diff --git a/data/delete_me/sparsesignatures/HCC1395_WXS_HCC1395_joint_table.tsv b/data/delete_me/sparsesignatures/HCC1395_WXS_HCC1395_joint_table.tsv new file mode 100644 index 000000000..9b162fa8c --- /dev/null +++ b/data/delete_me/sparsesignatures/HCC1395_WXS_HCC1395_joint_table.tsv @@ -0,0 +1,1826 @@ +chr from to ref alt NV DP VAF IMPACT SYMBOL Gene Consequence annotations from Ensembl VEP. Format: Allele Consequence Feature_type Feature BIOTYPE EXON INTRON HGVSc HGVSp s1 s2 cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation DISTANCE STRAND FLAGS VARIANT_CLASS SYMBOL_SOURCE HGNC_ID CANONICAL MANE_SELECT MANE_PLUS_CLINICAL TSL APPRIS CCDS ENSP SWISSPROT TREMBL UNIPARC UNIPROT_ISOFORM GENE_PHENO SIFT PolyPhen DOMAINS miRNA HGVS_OFFSET AF AFR_AF AMR_AF EAS_AF EUR_AF SAS_AF gnomADe_AF gnomADe_AFR_AF gnomADe_AMR_AF gnomADe_ASJ_AF gnomADe_EAS_AF gnomADe_FIN_AF gnomADe_NFE_AF gnomADe_OTH_AF gnomADe_SAS_AF gnomADg_AF gnomADg_AFR_AF gnomADg_AMI_AF gnomADg_AMR_AF gnomADg_ASJ_AF gnomADg_EAS_AF gnomADg_FIN_AF gnomADg_MID_AF gnomADg_NFE_AF gnomADg_OTH_AF gnomADg_SAS_AF MAX_AF MAX_AF_POPS CLIN_SIG SOMATIC PHENO PUBMED MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE TRANSCRIPTION_FACTORS ChromKey...89 ID QUAL FILTER AS_FilterStatus AS_SB_TABLE AS_UNIQ_ALT_READ_COUNT CONTQ ECNT GERMQ MBQ MFRL MMQ MPOS NALOD NCount NLOD OCM PON POPAF ROQ RPA RU SEQQ STR STRANDQ STRQ TLOD ChromKey...117 POS Indiv NR gt_AF gt_DP gt_F1R2 gt_F2R1 gt_FAD gt_GQ gt_GT gt_PGT gt_PID gt_PL gt_PS gt_SB gt_GT_alleles CANCER_TYPE CGC_CANCER_GENE is_driver driver_label mutation_id type karyotype segment_id QC_PASS matched purity +chr1 1049980 1049981 G C 168 168 1 MODERATE AGRN ENSG00000188157 C missense_variant Transcript ENST00000379370 protein_coding 27/36 ENST00000379370.7:c.4822G>C ENSP00000368678.2:p.E1608Q ENSP00000368678.2 p.E1608Q 4875 4822 1608 E/Q Gag/Cag COSV65069056 1 SNV HGNC HGNC:329 YES NM_198576.4 1 P1 CCDS30551.1 ENSP00000368678 O00468.205 UPI00001D7C8B O00468-6 1 tolerated_low_confidence(0.24) Gene3D:2.10.25.10&SMART:SM00181&PROSITE_profiles:PS50026&PANTHER:PTHR15036&AlphaFold_DB_import:AF-O00468-F1 1 1 1 NA NA PASS SITE 109,193|64,104 NA NA 1 93 20,20 154,157 60,60 35 2.30 NA 59.29 NA FALSE 6.00 93 NA NA NA FALSE NA NA 486.34 1 1049980 HCC1395_HCC1395T 0 0.991 168 0,50 0,47 0,108 NA 0/1 NA NA NA NA 0,0,64,104 G/C PANCANCER NA FALSE AGRN_p.E1608Q chr1:1049980:1049981:G:C SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 1212740 1212741 A C 125 125 1 MODIFIER SDF4 ENSG00000078808 C downstream_gene_variant Transcript ENST00000263741 protein_coding NA COSV55421527 4191 -1 SNV HGNC HGNC:24188 1 CCDS12.2 ENSP00000263741 A0A5F9UJX7.13 UPI00114AF40C 1 1 1 NA NA PASS SITE 63,80|49,76 NA NA 1 93 20,20 151,154 60,60 30 1.94 NA 25.89 NA FALSE 6.00 93 NA NA NA FALSE NA NA 341.76 1 1212740 HCC1395_HCC1395T 0 0.988 125 0,28 0,37 0,78 NA 0/1 NA NA NA NA 0,0,49,76 A/C PANCANCER NA FALSE SDF4 chr1:1212740:1212741:A:C SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 1263518 1263519 G A 15 18 0.833333333333333 MODIFIER UBE2J2 ENSG00000160087 A intron_variant Transcript ENST00000347370 protein_coding 2/6 ENST00000347370.6:c.-25-132C>T NA -1 SNV HGNC HGNC:19268 3 CCDS16.1 ENSP00000344857 A6NGS0.130 UPI00001D69FA 1 NA NA PASS SITE 1,22|0,15 NA NA 1 73 39,37 208,209 60,60 33 1.32 NA 5.72 NA FALSE 6.00 88 NA NA NA FALSE NA NA 58.73 1 1263518 HCC1395_HCC1395T 3 0.802 18 0,6 2,9 3,15 NA 0/1 NA NA NA NA 0,3,0,15 G/A PANCANCER NA FALSE UBE2J2 chr1:1263518:1263519:G:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 1320793 1320794 G A 188 188 1 MODIFIER INTS11 ENSG00000127054 A non_coding_transcript_exon_variant Transcript ENST00000323275 retained_intron 2/16 ENST00000323275.10:n.342C>T NA 342 -1 SNV HGNC HGNC:26052 1 1 NA NA PASS SITE 111,104|97,91 NA NA 1 93 20,20 157,171 60,60 31 2.17 NA 43.34 NA FALSE 6.00 93 NA NA NA FALSE NA NA 538.39 1 1320793 HCC1395_HCC1395T 0 0.992 188 0,50 0,67 0,123 NA 0/1 NA NA NA NA 0,0,97,91 G/A PANCANCER NA FALSE INTS11 chr1:1320793:1320794:G:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 1336326 1336327 G A 228 231 0.987012987012987 MODIFIER TAS1R3 ENSG00000169962 A downstream_gene_variant Transcript ENST00000339381 protein_coding NA rs1272007310 1012 1 SNV HGNC HGNC:15661 YES NM_152228.3 2 P1 CCDS30556.1 ENSP00000344411 Q7RTX0.169 UPI0000051F47 4.996e-06 0 0 0 0 0 0 0 3.547e-05 2.629e-05 4.826e-05 0 0 0 0.0001931 0 0 1.47e-05 0 0 0.0001931 gnomADg_EAS 1 NA NA PASS SITE 112,172|90,138 NA NA 1 93 20,20 161,174 60,60 31 2.29 NA 56.54 NA FALSE 4.31 93 NA NA NA FALSE NA NA 707.96 1 1336326 HCC1395_HCC1395T 3 0.982 231 1,70 1,76 2,160 NA 0/1 NA NA NA NA 1,2,90,138 G/A PANCANCER NA FALSE TAS1R3 chr1:1336326:1336327:G:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 1391558 1391559 C A 17 136 0.125 MODIFIER CCNL2 ENSG00000221978 A intron_variant Transcript ENST00000400809 protein_coding 5/10 ENST00000400809.8:c.660-693G>T NA -1 SNV HGNC HGNC:20570 YES NM_030937.6 1 P1 CCDS30557.1 ENSP00000383611 Q96S94.170 UPI00000713F5 Q96S94-1 1 NA NA PASS SITE 127,145|6,11 NA NA 1 93 20,20 165,166 60,60 26 1.99 NA 28.55 NA FALSE 6.00 35 NA NA NA FALSE NA NA 33.47 1 1391558 HCC1395_HCC1395T 119 0.132 136 22,4 47,7 78,11 NA 0/1 NA NA NA NA 51,68,6,11 C/A PANCANCER NA FALSE CCNL2 chr1:1391558:1391559:C:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 1574734 1574735 C T 66 66 1 MODIFIER SSU72 ENSG00000160075 T 5_prime_UTR_variant Transcript ENST00000291386 protein_coding 1/5 ENST00000291386.4:c.-177G>A NA 130 -1 SNV HGNC HGNC:25016 YES NM_014188.3 1 P1 CCDS32.1 ENSP00000291386 Q9NP77.162 UPI00000437EE Q9NP77-1 1 NA NA PASS SITE 31,46|31,35 NA NA 1 93 20,20 155,155 60,60 22 1.74 NA 15.65 NA FALSE 6.00 93 NA NA NA FALSE NA NA 188.82 1 1574734 HCC1395_HCC1395T 0 0.978 66 0,16 0,26 0,43 NA 0/1 NA NA NA NA 0,0,31,35 C/T PANCANCER NA FALSE SSU72 chr1:1574734:1574735:C:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 1634406 1634407 C G 6 6 1 MODIFIER CDK11B ENSG00000248333 G downstream_gene_variant Transcript ENST00000340677 protein_coding NA rs1479580586 1332 -1 SNV HGNC HGNC:1729 1 CCDS72682.1 ENSP00000464016 P21127.230 UPI0004423C02 P21127-9 0.005032 0.001963 0 0.005982 0.008741 0.007993 0.004367 0.01408 0.006092 0.009328 0.01284 0.01408 gnomADg_MID 1 NA NA PASS SITE 76,91|5,4 NA NA 1 93 20,20 163,152 60,33 27 0.314 NA 29.36 NA FALSE 6.00 75 NA NA NA FALSE NA NA 9.05 1 1634406 HCC1395_HCC1395T 0 0.833 6 0,1 0,3 0,4 NA 0/1 NA NA NA NA 0,0,4,2 C/G PANCANCER NA FALSE CDK11B chr1:1634406:1634407:C:G SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 1701561 1701562 C A 71 437 0.162471395881007 MODIFIER MMP23A ENSG00000215914 A intron_variant&non_coding_transcript_variant Transcript ENST00000234610 unprocessed_pseudogene 6/6 ENST00000234610.5:n.843-47C>A NA 1 SNV HGNC HGNC:7170 YES 1 NA NA PASS SITE 363,462|31,40 NA NA 1 93 20,20 159,166 51,53 28 2.47 NA 87.99 NA FALSE 6.00 57 NA NA NA FALSE NA NA 149.79 1 1701561 HCC1395_HCC1395T 366 0.168 437 72,11 92,24 237,47 NA 0/1 NA NA NA NA 154,212,31,40 C/A PANCANCER NA FALSE MMP23A chr1:1701561:1701562:C:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 2489143 2489144 G C 20 20 1 MODIFIER PLCH2 ENSG00000149527 C intron_variant Transcript ENST00000278878 protein_coding 6/18 ENST00000278878.6:c.811-64G>C NA 1 cds_start_NF SNV HGNC HGNC:29037 5 ENSP00000278878 B9DI82.112 UPI0002B8321E 1 NA NA PASS SITE 28,7|18,2 NA NA 1 93 37,38 200,180 60,60 21 1.48 NA 8.73 NA FALSE 6.00 93 NA NA NA FALSE NA NA 77.18 1 2489143 HCC1395_HCC1395T 0 0.952 20 0,5 0,13 0,18 NA 0/1 NA NA NA NA 0,0,18,2 G/C PANCANCER NA FALSE PLCH2 chr1:2489143:2489144:G:C SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 2591128 2591129 C G 243 243 1 MODIFIER MMEL1 ENSG00000142606 G intron_variant Transcript ENST00000378412 protein_coding 23/23 ENST00000378412.8:c.2241-39G>C NA -1 SNV HGNC HGNC:14668 YES NM_033467.4 2 P1 CCDS30569.2 ENSP00000367668 Q495T6.147 UPI0000047596 Q495T6-1 1 1 NA NA PASS SITE 145,153|117,126 NA NA 1 93 20,20 164,168 60,60 35 2.31 NA 60.71 NA FALSE 6.00 93 NA NA NA FALSE NA NA 765.12 1 2591128 HCC1395_HCC1395T 0 0.994 243 0,63 0,93 0,169 NA 0/1 NA NA NA NA 0,0,117,126 C/G PANCANCER NA FALSE MMEL1 chr1:2591128:2591129:C:G SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 6620200 6620201 C A 43 313 0.137380191693291 MODIFIER THAP3 ENSG00000041988 A upstream_gene_variant Transcript ENST00000054650 protein_coding NA 4668 1 SNV HGNC HGNC:20855 YES NM_001195753.2 1 P4 CCDS55572.1 ENSP00000054650 Q8WTV1.161 UPI000006CFCA Q8WTV1-1 1 NA NA PASS SITE 298,271|18,25 NA NA 1 93 20,20 157,161 60,60 42 2.29 NA 57.79 NA FALSE 6.00 41 NA NA NA FALSE NA NA 85.69 1 6620200 HCC1395_HCC1395T 270 0.134 313 61,7 115,19 180,27 NA 0/1 NA NA NA NA 145,125,18,25 C/A PANCANCER NA FALSE THAP3 chr1:6620200:6620201:C:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 10647466 10647467 C T 35 275 0.127272727272727 MODIFIER CASZ1 ENSG00000130940 T 3_prime_UTR_variant Transcript ENST00000344008 protein_coding 16/16 ENST00000344008.5:c.*331G>A NA 4152 rs946579497 -1 SNV HGNC HGNC:26002 2 CCDS120.2 ENSP00000339445 Q86V15.158 UPI0000470BA1 Q86V15-2 1 3.285e-05 0 0 0 0 0 0 0 5.88e-05 0.000478 0 0.000478 gnomADg_OTH 1 NA NA PASS SITE 223,224|17,18 NA NA 1 93 20,20 149,160 60,60 43 2.11 NA 38.13 NA FALSE 4.31 53 NA NA NA FALSE NA NA 69.34 1 10647466 HCC1395_HCC1395T 240 0.128 275 60,6 72,13 142,20 NA 0/1 NA NA NA NA 121,119,17,18 C/T PANCANCER NA FALSE CASZ1 chr1:10647466:10647467:C:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 12258129 12258130 C G 152 152 1 MODIFIER VPS13D ENSG00000048707 G downstream_gene_variant Transcript ENST00000489961 protein_coding_CDS_not_defined NA 174 1 SNV HGNC HGNC:23595 5 1 1 NA NA PASS SITE 47,75|52,100 NA NA 1 93 20,20 174,168 60,60 25 1.94 NA 25.58 NA FALSE 6.00 93 NA NA NA FALSE NA NA 481.50 1 12258129 HCC1395_HCC1395T 0 0.991 152 0,46 0,50 0,106 NA 0/1 NA NA NA NA 0,0,52,100 C/G PANCANCER NA FALSE VPS13D chr1:12258129:12258130:C:G SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 16006134 16006135 G T 150 151 0.993377483443709 MODERATE SRARP ENSG00000183888 T missense_variant Transcript ENST00000329454 protein_coding 2/2 ENST00000329454.2:c.298G>T ENSP00000332162.2:p.G100W ENSP00000332162.2 p.G100W 366 298 100 G/W Ggg/Tgg COSV61498146 1 SNV HGNC HGNC:28339 YES NM_178840.4 1 P1 CCDS166.1 ENSP00000332162 Q8NEQ6.124 UPI0000070801 tolerated(0.24) possibly_damaging(0.742) AlphaFold_DB_import:AF-Q8NEQ6-F1&Pfam:PF15547&PANTHER:PTHR38494 1 1 1 NA NA PASS SITE 70,67|77,73 NA NA 1 93 20,20 162,167 60,60 32 1.96 NA 27.09 NA FALSE 6.00 93 NA NA NA FALSE NA NA 449.58 1 16006134 HCC1395_HCC1395T 1 0.990 151 0,48 0,55 1,103 NA 0/1 NA NA NA NA 1,0,77,73 G/T PANCANCER NA FALSE SRARP_p.G100W chr1:16006134:16006135:G:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 16395272 16395273 C T 239 275 0.869090909090909 MODIFIER SPATA21 ENSG00000187144 T downstream_gene_variant Transcript ENST00000335496 protein_coding NA rs1034697774&COSV100131347 3371 -1 SNV HGNC HGNC:28026 YES NM_198546.1 1 P2 CCDS172.1 ENSP00000335612 Q7Z572.148 UPI00001B4B16 Q7Z572-1 1.314e-05 0 0 0 0 0 0 0 2.94e-05 0 0 2.94e-05 gnomADg_NFE 0&1 0&1 1 NA NA PASS SITE 107,170|90,149 NA NA 1 93 20,20 162,165 60,60 27 2.22 NA 48.72 NA FALSE 6.00 93 NA NA NA FALSE NA NA 698.23 1 16395272 HCC1395_HCC1395T 36 0.867 275 8,47 15,107 25,168 NA 0/1 NA NA NA NA 12,24,90,149 C/T PANCANCER NA FALSE SPATA21 chr1:16395272:16395273:C:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 16647080 16647081 C T 178 541 0.32902033271719 MODIFIER CROCCP2 ENSG00000291072 T upstream_gene_variant Transcript ENST00000362058 lncRNA NA rs1261876733 2397 -1 SNV EntrezGene HGNC:28170 2 0 0 0 0 0 0 0 0 0 0 0 0 gnomADg_AFR&gnomADg_AMI&gnomADg_AMR&gnomADg_ASJ&gnomADg_EAS&gnomADg_FIN&gnomADg_MID&gnomADg_NFE&gnomADg_OTH&gnomADg_SAS 1 NA NA PASS SITE 494,643|91,87 NA NA 1 93 20,20 163,151 27,43 41 2.72 NA 154.57 NA FALSE 6.00 93 NA NA NA FALSE NA NA 354.88 1 16647080 HCC1395_HCC1395T 363 0.311 541 123,52 76,37 205,92 NA 0/1 NA NA NA NA 169,194,91,87 C/T PANCANCER NA FALSE CROCCP2 chr1:16647080:16647081:C:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 16972418 16972419 C G 162 162 1 MODIFIER MFAP2 ENSG00000117122 G downstream_gene_variant Transcript ENST00000375534 protein_coding NA COSV100977605&COSV65003692&COSV65003720 2084 -1 SNV HGNC HGNC:7033 2 A1 CCDS44071.1 ENSP00000364684 P55001.171 UPI00004709D7 P55001-2 1&1&1 1&1&1 1 NA NA PASS SITE 90,105|69,93 NA NA 1 93 20,20 155,163 60,60 38 2.11 NA 37.91 NA FALSE 6.00 93 NA NA NA FALSE NA NA 480.69 1 16972418 HCC1395_HCC1395T 0 0.991 162 0,49 0,47 0,107 NA 0/1 NA NA NA NA 0,0,69,93 C/G PANCANCER NA FALSE MFAP2 chr1:16972418:16972419:C:G SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 17421003 17421004 T G 14 14 1 MODIFIER RCC2 ENSG00000179051 G intron_variant Transcript ENST00000375433 protein_coding 5/11 ENST00000375433.3:c.745-175A>C NA -1 SNV HGNC HGNC:30297 1 P1 CCDS181.1 ENSP00000364582 Q9P258.184 A0A024RAC5.62 UPI0000074608 1 NA NA PASS SITE 0,8|2,12 NA NA 1 48 33,38 190,198 60,60 37 0.974 NA 2.41 NA FALSE 6.00 93 NA NA NA FALSE NA NA 51.89 1 17421003 HCC1395_HCC1395T 0 0.929 14 0,6 0,6 0,12 NA 0/1 NA NA NA NA 0,0,2,12 T/G PANCANCER NA FALSE RCC2 chr1:17421003:17421004:T:G SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 18849578 18849579 G A 100 188 0.531914893617021 MODIFIER TAS1R2 ENSG00000179002 A intron_variant Transcript ENST00000375371 protein_coding 3/5 ENST00000375371.4:c.1258-28C>T NA COSV64748031 -1 SNV HGNC HGNC:14905 YES NM_152232.6 2 P1 CCDS187.1 ENSP00000364520 Q8TE23.169 UPI0000456168 1 1 1 NA NA PASS SITE 105,120|48,52 NA NA 1 93 20,20 158,167 60,60 31 1.98 NA 27.60 NA FALSE 6.00 93 NA NA NA FALSE NA NA 254.64 1 18849578 HCC1395_HCC1395T 88 0.527 188 20,19 34,43 58,65 NA 0/1 NA NA NA NA 43,45,48,52 G/A PANCANCER NA FALSE TAS1R2 chr1:18849578:18849579:G:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 19118771 19118772 C G 265 265 1 MODIFIER UBR4 ENSG00000127481 G 5_prime_UTR_variant Transcript ENST00000375218 protein_coding 1/5 ENST00000375218.3:c.-1075G>C NA 79 -1 SNV HGNC HGNC:30313 2 ENSP00000364366 Q5T4S7.170 UPI000006E63B Q5T4S7-6 1 NA NA PASS SITE 87,88|136,129 NA NA 1 93 20,20 166,171 60,60 27 2.11 NA 37.92 NA FALSE 6.00 93 NA NA NA FALSE NA NA 842.15 1 19118771 HCC1395_HCC1395T 0 0.995 265 0,63 0,113 0,184 NA 0/1 NA NA NA NA 0,0,136,129 C/G PANCANCER NA FALSE UBR4 chr1:19118771:19118772:C:G SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 22129569 22129571 CC TT 4 19 0.210526315789474 MODIFIER WNT4 ENSG00000162552 TT intron_variant Transcript ENST00000290167 protein_coding 2/4 ENST00000290167.11:c.313+46_313+47delinsAA NA -1 substitution HGNC HGNC:12783 YES NM_030761.5 1 P1 CCDS223.1 ENSP00000290167 P56705.194 UPI0000048EC6 P56705-1 1 1 NA NA PASS SITE 24,1|4,0 NA NA 1 30 39,35 222,210 60,60 22 1.04 NA 3.01 NA FALSE 6.00 13 NA NA NA FALSE NA NA 11.95 1 22129569 HCC1395_HCC1395T 15 0.249 19 4,1 8,2 14,4 NA 0/1 NA NA NA NA 14,1,4,0 CC/TT PANCANCER NA FALSE WNT4 chr1:22129569:22129571:CC:TT indel 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 22660991 22660992 G A 316 316 1 MODERATE C1QB ENSG00000173369 A missense_variant Transcript ENST00000432749 protein_coding 4/4 ENST00000432749.6:c.361G>A ENSP00000404606.2:p.A121T ENSP00000404606.2 p.A121T 652 361 121 A/T Gcc/Acc rs776292843&COSV59246258 1 cds_end_NF SNV HGNC HGNC:1242 2 ENSP00000404606 A0A0A0MSV6.49 UPI0003F47FF1 1 deleterious(0) possibly_damaging(0.881) PROSITE_profiles:PS50871&Pfam:PF00386&Gene3D:2.60.120.40&SMART:SM00110&Superfamily:SSF49842&AlphaFold_DB_import:AF-A0A0A0MSV6-F1 1.591e-05 0 0 0 0 0 2.637e-05 0 3.267e-05 1.976e-05 0 0 0 0 0 0 0 4.415e-05 0 0 4.415e-05 gnomADg_NFE 0&1 0&1 1 NA NA PASS SITE 162,209|137,180 NA NA 1 93 20,20 157,164 60,60 30 2.39 NA 72.61 NA FALSE 6.00 93 NA NA NA FALSE NA NA 936.21 1 22660991 HCC1395_HCC1395T 0 0.995 316 0,76 0,123 0,212 NA 0/1 NA NA NA NA 0,0,136,180 G/A PANCANCER NA FALSE C1QB_p.A121T chr1:22660991:22660992:G:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 23522118 23522119 C T 28 28 1 MODIFIER E2F2 ENSG00000007968 T intron_variant Transcript ENST00000361729 protein_coding 2/6 ENST00000361729.3:c.359-62G>A NA -1 SNV HGNC HGNC:3114 YES NM_004091.4 1 P1 CCDS236.1 ENSP00000355249 Q14209.198 UPI0000129AC1 1 NA NA PASS SITE 8,14|9,19 NA NA 1 88 20,26 181,155 60,60 22 1.20 NA 4.21 NA FALSE 6.00 93 NA NA NA FALSE NA NA 92.89 1 23522118 HCC1395_HCC1395T 0 0.956 28 0,9 0,8 0,20 NA 0/1 NA NA NA NA 0,0,9,19 C/T PANCANCER NA FALSE E2F2 chr1:23522118:23522119:C:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 25982249 25982250 G C 41 41 1 MODIFIER PAFAH2 ENSG00000158006 C intron_variant Transcript ENST00000374282 protein_coding 7/10 ENST00000374282.8:c.666+115C>G NA -1 SNV HGNC HGNC:8579 YES NM_000437.4 1 P1 CCDS270.1 ENSP00000363400 Q99487.172 UPI00001311EB 1 NA NA PASS SITE 25,10|36,5 NA NA 1 93 20,38 170,195 60,60 22 1.41 NA 7.53 NA FALSE 6.00 93 NA NA NA FALSE NA NA 156.57 1 25982249 HCC1395_HCC1395T 0 0.974 41 0,10 0,26 0,36 NA 0/1 NA NA NA NA 0,0,36,5 G/C PANCANCER NA FALSE PAFAH2 chr1:25982249:25982250:G:C SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 26039716 26039717 G T 67 67 1 MODIFIER SLC30A2 ENSG00000158014 T intron_variant Transcript ENST00000374276 protein_coding 7/7 ENST00000374276.4:c.973+61C>A NA -1 SNV HGNC HGNC:11013 YES NM_001004434.3 1 P1 CCDS30644.1 ENSP00000363394 Q9BRI3.168 UPI0000049F98 Q9BRI3-2 1 1 NA NA PASS SITE 24,23|35,32 NA NA 1 93 20,20 152,164 60,60 29 1.52 NA 9.63 NA FALSE 6.00 93 NA NA NA FALSE NA NA 185.71 1 26039716 HCC1395_HCC1395T 0 0.978 67 0,17 0,22 0,43 NA 0/1 NA NA NA NA 0,0,35,32 G/T PANCANCER NA FALSE SLC30A2 chr1:26039716:26039717:G:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 27793607 27793608 C G 93 95 0.978947368421053 MODERATE STX12 ENSG00000117758 G missense_variant Transcript ENST00000373943 protein_coding 3/9 ENST00000373943.9:c.263C>G ENSP00000363054.4:p.P88R ENSP00000363054.4 p.P88R 352 263 88 P/R cCc/cGc COSV105307378&COSV64250176 1 SNV HGNC HGNC:11430 YES NM_177424.3 1 P1 CCDS310.1 ENSP00000363054 Q86Y82.178 UPI000000DB92 deleterious(0) Gene3D:1.20.58.70&PDB-ENSP_mappings:2dnx.A&AlphaFold_DB_import:AF-Q86Y82-F1&Pfam:PF14523&PANTHER:PTHR19957&SMART:SM00503&Superfamily:SSF47661&CDD:cd00179&Low_complexity_(Seg):seg 1&1 1&1 1 NA NA PASS SITE 27,52|29,64 NA NA 1 93 20,20 157,163 60,60 30 1.73 NA 15.65 NA FALSE 6.00 93 NA NA NA FALSE NA NA 304.39 1 27793607 HCC1395_HCC1395T 2 0.972 95 0,23 1,36 1,69 NA 0/1 NA NA NA NA 1,1,29,64 C/G PANCANCER NA FALSE STX12_p.P88R chr1:27793607:27793608:C:G SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 28718082 28718083 C G 74 74 1 MODIFIER GMEB1 ENSG00000162419 G downstream_gene_variant Transcript ENST00000294409 protein_coding NA 3209 1 SNV HGNC HGNC:4370 1 CCDS327.1 ENSP00000294409 Q9Y692.187 UPI000012B8AB Q9Y692-1 1 NA NA PASS SITE 36,37|34,40 NA NA 1 93 20,38 165,171 60,60 30 1.72 NA 15.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 263.52 1 28718082 HCC1395_HCC1395T 0 0.984 74 0,17 0,35 0,59 NA 0/1 NA NA NA NA 0,0,34,40 C/G PANCANCER NA FALSE GMEB1 chr1:28718082:28718083:C:G SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 33567887 33567888 C G 86 86 1 MODIFIER CSMD2 ENSG00000121904 G intron_variant Transcript ENST00000373381 protein_coding 52/70 ENST00000373381.9:c.8132-46G>C NA -1 SNV HGNC HGNC:19290 YES NM_001281956.2 1 P2 CCDS60082.1 ENSP00000362479 Q7Z408.158 UPI0000578D0B Q7Z408-4 1 NA NA PASS SITE 33,37|43,43 NA NA 1 93 20,20 172,162 60,60 34 1.71 NA 15.05 NA FALSE 6.00 93 NA NA NA FALSE NA NA 266.31 1 33567887 HCC1395_HCC1395T 0 0.984 86 0,23 0,30 0,60 NA 0/1 NA NA NA NA 0,0,43,43 C/G PANCANCER NA FALSE CSMD2 chr1:33567887:33567888:C:G SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 35594531 35594532 G A 30 276 0.108695652173913 MODERATE TFAP2E ENSG00000116819 A missense_variant Transcript ENST00000373235 protein_coding 7/7 ENST00000373235.4:c.1184G>A ENSP00000362332.3:p.G395E ENSP00000362332.3 p.G395E 1448 1184 395 G/E gGg/gAg 1 SNV HGNC HGNC:30774 YES NM_178548.4 1 P1 CCDS393.2 ENSP00000362332 Q6VUC0.135 UPI0000203EFC deleterious_low_confidence(0) probably_damaging(0.999) AlphaFold_DB_import:AF-Q6VUC0-F1&Pfam:PF03299&PANTHER:PTHR10812 1 NA NA PASS SITE 221,250|15,15 NA NA 1 93 20,20 159,153 60,60 30 2.20 NA 46.91 NA FALSE 6.00 73 NA NA NA FALSE NA NA 63.30 1 35594531 HCC1395_HCC1395T 246 0.113 276 53,8 97,10 156,19 NA 0/1 NA NA NA NA 122,124,15,15 G/A PANCANCER NA FALSE TFAP2E_p.G395E chr1:35594531:35594532:G:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 36176447 36176448 G A 80 80 1 MODERATE MAP7D1 ENSG00000116871 A missense_variant Transcript ENST00000316156 protein_coding 6/16 ENST00000316156.8:c.988G>A ENSP00000320228.4:p.A330T ENSP00000320228.4 p.A330T 1441 988 330 A/T Gcc/Acc rs1453412747&COSV60215948 1 SNV HGNC HGNC:25514 1 A2 CCDS65493.1 ENSP00000320228 Q3KQU3.140 UPI00004561B1 Q3KQU3-2 deleterious(0.01) probably_damaging(0.981) AlphaFold_DB_import:AF-Q3KQU3-F1&PANTHER:PTHR15073 0 0 0 0 0 0 0 0 0 0 gnomADe_AFR&gnomADe_AMR&gnomADe_ASJ&gnomADe_EAS&gnomADe_FIN&gnomADe_NFE&gnomADe_OTH&gnomADe_SAS 0&1 0&1 1 NA NA PASS SITE 66,60|42,38 NA NA 1 93 20,20 162,157 60,60 41 1.95 NA 26.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 231.69 1 36176447 HCC1395_HCC1395T 0 0.982 80 0,27 0,24 0,53 NA 0/1 NA NA NA NA 0,0,42,38 G/A PANCANCER NA FALSE MAP7D1_p.A330T chr1:36176447:36176448:G:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 36179727 36179729 GG AA 24 63 0.380952380952381 MODERATE MAP7D1 ENSG00000116871 AA missense_variant Transcript ENST00000316156 protein_coding 14/16 ENST00000316156.8:c.2178_2179delinsAA ENSP00000320228.4:p.E727K ENSP00000320228.4 p.E727K 2631-2632 2178-2179 726-727 EE/EK gaGGag/gaAAag 1 substitution HGNC HGNC:25514 1 A2 CCDS65493.1 ENSP00000320228 Q3KQU3.140 UPI00004561B1 Q3KQU3-2 AlphaFold_DB_import:AF-Q3KQU3-F1&PANTHER:PTHR15073&MobiDB_lite:mobidb-lite 1 NA NA PASS SITE 53,37|12,12 NA NA 1 93 20,20 168,168 60,60 36 1.59 NA 11.14 NA FALSE 6.00 48 NA NA NA FALSE NA NA 94.09 1 36179727 HCC1395_HCC1395T 39 0.375 63 11,12 16,4 29,17 NA 0/1 NA NA NA NA 22,17,12,12 GG/AA PANCANCER NA FALSE MAP7D1_p.E727K chr1:36179727:36179729:GG:AA indel 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 39429922 39429923 G C 20 133 0.150375939849624 MODIFIER MACF1 ENSG00000127603 C non_coding_transcript_exon_variant Transcript ENST00000289893 retained_intron 29/64 ENST00000289893.8:n.12435G>C NA 12435 1 SNV HGNC HGNC:13664 5 1 1 NA NA PASS SITE 99,120|5,15 NA NA 1 93 20,41 154,183 60,60 36 1.85 NA 20.47 NA FALSE 6.00 75 NA NA NA FALSE NA NA 54.71 1 39429922 HCC1395_HCC1395T 113 0.193 133 25,5 40,9 70,16 NA 0/1 NA NA NA NA 49,64,5,15 G/C PANCANCER NA FALSE MACF1 chr1:39429922:39429923:G:C SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 41510892 41510893 G C 71 377 0.188328912466843 LOW HIVEP3 ENSG00000127124 C synonymous_variant Transcript ENST00000372583 protein_coding 9/9 ENST00000372583.6:c.6780C>G ENSP00000361664.1:p.V2260= ENSP00000361664.1 p.V2260= 8090 6780 2260 V gtC/gtG -1 SNV HGNC HGNC:13561 YES NM_024503.5 1 P5 CCDS463.1 ENSP00000361664 Q5T1R4.158 UPI000013CC24 Q5T1R4-1 Low_complexity_(Seg):seg&PANTHER:PTHR45944&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-Q5T1R4-F1 1 NA NA PASS SITE 364,412|36,35 NA NA 1 93 20,20 155,164 60,60 25 2.48 NA 89.95 NA FALSE 6.00 93 NA NA NA FALSE NA NA 157.66 1 41510892 HCC1395_HCC1395T 306 0.178 377 82,20 109,23 211,45 NA 0/1 NA NA NA NA 144,162,36,35 G/C PANCANCER NA FALSE HIVEP3_p.V2260= chr1:41510892:41510893:G:C SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 42179175 42179176 A T 34 130 0.261538461538462 MODIFIER FOXJ3 ENSG00000198815 T 3_prime_UTR_variant Transcript ENST00000361346 protein_coding 13/13 ENST00000361346.6:c.*535T>A NA 2598 -1 SNV HGNC HGNC:29178 YES NM_014947.5 1 P1 CCDS30689.1 ENSP00000354620 Q9UPW0.179 UPI000013D359 Q9UPW0-1 1 NA NA PASS SITE 51,119|9,25 NA NA 1 93 28,36 188,194 60,60 28 1.75 NA 16.25 NA FALSE 6.00 63 NA NA NA FALSE NA NA 89.76 1 42179175 HCC1395_HCC1395T 96 0.260 130 21,7 48,18 76,26 NA 0/1 NA NA NA NA 23,73,9,25 A/T PANCANCER NA FALSE FOXJ3 chr1:42179175:42179176:A:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 42794426 42794427 A T 57 210 0.271428571428571 LOW TMEM269 ENSG00000274386 T synonymous_variant&NMD_transcript_variant Transcript ENST00000421630 nonsense_mediated_decay 5/11 ENST00000421630.6:c.297A>T ENSP00000490287.1:p.T99= ENSP00000490287.1 p.T99= 471 297 99 T acA/acT 1 SNV HGNC HGNC:52381 5 CCDS90932.1 ENSP00000490287 A0A1B0GUR4.26 UPI0002B831D0 AlphaFold_DB_import:AF-A0A1B0GUR4-F1 1 NA NA PASS SITE 161,94|37,20 NA NA 1 93 26,20 163,167 60,60 26 1.90 NA 23.43 NA FALSE 6.00 93 NA NA NA FALSE NA NA 145.74 1 42794426 HCC1395_HCC1395T 153 0.275 210 35,18 76,24 115,43 NA 0/1 NA NA NA NA 95,58,37,20 A/T PANCANCER NA FALSE TMEM269_p.T99= chr1:42794426:42794427:A:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 43338032 43338033 G C 189 239 0.790794979079498 MODIFIER MPL ENSG00000117400 C intron_variant Transcript ENST00000372470 protein_coding 1/11 ENST00000372470.9:c.80-67G>C NA 1 SNV HGNC HGNC:7217 YES NM_005373.3 1 P1 CCDS483.1 ENSP00000361548 P40238.212 UPI000002DB88 P40238-1 1 1 NA NA PASS SITE 129,80|118,71 NA NA 1 93 20,23 166,169 60,60 28 2.06 NA 33.62 NA FALSE 6.00 93 NA NA NA FALSE NA NA 575.79 1 43338032 HCC1395_HCC1395T 50 0.770 239 23,40 17,95 42,143 NA 0/1 NA NA NA NA 33,17,118,71 G/C PANCANCER NA FALSE MPL chr1:43338032:43338033:G:C SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 43960390 43960391 G T 54 213 0.253521126760563 MODIFIER IPO13 ENSG00000117408 T intron_variant Transcript ENST00000372343 protein_coding 12/19 ENST00000372343.8:c.2109+61G>T NA 1 SNV HGNC HGNC:16853 YES NM_014652.4 1 P1 CCDS503.1 ENSP00000361418 O94829.176 UPI0000073F11 1 1 NA NA PASS SITE 145,144|28,26 NA NA 1 93 20,20 162,167 60,60 31 1.95 NA 26.79 NA FALSE 6.00 85 NA NA NA FALSE NA NA 126.17 1 43960390 HCC1395_HCC1395T 159 0.245 213 37,10 57,22 116,37 NA 0/1 NA NA NA NA 83,76,28,26 G/T PANCANCER NA FALSE IPO13 chr1:43960390:43960391:G:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 43977964 43977965 C T 108 433 0.249422632794457 LOW ATP6V0B ENSG00000117410 T splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000236067 protein_coding 6/6 ENST00000236067.8:c.451-17C>T NA 1 SNV HGNC HGNC:861 2 CCDS41315.1 ENSP00000236067 Q99437.185 UPI00005BC2CC Q99437-2 1 NA NA PASS SITE 271,318|46,62 NA NA 1 93 20,20 156,167 60,60 37 2.24 NA 51.18 NA FALSE 6.00 93 NA NA NA FALSE NA NA 249.29 1 43977964 HCC1395_HCC1395T 325 0.251 433 79,35 127,31 213,71 NA 0/1 NA NA NA NA 152,173,46,62 C/T PANCANCER NA FALSE ATP6V0B chr1:43977964:43977965:C:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 44219594 44219595 A T 19 96 0.197916666666667 MODIFIER DMAP1 ENSG00000178028 T intron_variant Transcript ENST00000315913 protein_coding 8/10 ENST00000315913.9:c.978+117A>T NA 1 SNV HGNC HGNC:18291 1 P1 CCDS509.1 ENSP00000312697 Q9NPF5.205 UPI00001294C6 1 NA NA PASS SITE 108,48|16,3 NA NA 1 93 33,34 180,202 60,60 23 1.82 NA 19.52 NA FALSE 6.00 50 NA NA NA FALSE NA NA 50.83 1 44219594 HCC1395_HCC1395T 77 0.229 96 22,5 39,13 63,18 NA 0/1 NA NA NA NA 52,25,16,3 A/T PANCANCER NA FALSE DMAP1 chr1:44219594:44219595:A:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 45051304 45051305 GT G 28 140 0.2 MODIFIER ZSWIM5 ENSG00000162415 - intron_variant Transcript ENST00000359600 protein_coding 4/13 ENST00000359600.6:c.1253-52del NA -1 deletion HGNC HGNC:29299 YES NM_020883.2 1 P1 CCDS41319.1 ENSP00000352614 Q9P217.136 UPI00001C1D76 1 NA NA PASS SITE 62,139|10,18 NA NA 1 93 20,20 171,189 60,60 32 1.83 NA 19.56 NA FALSE 6.00 93 NA NA NA FALSE NA NA 51.29 1 45051304 HCC1395_HCC1395T 112 0.184 140 17,3 27,9 83,18 NA 0/1 NA NA NA NA 34,78,10,18 GT/G PANCANCER NA FALSE ZSWIM5 chr1:45051304:45051305:GT:G indel 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 46658589 46658590 C T 33 162 0.203703703703704 MODIFIER ATPAF1 ENSG00000123472 T intron_variant Transcript ENST00000329231 protein_coding 3/6 ENST00000329231.8:c.495+98G>A NA -1 SNV HGNC HGNC:18803 2 CCDS41327.2 ENSP00000330685 A8MRA7.93 UPI000222BB4F 1 1 NA NA PASS SITE 126,94|19,14 NA NA 1 93 20,34 165,188 60,60 26 1.79 NA 17.76 NA FALSE 6.00 66 NA NA NA FALSE NA NA 86.67 1 46658589 HCC1395_HCC1395T 129 0.233 162 31,8 53,18 91,27 NA 0/1 NA NA NA NA 73,56,19,14 C/T PANCANCER NA FALSE ATPAF1 chr1:46658589:46658590:C:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 47118370 47118371 G C 40 51 0.784313725490196 MODIFIER CYP4Z1 ENSG00000186160 C downstream_gene_variant Transcript ENST00000334194 protein_coding NA 52 1 SNV HGNC HGNC:20583 YES NM_178134.3 1 P1 CCDS545.1 ENSP00000334246 Q86W10.159 UPI00000477F8 1 NA NA PASS SITE 0,39|0,40 NA NA 1 88 39,40 211,226 60,60 28 1.47 NA 8.43 NA FALSE 6.00 93 NA NA NA FALSE NA NA 163.39 1 47118370 HCC1395_HCC1395T 11 0.774 51 8,17 3,22 11,40 NA 0/1 NA NA NA NA 0,11,0,40 G/C PANCANCER NA FALSE CYP4Z1 chr1:47118370:47118371:G:C SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 52055641 52055642 G A 45 206 0.218446601941748 MODIFIER BTF3L4 ENSG00000134717 A upstream_gene_variant Transcript ENST00000313334 protein_coding NA 654 1 SNV HGNC HGNC:30547 YES NM_152265.5 1 P1 CCDS30713.1 ENSP00000360664 Q96K17.158 UPI00000299AB Q96K17-1 1 NA NA PASS SITE 151,162|20,25 NA NA 1 93 20,20 158,159 60,60 34 2.00 NA 29.45 NA FALSE 6.00 93 NA NA NA FALSE NA NA 106.78 1 52055641 HCC1395_HCC1395T 161 0.246 206 40,14 53,16 97,31 NA 0/1 NA NA NA NA 76,85,20,25 G/A PANCANCER NA FALSE BTF3L4 chr1:52055641:52055642:G:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 52894697 52894698 A C 259 417 0.621103117505995 MODIFIER ECHDC2 ENSG00000121310 C downstream_gene_variant Transcript ENST00000358358 protein_coding NA 1536 -1 SNV HGNC HGNC:23408 2 CCDS571.1 ENSP00000351125 Q86YB7.138 UPI000013D2F7 Q86YB7-2 1 NA NA PASS SITE 271,276|135,124 NA NA 1 93 20,20 163,171 60,60 28 2.43 NA 80.32 NA FALSE 6.00 93 NA NA NA FALSE NA NA 739.47 1 52894697 HCC1395_HCC1395T 158 0.626 417 34,62 67,107 111,187 NA 0/1 NA NA NA NA 79,79,135,124 A/C PANCANCER NA FALSE ECHDC2 chr1:52894697:52894698:A:C SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 52941964 52941965 A G 12 21 0.571428571428571 MODIFIER SCP2 ENSG00000116171 G intron_variant Transcript ENST00000371509 protein_coding 2/14 ENST00000371509.8:c.127+111A>G NA 1 SNV HGNC HGNC:10606 1 CCDS53317.1 ENSP00000360564 P22307.233 UPI0000D61F1F P22307-7 1 1 NA NA PASS SITE 1,33|1,11 NA NA 1 73 36,39 198,211 60,60 30 1.41 NA 7.22 NA FALSE 6.00 58 NA NA NA FALSE NA NA 41.74 1 52941964 HCC1395_HCC1395T 9 0.545 21 3,4 6,6 9,11 NA 0/1 NA NA NA NA 0,9,1,11 A/G PANCANCER NA FALSE SCP2 chr1:52941964:52941965:A:G SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 52961570 52961571 C A 102 195 0.523076923076923 MODERATE SCP2 ENSG00000116171 A missense_variant Transcript ENST00000371509 protein_coding 5/15 ENST00000371509.8:c.332C>A ENSP00000360564.4:p.A111D ENSP00000360564.4 p.A111D 443 332 111 A/D gCt/gAt COSV65262926 1 SNV HGNC HGNC:10606 1 CCDS53317.1 ENSP00000360564 P22307.233 UPI0000D61F1F P22307-7 1 tolerated(0.09) Gene3D:3.40.47.10&Pfam:PF00108&Superfamily:SSF53901&AlphaFold_DB_import:AF-P22307-F1 1 1 1 NA NA PASS SITE 103,141|43,59 NA NA 1 93 20,20 162,160 60,60 35 2.01 NA 30.01 NA FALSE 6.00 93 NA NA NA FALSE NA NA 250.32 1 52961570 HCC1395_HCC1395T 93 0.511 195 17,25 31,30 61,64 NA 0/1 NA NA NA NA 37,56,43,59 C/A PANCANCER NA FALSE SCP2_p.A111D chr1:52961570:52961571:C:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 54405449 54405450 C A 51 163 0.312883435582822 MODIFIER SSBP3 ENSG00000157216 A intron_variant Transcript ENST00000357475 protein_coding 1/16 ENST00000357475.9:c.56+504G>T NA rs1007386860 -1 SNV HGNC HGNC:15674 1 CCDS590.1 ENSP00000350067 Q9BWW4.170 UPI000002B437 Q9BWW4-3 4.603e-05 0.0001449 0 0 0 0 0 0 0 0 0.0002071 0.0002071 gnomADg_SAS 1 NA NA PASS SITE 169,190|22,29 NA NA 1 93 20,20 150,136 60,60 35 2.19 NA 46.65 NA FALSE 4.61 93 NA NA NA FALSE NA NA 114.67 1 54405449 HCC1395_HCC1395T 112 0.298 163 30,14 37,14 72,30 NA 0/1 NA NA NA NA 50,62,22,29 C/A PANCANCER NA FALSE SSBP3 chr1:54405449:54405450:C:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 56726645 56726646 C G 5 17 0.294117647058824 MODIFIER FYB2 ENSG00000187889 G intron_variant Transcript ENST00000343433 protein_coding 15/19 ENST00000343433.7:c.1794-62G>C NA -1 SNV HGNC HGNC:27295 YES NM_001004303.5 1 P1 CCDS30729.1 ENSP00000345972 Q5VWT5.133 UPI000022AE5B Q5VWT5-1 1 NA NA PASS SITE 0,31|0,5 NA NA 1 58 40,38 205,249 60,60 31 1.34 NA 5.72 NA FALSE 6.00 47 NA NA NA FALSE NA NA 13.85 1 56726645 HCC1395_HCC1395T 12 0.314 17 3,3 8,1 12,5 NA 0/1 NA NA NA NA 0,12,0,5 C/G PANCANCER NA FALSE FYB2 chr1:56726645:56726646:C:G SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 56867776 56867777 C A 48 121 0.396694214876033 MODIFIER C8A ENSG00000157131 A intron_variant Transcript ENST00000361249 protein_coding 2/10 ENST00000361249.4:c.171+74C>A NA 1 SNV HGNC HGNC:1352 YES NM_000562.3 1 P4 CCDS606.1 ENSP00000354458 P07357.220 UPI0000127C5A 1 1 NA NA PASS SITE 82,104|20,30 NA NA 1 93 20,20 168,161 60,60 33 -1.092e+00 NA 19.46 NA FALSE 6.00 60 NA NA NA FALSE NA NA 119.02 1 56867776 HCC1395_HCC1395T 73 0.397 121 17,9 27,19 49,32 NA 0/1 NA NA NA NA 33,40,19,29 C/A PANCANCER NA FALSE C8A chr1:56867776:56867777:C:A SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 57010975 57010976 C T 23 58 0.396551724137931 MODIFIER DAB1 ENSG00000173406 T intron_variant Transcript ENST00000371231 protein_coding 14/14 ENST00000371231.5:c.1671+170G>A NA -1 SNV HGNC HGNC:2661 5 ENSP00000360275 O75553.178 A0A3G6VF52.20 UPI000040DC2E O75553-1 1 1 NA NA PASS SITE 55,36|12,11 NA NA 1 93 20,20 166,177 60,60 41 1.60 NA 11.43 NA FALSE 6.00 51 NA NA NA FALSE NA NA 52.15 1 57010975 HCC1395_HCC1395T 35 0.375 58 8,4 16,10 24,14 NA 0/1 NA NA NA NA 23,12,12,11 C/T PANCANCER NA FALSE DAB1 chr1:57010975:57010976:C:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 59858483 59858484 C T 106 175 0.605714285714286 MODERATE HOOK1 ENSG00000134709 T missense_variant Transcript ENST00000371208 protein_coding 13/22 ENST00000371208.5:c.1298C>T ENSP00000360252.3:p.S433L ENSP00000360252.3 p.S433L 1467 1298 433 S/L tCa/tTa COSV64621280 1 SNV HGNC HGNC:19884 YES NM_015888.6 1 P1 CCDS612.1 ENSP00000360252 Q9UJC3.173 UPI0000071E61 Q9UJC3-1 deleterious(0) PANTHER:PTHR18947&Pfam:PF05622&Coiled-coils_(Ncoils):Coil&AlphaFold_DB_import:AF-Q9UJC3-F1 1 1 1 NA NA PASS SITE 135,114|57,49 NA NA 1 93 20,20 158,154 60,60 45 2.05 NA 33.40 NA FALSE 6.00 93 NA NA NA FALSE NA NA 255.90 1 59858483 HCC1395_HCC1395T 69 0.582 175 14,18 28,43 45,63 NA 0/1 NA NA NA NA 37,32,57,49 C/T PANCANCER NA FALSE HOOK1_p.S433L chr1:59858483:59858484:C:T SNV 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 59893839 59893840 AAAATC A 86 154 0.558441558441558 LOW CYP2J2 ENSG00000134716 - splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000371204 protein_coding 8/8 ENST00000371204.4:c.1331-15_1331-11del NA -1 deletion HGNC HGNC:2634 YES NM_000775.4 1 P1 CCDS613.1 ENSP00000360247 P51589.200 UPI00001282BF 1 NA NA PASS SITE 107,132|32,54 NA NA 1 93 20,20 156,185 60,60 31 2.02 NA 30.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 349.60 1 59893839 HCC1395_HCC1395T 68 0.593 154 13,13 18,26 43,63 NA 0/1 NA NA NA NA 27,41,32,54 AAAATC/A PANCANCER NA FALSE CYP2J2 chr1:59893839:59893840:AAAATC:A indel 3:0 chr1:873251:61875183:3:0:1 NA NA 0.96 +chr1 63437079 63437080 G T 32 113 0.283185840707965 MODIFIER ALG6 ENSG00000088035 T 3_prime_UTR_variant Transcript ENST00000263440 protein_coding 15/15 ENST00000263440.6:c.*59G>T NA 1851 rs904481709 1 SNV HGNC HGNC:23157 YES NM_013339.4 5 P1 CCDS30735.1 ENSP00000263440 Q9Y672.185 UPI00001E057D 1 1 NA NA PASS SITE 151,74|23,9 NA NA 1 93 20,36 180,194 60,60 30 2.03 NA 31.60 NA FALSE 6.00 88 NA NA NA FALSE NA NA 85.05 1 63437079 HCC1395_HCC1395T 81 0.289 113 22,14 39,11 63,25 NA 0/1 NA NA NA NA 56,25,23,9 G/T PANCANCER NA FALSE ALG6 chr1:63437079:63437080:G:T SNV 2:0 chr1:61899545:84414697:2:0:1 TRUE NA 0.96 +chr1 64832540 64832541 C T 63 245 0.257142857142857 MODIFIER RAVER2 ENSG00000162437 T 3_prime_UTR_variant Transcript ENST00000294428 protein_coding 12/12 ENST00000294428.8:c.*1555C>T NA 3729 1 SNV HGNC HGNC:25577 YES NM_001366165.2 5 A2 CCDS90967.1 ENSP00000294428 Q9HCJ3.166 UPI000050AAAF Q9HCJ3-1 1 NA NA PASS SITE 182,238|23,40 NA NA 1 93 20,32 163,183 60,60 32 2.20 NA 47.56 NA FALSE 6.00 93 NA NA NA FALSE NA NA 159.76 1 64832540 HCC1395_HCC1395T 182 0.288 245 35,16 70,28 120,48 NA 0/1 NA NA NA NA 73,109,23,40 C/T PANCANCER NA FALSE RAVER2 chr1:64832540:64832541:C:T SNV 2:0 chr1:61899545:84414697:2:0:1 TRUE NA 0.96 +chr1 65637992 65637993 A C 17 48 0.354166666666667 MODIFIER LEPR ENSG00000116678 C 3_prime_UTR_variant Transcript ENST00000349533 protein_coding 20/20 ENST00000349533.11:c.*977A>C NA 4644 1 SNV HGNC HGNC:6554 YES NM_002303.6 1 P4 CCDS631.1 ENSP00000330393 P48357.224 UPI000014C37B P48357-1 1 1 NA NA PASS SITE 32,58|7,10 NA NA 1 93 20,20 188,169 60,60 24 1.63 NA 12.60 NA FALSE 6.00 79 NA NA NA FALSE NA NA 44.38 1 65637992 HCC1395_HCC1395T 31 0.326 48 9,7 15,4 26,12 NA 0/1 NA NA NA NA 9,22,7,10 A/C PANCANCER NA FALSE LEPR chr1:65637992:65637993:A:C SNV 2:0 chr1:61899545:84414697:2:0:1 TRUE NA 0.96 +chr1 66834006 66834007 C G 48 74 0.648648648648649 MODIFIER DNAI4 ENSG00000152763 G downstream_gene_variant Transcript ENST00000371023 protein_coding NA 3597 -1 SNV HGNC HGNC:26252 1 CCDS44157.1 ENSP00000360062 Q5VTH9.155 UPI0000366548 Q5VTH9-2 1 NA NA PASS SITE 64,36|29,19 NA NA 1 93 20,20 170,169 60,60 23 1.73 NA 15.65 NA FALSE 6.00 93 NA NA NA FALSE NA NA 131.74 1 66834006 HCC1395_HCC1395T 26 0.630 74 6,11 13,22 19,33 NA 0/1 NA NA NA NA 19,7,29,19 C/G PANCANCER NA FALSE DNAI4 chr1:66834006:66834007:C:G SNV 2:0 chr1:61899545:84414697:2:0:1 TRUE NA 0.96 +chr1 67052899 67052900 G A 32 99 0.323232323232323 MODIFIER SLC35D1 ENSG00000116704 A intron_variant Transcript ENST00000235345 protein_coding 2/11 ENST00000235345.6:c.238-42C>T NA -1 SNV HGNC HGNC:20800 YES NM_015139.3 1 P1 CCDS636.1 ENSP00000235345 Q9NTN3.166 UPI0000137AF8 Q9NTN3-1 1 1 NA NA PASS SITE 92,91|16,16 NA NA 1 93 20,20 172,154 60,60 34 1.94 NA 25.27 NA FALSE 6.00 45 NA NA NA FALSE NA NA 77.15 1 67052899 HCC1395_HCC1395T 67 0.315 99 20,13 25,4 49,22 NA 0/1 NA NA NA NA 34,33,16,16 G/A PANCANCER NA FALSE SLC35D1 chr1:67052899:67052900:G:A SNV 2:0 chr1:61899545:84414697:2:0:1 TRUE NA 0.96 +chr1 76627440 76627441 C T 40 211 0.18957345971564 LOW ST6GALNAC3 ENSG00000184005 T splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000328299 protein_coding 3/4 ENST00000328299.4:c.624-12C>T NA rs746506226 1 SNV HGNC HGNC:19343 YES NM_152996.4 1 P1 CCDS672.1 ENSP00000329214 Q8NDV1.166 UPI000006F75A Q8NDV1-1 4.006e-06 0 0 0 5.444e-05 0 0 0 0 5.444e-05 gnomADe_EAS 1 NA NA PASS SITE 205,148|22,18 NA NA 1 93 20,20 157,161 60,60 45 2.08 NA 35.47 NA FALSE 6.00 89 NA NA NA FALSE NA NA 81.54 1 76627440 HCC1395_HCC1395T 171 0.195 211 35,10 71,13 109,26 NA 0/1 NA NA NA NA 100,71,22,18 C/T PANCANCER NA FALSE ST6GALNAC3 chr1:76627440:76627441:C:T SNV 2:0 chr1:61899545:84414697:2:0:1 TRUE NA 0.96 +chr1 77559130 77559131 T G 61 137 0.445255474452555 MODIFIER AK5 ENSG00000154027 G 3_prime_UTR_variant Transcript ENST00000344720 protein_coding 14/14 ENST00000344720.9:c.*460T>G NA 3097 1 SNV HGNC HGNC:365 1 CCDS676.1 ENSP00000341430 Q9Y6K8.189 UPI0000167E21 Q9Y6K8-3 1 NA NA PASS SITE 92,122|30,31 NA NA 1 93 20,20 167,180 60,60 31 2.03 NA 31.51 NA FALSE 6.00 93 NA NA NA FALSE NA NA 160.92 1 77559130 HCC1395_HCC1395T 76 0.435 137 18,16 28,22 54,41 NA 0/1 NA NA NA NA 35,41,30,31 T/G PANCANCER NA FALSE AK5 chr1:77559130:77559131:T:G SNV 2:0 chr1:61899545:84414697:2:0:1 TRUE NA 0.96 +chr1 83904034 83904035 A G 28 60 0.466666666666667 MODIFIER TTLL7 ENSG00000137941 G intron_variant Transcript ENST00000260505 protein_coding 18/20 ENST00000260505.13:c.2208+45T>C NA rs756255058 -1 SNV HGNC HGNC:26242 YES NM_024686.6 2 P1 CCDS690.2 ENSP00000260505 Q6ZT98.145 UPI000020391D Q6ZT98-1 8.089e-06 0 0 0 0 0 1.781e-05 0 0 1.781e-05 gnomADe_NFE 1 NA NA PASS SITE 60,25|19,9 NA NA 1 93 20,38 164,185 60,60 30 1.61 NA 11.44 NA FALSE 4.61 93 NA NA NA FALSE NA NA 87.62 1 83904034 HCC1395_HCC1395T 32 0.490 60 9,9 15,12 24,23 NA 0/1 NA NA NA NA 23,9,19,9 A/G PANCANCER NA FALSE TTLL7 chr1:83904034:83904035:A:G SNV 2:0 chr1:61899545:84414697:2:0:1 TRUE NA 0.96 +chr1 86063856 86063857 G C 42 83 0.506024096385542 MODIFIER COL24A1 ENSG00000171502 C intron_variant Transcript ENST00000370571 protein_coding 7/59 ENST00000370571.7:c.1708-97C>G NA -1 SNV HGNC HGNC:20821 YES NM_152890.7 1 P1 CCDS41353.1 ENSP00000359603 Q17RW2.139 UPI000013E81F Q17RW2-1 1 NA NA PASS SITE 11,51|7,35 NA NA 1 68 39,31 165,182 60,60 22 1.28 NA 5.12 NA FALSE 6.00 93 NA NA NA FALSE NA NA 112.69 1 86063856 HCC1395_HCC1395T 41 0.506 83 8,10 23,21 34,35 NA 0/1 NA NA NA NA 7,34,7,35 G/C PANCANCER NA FALSE COL24A1 chr1:86063856:86063857:G:C SNV 5:0 chr1:85018593:86385737:5:0:1 NA NA 0.96 +chr1 86453474 86453475 G A 334 565 0.591150442477876 MODERATE CLCA2 ENSG00000137975 A missense_variant Transcript ENST00000370565 protein_coding 13/14 ENST00000370565.5:c.2261G>A ENSP00000359596.4:p.G754E ENSP00000359596.4 p.G754E 2338 2261 754 G/E gGa/gAa COSV65289124 1 SNV HGNC HGNC:2016 YES NM_006536.7 1 P1 CCDS708.1 ENSP00000359596 Q9UQC9.156 UPI0000035838 tolerated(0.11) possibly_damaging(0.583) AlphaFold_DB_import:AF-Q9UQC9-F1&PANTHER:PTHR10579&TIGRFAM:TIGR00868&Low_complexity_(Seg):seg 1 1 1 NA NA PASS SITE 262,165|194,140 NA NA 1 93 20,20 164,164 60,60 32 2.13 NA 39.03 NA FALSE 6.00 93 NA NA NA FALSE NA NA 837.62 1 86453474 HCC1395_HCC1395T 231 0.577 565 60,53 94,153 158,216 NA 0/1 NA NA NA NA 147,84,194,140 G/A PANCANCER NA FALSE CLCA2_p.G754E chr1:86453474:86453475:G:A SNV 4:0 chr1:86386938:97883329:4:0:1 NA NA 0.96 +chr1 87107554 87107555 G A 16 26 0.615384615384615 MODIFIER HS2ST1 ENSG00000153936 A 3_prime_UTR_variant Transcript ENST00000370550 protein_coding 7/7 ENST00000370550.10:c.*2858G>A NA 4331 1 SNV HGNC HGNC:5193 YES NM_012262.4 1 P1 CCDS711.1 ENSP00000359581 Q7LGA3.154 UPI0000073F43 Q7LGA3-1 1 1 NA NA PASS SITE 4,27|0,16 NA NA 1 50 38,37 177,203 60,60 11 1.26 NA 5.07 NA FALSE 6.00 30 NA NA NA FALSE NA NA 58.27 1 87107554 HCC1395_HCC1395T 10 0.607 26 2,2 8,13 10,16 NA 0/1 NA NA NA NA 0,10,0,16 G/A PANCANCER NA FALSE HS2ST1 chr1:87107554:87107555:G:A SNV 4:0 chr1:86386938:97883329:4:0:1 NA NA 0.96 +chr1 90714575 90714576 G C 31 139 0.223021582733813 LOW BARHL2 ENSG00000143032 C synonymous_variant Transcript ENST00000370445 protein_coding 2/3 ENST00000370445.5:c.807C>G ENSP00000359474.3:p.L269= ENSP00000359474.3 p.L269= 914 807 269 L ctC/ctG COSV64981379 -1 SNV HGNC HGNC:954 YES NM_020063.2 1 P1 CCDS730.1 ENSP00000359474 Q9NY43.164 UPI00001B50ED CDD:cd00086&Pfam:PF00046&Gene3D:1.10.10.60&SMART:SM00389&Superfamily:SSF46689&PROSITE_profiles:PS50071&PANTHER:PTHR24330&PROSITE_patterns:PS00027&Prints:PR00024&AlphaFold_DB_import:AF-Q9NY43-F1 1 1 1 NA NA PASS SITE 88,91|13,18 NA NA 1 93 20,20 163,155 60,60 33 1.69 NA 14.45 NA FALSE 6.00 93 NA NA NA FALSE NA NA 67.66 1 90714575 HCC1395_HCC1395T 108 0.215 139 36,8 31,10 72,19 NA 0/1 NA NA NA NA 51,57,13,18 G/C PANCANCER NA FALSE BARHL2_p.L269= chr1:90714575:90714576:G:C SNV 4:0 chr1:86386938:97883329:4:0:1 NA NA 0.96 +chr1 92300283 92300284 C G 13 58 0.224137931034483 MODIFIER GLMN ENSG00000174842 G upstream_gene_variant Transcript ENST00000370360 protein_coding NA rs542697396 1296 -1 SNV HGNC HGNC:14373 YES NM_053274.3 1 P1 CCDS738.1 ENSP00000359385 Q92990.178 UPI0000040A53 Q92990-1 1 0.0002 0 0 0 0.001 0 0 0 0 0 0 0 0 0 0 0.001 EUR 1 NA NA PASS SITE 34,57|3,10 NA NA 1 93 36,38 189,211 60,60 29 1.56 NA 10.53 NA FALSE 6.00 48 NA NA NA FALSE NA NA 41.85 1 92300283 HCC1395_HCC1395T 45 0.250 58 15,3 22,10 41,13 NA 0/1 NA NA NA NA 13,32,3,10 C/G PANCANCER NA FALSE GLMN chr1:92300283:92300284:C:G SNV 4:0 chr1:86386938:97883329:4:0:1 NA NA 0.96 +chr1 92847140 92847141 G T 77 105 0.733333333333333 MODIFIER DIPK1A ENSG00000154511 T intron_variant Transcript ENST00000370310 protein_coding 4/4 ENST00000370310.5:c.474+43C>A NA -1 SNV HGNC HGNC:32213 YES NM_001006605.5 2 P1 CCDS44173.1 ENSP00000359333 Q5T7M9.135 UPI0000037783 Q5T7M9-1 1 NA NA PASS SITE 56,47|43,34 NA NA 1 93 20,20 151,165 60,60 40 1.68 NA 14.05 NA FALSE 6.00 93 NA NA NA FALSE NA NA 208.49 1 92847140 HCC1395_HCC1395T 28 0.732 105 7,16 10,32 18,51 NA 0/1 NA NA NA NA 14,14,43,34 G/T PANCANCER NA FALSE DIPK1A chr1:92847140:92847141:G:T SNV 4:0 chr1:86386938:97883329:4:0:1 NA NA 0.96 +chr1 94036625 94036626 T A 5 9 0.555555555555556 MODIFIER ABCA4 ENSG00000198691 A intron_variant Transcript ENST00000370225 protein_coding 26/49 ENST00000370225.4:c.3862+115A>T NA -1 SNV HGNC HGNC:34 YES NM_000350.3 1 P1 CCDS747.1 ENSP00000359245 P78363.212 UPI000012511C 1 1 NA NA PASS SITE 12,3|3,2 NA NA 1 25 36,20 212,143 60,60 29 0.954 NA 2.41 NA FALSE 6.00 33 NA NA NA FALSE NA NA 11.69 1 94036625 HCC1395_HCC1395T 4 0.444 9 2,2 2,1 4,3 NA 0/1 NA NA NA NA 4,0,3,2 T/A PANCANCER NA FALSE ABCA4 chr1:94036625:94036626:T:A SNV 4:0 chr1:86386938:97883329:4:0:1 NA NA 0.96 +chr1 107403782 107403783 G A 79 171 0.461988304093567 MODIFIER NTNG1 ENSG00000162631 A intron_variant&non_coding_transcript_variant Transcript ENST00000294649 retained_intron 4/4 ENST00000294649.8:n.1800-3900G>A NA 1 SNV HGNC HGNC:23319 1 1 1 NA NA PASS SITE 97,123|39,41 NA NA 1 93 20,20 153,159 60,60 43 1.95 NA 26.15 NA FALSE 6.00 90 NA NA NA FALSE NA NA 180.84 1 107403782 HCC1395_HCC1395T 92 0.431 171 18,13 25,26 61,46 NA 0/1 NA NA NA NA 43,49,38,41 G/A PANCANCER NA FALSE NTNG1 chr1:107403782:107403783:G:A SNV 2:0 chr1:98685079:117965270:2:0:1 TRUE NA 0.96 +chr1 109265333 109265334 C G 14 50 0.28 MODIFIER CELSR2 ENSG00000143126 G intron_variant Transcript ENST00000271332 protein_coding 13/33 ENST00000271332.4:c.5727+22C>G NA 1 SNV HGNC HGNC:3231 YES NM_001408.3 1 P1 CCDS796.1 ENSP00000271332 Q9HCU4.193 UPI00000015B6 1 NA NA PASS SITE 45,70|3,11 NA NA 1 93 20,40 159,188 60,60 28 1.71 NA 15.05 NA FALSE 6.00 78 NA NA NA FALSE NA NA 40.33 1 109265333 HCC1395_HCC1395T 36 0.341 50 15,5 10,6 25,13 NA 0/1 NA NA NA NA 14,22,3,11 C/G PANCANCER NA FALSE CELSR2 chr1:109265333:109265334:C:G SNV 2:0 chr1:98685079:117965270:2:0:1 TRUE NA 0.96 +chr1 109267889 109267890 A C 65 119 0.546218487394958 LOW CELSR2 ENSG00000143126 C synonymous_variant Transcript ENST00000271332 protein_coding 17/34 ENST00000271332.4:c.6147A>C ENSP00000271332.3:p.S2049= ENSP00000271332.3 p.S2049= 6688 6147 2049 S tcA/tcC 1 SNV HGNC HGNC:3231 YES NM_001408.3 1 P1 CCDS796.1 ENSP00000271332 Q9HCU4.193 UPI00000015B6 Gene3D:1.25.40.610&PANTHER:PTHR24026 1 NA NA PASS SITE 120,100|34,31 NA NA 1 93 20,20 150,170 60,60 33 2.03 NA 31.60 NA FALSE 6.00 93 NA NA NA FALSE NA NA 157.15 1 109267889 HCC1395_HCC1395T 54 0.519 119 14,14 20,22 37,40 NA 0/1 NA NA NA NA 31,23,34,31 A/C PANCANCER NA FALSE CELSR2_p.S2049= chr1:109267889:109267890:A:C SNV 2:0 chr1:98685079:117965270:2:0:1 TRUE NA 0.96 +chr1 109509577 109509578 C G 17 40 0.425 MODIFIER AMIGO1 ENSG00000181754 G 5_prime_UTR_variant Transcript ENST00000369862 protein_coding 1/2 ENST00000369862.1:c.-223G>C NA 162 -1 SNV HGNC HGNC:20824 5 P1 CCDS30795.1 ENSP00000358878 Q86WK6.164 UPI0000035067 1 NA NA PASS SITE 26,55|7,10 NA NA 1 93 20,20 149,174 60,60 20 1.61 NA 11.99 NA FALSE 6.00 92 NA NA NA FALSE NA NA 44.05 1 109509577 HCC1395_HCC1395T 23 0.394 40 8,6 11,5 19,12 NA 0/1 NA NA NA NA 6,17,7,10 C/G PANCANCER NA FALSE AMIGO1 chr1:109509577:109509578:C:G SNV 2:0 chr1:98685079:117965270:2:0:1 TRUE NA 0.96 +chr1 109621023 109621024 C A 101 170 0.594117647058824 MODIFIER AMPD2 ENSG00000116337 A 5_prime_UTR_variant Transcript ENST00000256578 protein_coding 1/18 ENST00000256578.8:c.-153C>A NA 370 COSV56649690&COSV56650225 1 SNV HGNC HGNC:469 5 P1 CCDS805.2 ENSP00000256578 A0A5F9UK94.14 UPI00103253B3 1 1&1 1&1 1 NA NA PASS SITE 162,128|55,46 NA NA 1 93 20,20 152,161 60,60 37 2.14 NA 40.94 NA FALSE 6.00 93 NA NA NA FALSE NA NA 252.89 1 109621023 HCC1395_HCC1395T 69 0.594 170 20,26 20,33 42,62 NA 0/1 NA NA NA NA 39,30,55,46 C/A PANCANCER NA FALSE AMPD2 chr1:109621023:109621024:C:A SNV 2:0 chr1:98685079:117965270:2:0:1 TRUE NA 0.96 +chr1 111488999 111489000 G C 68 161 0.422360248447205 MODIFIER RNU6-792P ENSG00000200360 C downstream_gene_variant Transcript ENST00000363490 snRNA NA rs777715402 1318 -1 SNV HGNC HGNC:47755 YES 6.436e-05 0 0 0 0 0 0 0.0003273 0.0004586 0.0004586 gnomADe_SAS 1 NA NA PASS SITE 112,172|28,40 NA NA 1 93 20,20 162,169 60,60 33 2.11 NA 37.62 NA FALSE 6.00 93 NA NA NA FALSE NA NA 169.22 1 111488999 HCC1395_HCC1395T 93 0.427 161 22,17 33,22 58,43 NA 0/1 NA NA NA NA 38,55,28,40 G/C PANCANCER NA FALSE RNU6-792P chr1:111488999:111489000:G:C SNV 2:0 chr1:98685079:117965270:2:0:1 TRUE NA 0.96 +chr1 111715329 111715330 C T 21 42 0.5 MODIFIER RAP1A ENSG00000116473 T downstream_gene_variant Transcript ENST00000356415 protein_coding NA rs921889262 2216 1 SNV HGNC HGNC:9855 1 P1 CCDS840.1 ENSP00000348786 P62834.191 A8KAH9.125 UPI0000001250 1 NA NA PASS SITE 57,8|17,4 NA NA 1 93 38,35 177,159 60,60 20 1.61 NA 11.43 NA FALSE 6.00 93 NA NA NA FALSE NA NA 65.73 1 111715329 HCC1395_HCC1395T 21 0.487 42 5,9 14,9 19,18 NA 0/1 NA NA NA NA 19,2,17,4 C/T PANCANCER NA FALSE RAP1A chr1:111715329:111715330:C:T SNV 2:0 chr1:98685079:117965270:2:0:1 TRUE NA 0.96 +chr1 111982877 111982878 C T 16 30 0.533333333333333 MODIFIER KCND3 ENSG00000171385 T intron_variant Transcript ENST00000302127 protein_coding 1/7 ENST00000302127.5:c.-72-79G>A NA -1 SNV HGNC HGNC:6239 YES NM_001378969.1 5 P3 CCDS843.1 ENSP00000306923 Q9UK17.197 UPI000003050A Q9UK17-1 1 1 NA NA PASS SITE 13,43|3,13 NA NA 1 93 34,33 175,210 60,60 15 1.52 NA 9.58 NA FALSE 6.00 73 NA NA NA FALSE NA NA 45.20 1 111982877 HCC1395_HCC1395T 14 0.519 30 4,5 7,7 12,13 NA 0/1 NA NA NA NA 2,12,3,13 C/T PANCANCER NA FALSE KCND3 chr1:111982877:111982878:C:T SNV 2:0 chr1:98685079:117965270:2:0:1 TRUE NA 0.96 +chr1 112956212 112956213 G A 68 135 0.503703703703704 MODIFIER SLC16A1 ENSG00000155380 A upstream_gene_variant Transcript ENST00000369626 protein_coding NA 16 -1 SNV HGNC HGNC:10922 YES NM_003051.4 1 P1 CCDS858.1 ENSP00000358640 P53985.211 A0A024R0H1.52 UPI00000012F5 P53985-1 1 1 NA NA PASS SITE 139,154|29,39 NA NA 1 93 20,20 153,158 60,60 30 2.18 NA 44.15 NA FALSE 6.00 93 NA NA NA FALSE NA NA 170.41 1 112956212 HCC1395_HCC1395T 67 0.500 135 22,17 18,22 43,43 NA 0/1 NA NA NA NA 27,40,29,39 G/A PANCANCER NA FALSE SLC16A1 chr1:112956212:112956213:G:A SNV 2:0 chr1:98685079:117965270:2:0:1 TRUE NA 0.96 +chr1 116111759 116111760 T C 13 26 0.5 MODIFIER MAB21L3 ENSG00000173212 C 5_prime_UTR_variant Transcript ENST00000369500 protein_coding 2/8 ENST00000369500.4:c.-261T>C NA 243 1 SNV HGNC HGNC:26787 YES NM_152367.3 2 P1 CCDS886.1 ENSP00000358512 Q8N8X9.123 UPI000013EFA5 1 NA NA PASS SITE 31,29|6,7 NA NA 1 91 20,20 167,136 60,60 25 1.48 NA 8.73 NA FALSE 6.00 64 NA NA NA FALSE NA NA 31.65 1 116111759 HCC1395_HCC1395T 13 0.500 26 3,4 6,4 9,9 NA 0/1 NA NA NA NA 6,7,6,7 T/C PANCANCER NA FALSE MAB21L3 chr1:116111759:116111760:T:C SNV 2:0 chr1:98685079:117965270:2:0:1 TRUE NA 0.96 +chr1 116579677 116579681 C CCTA 114 211 0.540284360189573 HIGH IGSF3 ENSG00000143061 CTA stop_gained&inframe_insertion Transcript ENST00000318837 protein_coding 10/11 ENST00000318837.6:c.3108_3109insTAG ENSP00000321184.6:p.E1036_E1037ins* ENSP00000321184.6 p.E1036_E1037ins* 3213-3214 3108-3109 1036-1037 -/* -/TAG -1 insertion HGNC HGNC:5950 2 P4 CCDS30814.1 ENSP00000321184 O75054.163 UPI0000140437 O75054-2 1 Gene3D:2.60.40.10&AlphaFold_DB_import:AF-O75054-F1&Coiled-coils_(Ncoils):Coil&PROSITE_profiles:PS50835&SMART:SM00409&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg 1 NA NA PASS SITE 203,181|61,53 NA NA 1 93 20,34 163,161 60,60 28 1.99 NA 56.38 NA FALSE 6.00 93 NA NA NA FALSE NA NA 209.50 1 116579677 HCC1395_HCC1395T 97 0.546 211 19,28 37,29 65,79 NA 0/1 NA NA NA NA 54,43,61,53 C/CCTA PANCANCER NA FALSE IGSF3_p.E1036_E1037ins* chr1:116579677:116579681:C:CCTA indel 2:0 chr1:98685079:117965270:2:0:1 TRUE NA 0.96 +chr1 119622238 119622239 G C 27 168 0.160714285714286 MODIFIER ZNF697 ENSG00000143067 C 3_prime_UTR_variant Transcript ENST00000421812 protein_coding 3/3 ENST00000421812.3:c.*467C>G NA 2718 -1 SNV HGNC HGNC:32034 YES NM_001080470.2 3 P1 CCDS44202.1 ENSP00000396857 Q5TEC3.138 UPI0000DD78D7 1 NA NA PASS SITE 115,104|13,14 NA NA 1 93 20,20 162,173 60,60 31 1.74 NA 15.94 NA FALSE 6.00 80 NA NA NA FALSE NA NA 65.95 1 119622238 HCC1395_HCC1395T 141 0.178 168 35,6 53,12 91,19 NA 0/1 NA NA NA NA 76,65,13,14 G/C PANCANCER NA FALSE ZNF697 chr1:119622238:119622239:G:C SNV 5:0 chr1:118023330:120533204:5:0:1 NA NA 0.96 +chr1 119895936 119895937 C T 99 570 0.173684210526316 MODERATE ADAM30 ENSG00000134249 T missense_variant Transcript ENST00000369400 protein_coding 1/1 ENST00000369400.2:c.401G>A ENSP00000358407.1:p.R134Q ENSP00000358407.1 p.R134Q 580 401 134 R/Q cGa/cAa rs1037978740&COSV65560937 -1 SNV HGNC HGNC:208 YES NM_021794.4 P1 CCDS907.1 ENSP00000358407 Q9UKF2.185 UPI000004C638 Q9UKF2-1 deleterious(0.03) benign(0.319) AlphaFold_DB_import:AF-Q9UKF2-F1&Pfam:PF01562&PANTHER:PTHR11905 0&1 0&1 1 NA NA PASS SITE 384,384|49,50 NA NA 1 93 20,20 161,174 60,60 34 2.31 NA 60.50 NA FALSE 6.00 93 NA NA NA FALSE NA NA 221.67 1 119895936 HCC1395_HCC1395T 471 0.173 570 127,22 190,45 331,69 NA 0/1 NA NA NA NA 237,234,49,50 C/T PANCANCER NA FALSE ADAM30_p.R134Q chr1:119895936:119895937:C:T SNV 5:0 chr1:118023330:120533204:5:0:1 NA NA 0.96 +chr1 119914435 119914436 C T 20 43 0.465116279069767 MODIFIER NOTCH2 ENSG00000134250 T 3_prime_UTR_variant Transcript ENST00000256646 protein_coding 34/34 ENST00000256646.7:c.*871G>A NA 8543 -1 SNV HGNC HGNC:7882 YES NM_024408.4 1 P1 CCDS908.1 ENSP00000256646 Q04721.243 UPI000013CF1D 1 1 NA NA PASS SITE 21,22|12,8 NA NA 1 52 34,20 179,192 60,60 32 1.20 NA 4.52 NA FALSE 6.00 40 NA NA NA FALSE NA NA 53.69 1 119914435 HCC1395_HCC1395T 23 0.441 43 2,3 16,11 19,15 NA 0/1 NA NA NA NA 11,12,12,8 C/T PANCANCER TRUE FALSE NOTCH2 chr1:119914435:119914436:C:T SNV 5:0 chr1:118023330:120533204:5:0:1 NA NA 0.96 +chr1 119966549 119966550 G A 48 224 0.214285714285714 MODIFIER NOTCH2 ENSG00000134250 A intron_variant Transcript ENST00000256646 protein_coding 8/33 ENST00000256646.7:c.1454-60C>T NA -1 SNV HGNC HGNC:7882 YES NM_024408.4 1 P1 CCDS908.1 ENSP00000256646 Q04721.243 UPI000013CF1D 1 1 NA NA PASS SITE 113,176|15,33 NA NA 1 93 20,20 180,185 60,60 36 1.91 NA 24.33 NA FALSE 6.00 68 NA NA NA FALSE NA NA 114.93 1 119966549 HCC1395_HCC1395T 176 0.212 224 37,10 85,23 133,35 NA 0/1 NA NA NA NA 69,107,15,33 G/A PANCANCER TRUE FALSE NOTCH2 chr1:119966549:119966550:G:A SNV 5:0 chr1:118023330:120533204:5:0:1 NA NA 0.96 +chr1 120160393 120160394 C T 28 119 0.235294117647059 MODERATE SEC22B ENSG00000265808 T missense_variant Transcript ENST00000578049 protein_coding 4/5 ENST00000578049.4:c.484G>A ENSP00000463393.1:p.A162T ENSP00000463393.1 p.A162T 623 484 162 A/T Gca/Aca -1 SNV HGNC HGNC:10700 YES NM_004892.6 1 P1 CCDS83523.1 ENSP00000463393 O75396.197 UPI0000022D17 tolerated(0.13) benign(0.143) PDB-ENSP_mappings:2nup.C&PDB-ENSP_mappings:2nut.C&Low_complexity_(Seg):seg&PROSITE_profiles:PS50892&CDD:cd15866&PANTHER:PTHR45837&Gene3D:1.20.5.110&Pfam:PF00957&Superfamily:SSF58038&Prints:PR00219&AlphaFold_DB_import:AF-O75396-F1 1 NA NA PASS SITE 111,66|22,6 NA NA 1 93 20,31 159,196 58,58 31 1.77 NA 17.10 NA FALSE 6.00 41 NA NA NA FALSE NA NA 67.49 1 120160393 HCC1395_HCC1395T 91 0.271 119 34,16 26,5 60,22 NA 0/1 NA NA NA NA 60,31,22,6 C/T PANCANCER NA FALSE SEC22B_p.A162T chr1:120160393:120160394:C:T SNV 5:0 chr1:118023330:120533204:5:0:1 NA NA 0.96 +chr1 120233174 120233175 G C 29 40 0.725 MODIFIER ENSG00000274642 C intron_variant&non_coding_transcript_variant Transcript ENST00000612320 unprocessed_pseudogene 1/5 ENST00000612320.1:n.234-18240G>C NA 1 SNV YES 1 NA NA PASS SITE 31,43|4,25 NA NA 1 93 38,40 185,212 25,42 15 1.75 NA 15.64 NA FALSE 6.00 93 NA NA NA FALSE NA NA 95.35 1 120233174 HCC1395_HCC1395T 11 0.710 40 8,16 2,9 10,26 NA 0/1 NA NA NA NA 1,10,4,25 G/C PANCANCER NA FALSE chr1:120233174:120233175:G:C SNV 5:0 chr1:118023330:120533204:5:0:1 NA NA 0.96 +chr1 147757950 147757951 G C 40 53 0.754716981132076 MODIFIER GJA5 ENSG00000265107 C downstream_gene_variant Transcript ENST00000430508 protein_coding NA 534 -1 cds_end_NF SNV HGNC HGNC:4279 2 ENSP00000407645 A0A0B4J1Y3.50 UPI0003F47BF3 1 1 NA NA PASS SITE 30,36|14,26 NA NA 1 93 34,20 166,175 60,60 29 1.60 NA 11.74 NA FALSE 6.00 70 NA NA NA FALSE NA NA 111.35 1 147757950 HCC1395_HCC1395T 13 0.697 53 4,4 6,21 12,29 NA 0/1 NA NA NA NA 5,8,14,26 G/C PANCANCER NA FALSE GJA5 chr1:147757950:147757951:G:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 149899625 149899626 G C 135 196 0.688775510204082 MODIFIER SV2A ENSG00000159164 C downstream_gene_variant Transcript ENST00000369146 protein_coding NA 3693 -1 SNV HGNC HGNC:20566 YES NM_014849.5 1 P1 CCDS940.1 ENSP00000358142 Q7L0J3.172 UPI000000DAD2 Q7L0J3-1 1 NA NA PASS SITE 109,84|85,50 NA NA 1 93 20,20 170,173 60,60 34 1.99 NA 28.85 NA FALSE 6.00 93 NA NA NA FALSE NA NA 396.78 1 149899625 HCC1395_HCC1395T 61 0.685 196 20,48 22,46 44,97 NA 0/1 NA NA NA NA 37,24,85,50 G/C PANCANCER NA FALSE SV2A chr1:149899625:149899626:G:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 149930147 149930148 G C 31 109 0.284403669724771 MODIFIER SF3B4 ENSG00000143368 C upstream_gene_variant Transcript ENST00000271628 protein_coding NA 2344 -1 SNV HGNC HGNC:10771 YES NM_005850.5 1 P1 CCDS72900.1 ENSP00000271628 Q15427.218 UPI0000135472 1 1 NA NA PASS SITE 50,74|12,19 NA NA 1 93 20,20 168,159 60,60 31 1.54 NA 10.19 NA FALSE 6.00 78 NA NA NA FALSE NA NA 71.88 1 149930147 HCC1395_HCC1395T 78 0.286 109 20,11 27,6 49,19 NA 0/1 NA NA NA NA 34,44,12,19 G/C PANCANCER NA FALSE SF3B4 chr1:149930147:149930148:G:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 150159834 150159835 G C 60 88 0.681818181818182 MODIFIER PLEKHO1 ENSG00000023902 C 3_prime_UTR_variant Transcript ENST00000369124 protein_coding 6/6 ENST00000369124.5:c.*311G>C NA 1883 1 SNV HGNC HGNC:24310 YES NM_016274.6 1 P1 CCDS945.1 ENSP00000358120 Q53GL0.133 UPI000006DFAC Q53GL0-1 1 NA NA PASS SITE 48,59|29,31 NA NA 1 93 20,20 155,159 60,60 44 1.73 NA 15.64 NA FALSE 6.00 93 NA NA NA FALSE NA NA 184.93 1 150159834 HCC1395_HCC1395T 28 0.710 88 10,18 7,24 18,45 NA 0/1 NA NA NA NA 12,16,29,31 G/C PANCANCER NA FALSE PLEKHO1 chr1:150159834:150159835:G:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 150261629 150261630 G A 94 232 0.405172413793103 MODIFIER APH1A ENSG00000117362 A downstream_gene_variant Transcript ENST00000360244 protein_coding NA rs139115533 3777 -1 SNV HGNC HGNC:29509 1 CCDS41391.1 ENSP00000353380 Q96BI3.180 UPI0000048EEC Q96BI3-2 1.598e-05 0 0 0 0 0 3.543e-05 0 0 3.287e-05 2.415e-05 0 0 0 0 0 0 5.88e-05 0 0 5.88e-05 gnomADg_NFE 1 NA NA PASS SITE 139,207|36,58 NA NA 1 93 20,20 155,168 60,60 29 2.13 NA 40.03 NA FALSE 6.00 93 NA NA NA FALSE NA NA 235.37 1 150261629 HCC1395_HCC1395T 138 0.409 232 43,21 39,35 87,60 NA 0/1 NA NA NA NA 57,81,36,58 G/A PANCANCER NA FALSE APH1A chr1:150261629:150261630:G:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 150273912 150273913 G T 3 4 0.75 MODIFIER APH1A ENSG00000117362 T upstream_gene_variant Transcript ENST00000236017 protein_coding NA 4889 -1 cds_end_NF SNV HGNC HGNC:29509 2 ENSP00000236017 Q5TB21.116 UPI0000470B54 1 NA NA PASS SITE 10,1|3,0 NA NA 1 30 39,37 242,201 60,60 42 1.02 NA 2.71 NA FALSE 6.00 39 NA NA NA FALSE NA NA 11.33 1 150273912 HCC1395_HCC1395T 1 0.667 4 1,1 0,2 1,3 NA 0/1 NA NA NA NA 1,0,3,0 G/T PANCANCER NA FALSE APH1A chr1:150273912:150273913:G:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 151831100 151831101 C T 47 157 0.299363057324841 MODIFIER RORC ENSG00000143365 T intron_variant Transcript ENST00000318247 protein_coding 1/10 ENST00000318247.7:c.40+625G>A NA -1 SNV HGNC HGNC:10260 YES NM_005060.4 1 P2 CCDS1004.1 ENSP00000327025 P51449.207 Q6I9R9.156 UPI000006FBD8 P51449-1 1 1 NA NA PASS SITE 93,107|22,25 NA NA 1 93 20,20 160,155 60,60 32 1.77 NA 17.46 NA FALSE 6.00 85 NA NA NA FALSE NA NA 105.62 1 151831100 HCC1395_HCC1395T 110 0.308 157 22,16 37,10 64,28 NA 0/1 NA NA NA NA 54,56,22,25 C/T PANCANCER NA FALSE RORC chr1:151831100:151831101:C:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 153689508 153689509 T A 62 369 0.168021680216802 MODIFIER NPR1 ENSG00000169418 A non_coding_transcript_exon_variant Transcript ENST00000368677 retained_intron 3/6 ENST00000368677.2:n.556T>A NA 556 1 SNV HGNC HGNC:7943 5 1 NA NA PASS SITE 252,332|27,35 NA NA 1 93 20,20 160,152 60,60 24 2.24 NA 51.72 NA FALSE 6.00 93 NA NA NA FALSE NA NA 123.30 1 153689508 HCC1395_HCC1395T 307 0.157 369 77,16 92,18 197,36 NA 0/1 NA NA NA NA 129,178,27,35 T/A PANCANCER NA FALSE NPR1 chr1:153689508:153689509:T:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 154480758 154480759 A G 53 263 0.201520912547529 MODIFIER SHE ENSG00000169291 G 3_prime_UTR_variant Transcript ENST00000304760 protein_coding 6/6 ENST00000304760.3:c.*3391T>C NA 5265 rs1055960808 -1 SNV HGNC HGNC:27004 YES NM_001010846.3 1 P1 CCDS30877.1 ENSP00000307369 Q5VZ18.128 UPI00004588E0 1.314e-05 4.825e-05 0 0 0 0 0 0 0 0 0 4.825e-05 gnomADg_AFR 1 NA NA PASS SITE 170,213|23,30 NA NA 1 93 20,20 180,177 60,60 44 2.10 NA 36.97 NA FALSE 6.00 93 NA NA NA FALSE NA NA 126.93 1 154480758 HCC1395_HCC1395T 210 0.212 263 55,15 85,20 146,39 NA 0/1 NA NA NA NA 92,118,23,30 A/G PANCANCER NA FALSE SHE chr1:154480758:154480759:A:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 154579186 154579187 G C 26 71 0.366197183098592 MODIFIER ADAR ENSG00000160710 C downstream_gene_variant Transcript ENST00000368471 protein_coding NA 2881 -1 SNV HGNC HGNC:225 1 CCDS30879.1 ENSP00000357456 P55265.225 UPI0000458ADB P55265-5 1 1 NA NA PASS SITE 55,41|14,12 NA NA 1 93 20,20 156,164 60,60 37 1.51 NA 9.33 NA FALSE 6.00 93 NA NA NA FALSE NA NA 59.40 1 154579186 HCC1395_HCC1395T 45 0.340 71 9,7 21,8 32,16 NA 0/1 NA NA NA NA 28,17,14,12 G/C PANCANCER NA FALSE ADAR chr1:154579186:154579187:G:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 154590263 154590264 T A 59 205 0.28780487804878 MODERATE ADAR ENSG00000160710 A missense_variant Transcript ENST00000368471 protein_coding 7/15 ENST00000368471.8:c.1532A>T ENSP00000357456.3:p.E511V ENSP00000357456.3 p.E511V 2516 1532 511 E/V gAg/gTg rs144119808&COSV52722431 -1 SNV HGNC HGNC:225 1 CCDS30879.1 ENSP00000357456 P55265.225 UPI0000458ADB P55265-5 1 deleterious_low_confidence(0.01) probably_damaging(0.992) AlphaFold_DB_import:AF-P55265-F1&PANTHER:PTHR10910 3.977e-06 6.152e-05 0 0 0 0 0 0 0 6.593e-06 2.426e-05 0 0 0 0 0 0 0 0 0 6.152e-05 gnomADe_AFR 0&1 0&1 1 NA NA PASS SITE 136,144|31,28 NA NA 1 93 20,20 164,145 60,60 27 1.95 NA 26.44 NA FALSE 6.00 88 NA NA NA FALSE NA NA 134.24 1 154590263 HCC1395_HCC1395T 146 0.298 205 38,12 51,23 91,38 NA 0/1 NA NA NA NA 73,73,31,28 T/A PANCANCER NA FALSE ADAR_p.E511V chr1:154590263:154590264:T:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 155086199 155086200 GTGCTGGGTGAGTCTGCGCAGCGCCCTCTGGTGGCCAC G 82 185 0.443243243243243 HIGH EFNA3 ENSG00000143590 - splice_donor_variant&splice_donor_5th_base_variant&coding_sequence_variant&intron_variant Transcript ENST00000368408 protein_coding 4/5 4/4 ENST00000368408.4:c.586+1_586+37del NA 686-? 581-? 194-? 1 deletion HGNC HGNC:3223 YES NM_004952.5 1 P1 CCDS1090.1 ENSP00000357393 P52797.182 UPI0000129C8F P52797-1 6 1 NA NA PASS SITE 184,201|34,48 NA NA 1 93 20,20 146,181 60,60 41 2.21 NA 47.91 NA FALSE 6.00 93 NA NA NA FALSE NA NA 336.77 1 155086199 HCC1395_HCC1395T 103 0.508 185 14,18 33,29 57,57 NA 0/1 NA NA NA NA 51,52,34,48 GTGCTGGGTGAGTCTGCGCAGCGCCCTCTGGTGGCCAC/G PANCANCER NA FALSE EFNA3 chr1:155086199:155086200:GTGCTGGGTGAGTCTGCGCAGCGCCCTCTGGTGGCCAC:G indel 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 155207642 155207643 C T 19 36 0.527777777777778 MODIFIER MTX1 ENSG00000173171 T upstream_gene_variant Transcript ENST00000316721 protein_coding NA 1155 1 SNV HGNC HGNC:7504 1 CCDS1101.1 ENSP00000317106 Q13505.177 UPI00004432EB Q13505-2 1 NA NA PASS SITE 44,22|12,7 NA NA 1 93 20,20 155,162 60,60 28 1.53 NA 9.93 NA FALSE 6.00 67 NA NA NA FALSE NA NA 50.24 1 155207642 HCC1395_HCC1395T 17 0.536 36 5,6 7,7 12,14 NA 0/1 NA NA NA NA 11,6,12,7 C/T PANCANCER NA FALSE MTX1 chr1:155207642:155207643:C:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 155868563 155868564 G A 55 206 0.266990291262136 LOW SYT11 ENSG00000132718 A synonymous_variant Transcript ENST00000368324 protein_coding 2/4 ENST00000368324.5:c.633G>A ENSP00000357307.4:p.K211= ENSP00000357307.4 p.K211= 828 633 211 K aaG/aaA 1 SNV HGNC HGNC:19239 YES NM_152280.5 1 P1 CCDS1122.1 ENSP00000357307 Q9BT88.189 UPI00002049CC PROSITE_profiles:PS50004&CDD:cd08388&PANTHER:PTHR10024&Pfam:PF00168&Gene3D:2.60.40.150&SMART:SM00239&Superfamily:SSF49562&AlphaFold_DB_import:AF-Q9BT88-F1 1 NA NA PASS SITE 191,204|29,26 NA NA 1 93 20,20 162,162 60,60 22 2.23 NA 50.57 NA FALSE 6.00 78 NA NA NA FALSE NA NA 142.29 1 155868563 HCC1395_HCC1395T 151 0.283 206 44,12 49,25 103,40 NA 0/1 NA NA NA NA 73,78,29,26 G/A PANCANCER NA FALSE SYT11_p.K211= chr1:155868563:155868564:G:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 156042053 156042054 G A 105 314 0.334394904458599 MODIFIER UBQLN4 ENSG00000160803 A intron_variant Transcript ENST00000368309 protein_coding 8/10 ENST00000368309.4:c.1351-66C>T NA -1 SNV HGNC HGNC:1237 YES NM_020131.5 1 P1 CCDS1127.1 ENSP00000357292 Q9NRR5.182 UPI000013E0AB Q9NRR5-1 1 NA NA PASS SITE 304,191|64,42 NA NA 1 93 20,20 166,166 60,60 24 2.31 NA 60.06 NA FALSE 6.00 93 NA NA NA FALSE NA NA 254.10 1 156042053 HCC1395_HCC1395T 209 0.325 314 47,22 93,48 150,72 NA 0/1 NA NA NA NA 130,79,63,42 G/A PANCANCER NA FALSE UBQLN4 chr1:156042053:156042054:G:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 157520391 157520392 G A 43 121 0.355371900826446 MODIFIER FCRL5 ENSG00000143297 A intron_variant Transcript ENST00000361835 protein_coding 12/16 ENST00000361835.8:c.2632+40C>T NA -1 SNV HGNC HGNC:18508 YES NM_031281.3 1 P1 CCDS1165.1 ENSP00000354691 Q96RD9.177 UPI0000458907 Q96RD9-1 1 NA NA PASS SITE 105,82|23,20 NA NA 1 93 20,20 169,169 60,60 26 1.91 NA 24.08 NA FALSE 6.00 93 NA NA NA FALSE NA NA 105.11 1 157520391 HCC1395_HCC1395T 78 0.366 121 26,13 22,16 51,29 NA 0/1 NA NA NA NA 42,36,23,20 G/A PANCANCER NA FALSE FCRL5 chr1:157520391:157520392:G:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 158638013 158638014 T C 48 65 0.738461538461539 MODIFIER SPTA1 ENSG00000163554 C upstream_gene_variant Transcript ENST00000461624 retained_intron NA 3360 -1 SNV HGNC HGNC:11272 2 1 1 NA NA PASS SITE 53,23|37,11 NA NA 1 93 34,36 172,177 60,60 21 1.64 NA 12.94 NA FALSE 6.00 92 NA NA NA FALSE NA NA 153.49 1 158638013 HCC1395_HCC1395T 17 0.722 65 3,11 11,25 14,38 NA 0/1 NA NA NA NA 14,3,37,11 T/C PANCANCER NA FALSE SPTA1 chr1:158638013:158638014:T:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 158663052 158663053 C A 28 64 0.4375 MODIFIER SPTA1 ENSG00000163554 A intron_variant Transcript ENST00000643759 protein_coding 16/51 ENST00000643759.2:c.2221-107G>T NA -1 SNV HGNC HGNC:11272 YES NM_003126.4 P1 CCDS41423.1 ENSP00000495214 P02549.244 UPI0000458906 P02549-1 1 1 NA NA PASS SITE 17,47|9,19 NA NA 1 70 20,20 188,171 60,60 31 1.34 NA 6.32 NA FALSE 6.00 55 NA NA NA FALSE NA NA 76.00 1 158663052 HCC1395_HCC1395T 36 0.426 64 8,6 12,11 26,19 NA 0/1 NA NA NA NA 10,26,9,19 C/A PANCANCER NA FALSE SPTA1 chr1:158663052:158663053:C:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 160038404 160038405 C G 46 71 0.647887323943662 MODIFIER KCNJ10 ENSG00000177807 G intron_variant Transcript ENST00000509700 protein_coding 1/1 ENST00000509700.2:c.671+3430G>C NA -1 cds_start_NF SNV HGNC HGNC:6256 5 ENSP00000491416 A0A1W2PPI0.27 UPI00097BA569 1 1 NA NA PASS SITE 63,39|29,17 NA NA 1 93 20,20 162,166 60,60 25 1.71 NA 15.00 NA FALSE 6.00 86 NA NA NA FALSE NA NA 135.07 1 160038404 HCC1395_HCC1395T 25 0.630 71 7,8 12,23 19,33 NA 0/1 NA NA NA NA 16,9,29,17 C/G PANCANCER NA FALSE KCNJ10 chr1:160038404:160038405:C:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 160175883 160175884 G T 45 73 0.616438356164384 MODIFIER ATP1A4 ENSG00000132681 T intron_variant Transcript ENST00000368081 protein_coding 15/21 ENST00000368081.9:c.2312-209G>T NA 1 SNV HGNC HGNC:14073 YES NM_144699.4 1 P1 CCDS1197.1 ENSP00000357060 Q13733.202 UPI0000124FC5 Q13733-1 1 NA NA PASS SITE 82,44|29,16 NA NA 1 93 20,20 164,170 60,60 33 1.82 NA 19.26 NA FALSE 6.00 93 NA NA NA FALSE NA NA 122.17 1 160175883 HCC1395_HCC1395T 28 0.611 73 4,11 16,20 20,32 NA 0/1 NA NA NA NA 20,8,29,16 G/T PANCANCER NA FALSE ATP1A4 chr1:160175883:160175884:G:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 160876801 160876802 C T 38 113 0.336283185840708 MODERATE ITLN1 ENSG00000179914 T missense_variant Transcript ENST00000326245 protein_coding 8/8 ENST00000326245.4:c.805G>A ENSP00000323587.3:p.G269R ENSP00000323587.3 p.G269R 931 805 269 G/R Gga/Aga rs1250225298&COSV58277219 -1 SNV HGNC HGNC:18259 YES NM_017625.3 1 P1 CCDS1211.1 ENSP00000323587 Q8WWA0.152 UPI0000032AA3 deleterious(0) probably_damaging(0.99) PDB-ENSP_mappings:4wmq.A&PDB-ENSP_mappings:4wmq.B&PDB-ENSP_mappings:4wmy.A&PDB-ENSP_mappings:4wmy.B&PDB-ENSP_mappings:6usc.A&PDB-ENSP_mappings:6usc.B&PANTHER:PTHR16146&AlphaFold_DB_import:AF-Q8WWA0-F1 7.968e-06 0 0 0 0 0 1.764e-05 0 0 1.314e-05 0 0 0 0 0 0 0 2.939e-05 0 0 2.939e-05 gnomADg_NFE 0&1 0&1 1 NA NA PASS SITE 75,88|17,21 NA NA 1 93 20,20 162,159 60,60 31 1.78 NA 17.71 NA FALSE 6.00 67 NA NA NA FALSE NA NA 92.05 1 160876801 HCC1395_HCC1395T 75 0.338 113 22,7 25,15 50,25 NA 0/1 NA NA NA NA 32,43,17,21 C/T PANCANCER NA FALSE ITLN1_p.G269R chr1:160876801:160876802:C:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 160880550 160880551 T A 94 161 0.583850931677019 MODIFIER ITLN1 ENSG00000179914 A intron_variant Transcript ENST00000326245 protein_coding 6/7 ENST00000326245.4:c.685+38A>T NA -1 SNV HGNC HGNC:18259 YES NM_017625.3 1 P1 CCDS1211.1 ENSP00000323587 Q8WWA0.152 UPI0000032AA3 1 NA NA PASS SITE 121,83|57,37 NA NA 1 93 20,20 158,166 60,60 27 1.96 NA 26.79 NA FALSE 6.00 93 NA NA NA FALSE NA NA 251.25 1 160880550 HCC1395_HCC1395T 67 0.569 161 14,22 29,36 46,61 NA 0/1 NA NA NA NA 39,28,57,37 T/A PANCANCER NA FALSE ITLN1 chr1:160880550:160880551:T:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 161623483 161623484 G A 113 376 0.300531914893617 MODIFIER FCGR3B ENSG00000162747 A 3_prime_UTR_variant Transcript ENST00000367964 protein_coding 6/6 ENST00000367964.6:c.*1032C>T NA 1856 -1 SNV HGNC HGNC:3620 5 P2 CCDS41433.1 ENSP00000356941 O75015.198 UPI0000D62032 1 1 NA NA PASS SITE 161,340|33,80 NA NA 1 93 20,33 178,174 60,60 27 2.23 NA 50.98 NA FALSE 6.00 93 NA NA NA FALSE NA NA 288.84 1 161623483 HCC1395_HCC1395T 263 0.321 376 74,37 88,39 184,87 NA 0/1 NA NA NA NA 82,181,33,80 G/A PANCANCER NA FALSE FCGR3B chr1:161623483:161623484:G:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 161752393 161752394 C G 37 93 0.397849462365591 LOW DUSP12 ENSG00000081721 G synonymous_variant Transcript ENST00000367943 protein_coding 4/6 ENST00000367943.5:c.603C>G ENSP00000356920.4:p.L201= ENSP00000356920.4 p.L201= 619 603 201 L ctC/ctG COSV63411844 1 SNV HGNC HGNC:3067 YES NM_007240.3 1 P1 CCDS1234.1 ENSP00000356920 Q9UNI6.190 UPI0000034737 AlphaFold_DB_import:AF-Q9UNI6-F1&PIRSF:PIRSF000941&PANTHER:PTHR45848 1 1 1 NA NA PASS SITE 64,46|22,15 NA NA 1 93 20,20 170,149 60,60 28 1.57 NA 10.84 NA FALSE 6.00 93 NA NA NA FALSE NA NA 94.17 1 161752393 HCC1395_HCC1395T 56 0.417 93 8,10 25,12 34,24 NA 0/1 NA NA NA NA 32,24,22,15 C/G PANCANCER NA FALSE DUSP12_p.L201= chr1:161752393:161752394:C:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 165437329 165437330 A C 20 55 0.363636363636364 MODIFIER RXRG ENSG00000143171 C intron_variant Transcript ENST00000359842 protein_coding 1/9 ENST00000359842.10:c.49+7516T>G NA -1 SNV HGNC HGNC:10479 YES NM_006917.5 1 P1 CCDS1248.1 ENSP00000352900 P48443.211 F1D8Q7.99 UPI000004989F 1 NA NA PASS SITE 27,44|6,14 NA NA 1 77 20,20 173,168 60,60 18 1.41 NA 7.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 44.75 1 165437329 HCC1395_HCC1395T 35 0.371 55 14,7 7,6 24,14 NA 0/1 NA NA NA NA 15,20,6,14 A/C PANCANCER NA FALSE RXRG chr1:165437329:165437330:A:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 167383891 167383892 A G 53 205 0.258536585365854 MODIFIER POU2F1 ENSG00000143190 G 3_prime_UTR_variant&NMD_transcript_variant Transcript ENST00000271411 nonsense_mediated_decay 9/17 ENST00000271411.8:c.*680A>G NA 862 1 SNV HGNC HGNC:9212 1 ENSP00000271411 Q16075.101 UPI00000738CA 1 NA NA PASS SITE 161,171|25,28 NA NA 1 93 20,20 149,157 60,60 43 2.04 NA 32.81 NA FALSE 6.00 89 NA NA NA FALSE NA NA 118.72 1 167383891 HCC1395_HCC1395T 152 0.269 205 32,11 48,16 89,32 NA 0/1 NA NA NA NA 72,80,25,28 A/G PANCANCER NA FALSE POU2F1 chr1:167383891:167383892:A:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 168300462 168300463 C A 15 111 0.135135135135135 MODERATE TBX19 ENSG00000143178 A missense_variant Transcript ENST00000367821 protein_coding 5/8 ENST00000367821.8:c.706C>A ENSP00000356795.3:p.Q236K ENSP00000356795.3 p.Q236K 920 706 236 Q/K Cag/Aag 1 SNV HGNC HGNC:11596 YES NM_005149.3 1 P1 CCDS1272.1 ENSP00000356795 O60806.178 UPI000003176C 1 deleterious(0) benign(0) PANTHER:PTHR11267&AlphaFold_DB_import:AF-O60806-F1 1 NA NA PASS SITE 76,118|5,10 NA NA 1 93 20,20 165,175 60,60 32 1.82 NA 19.22 NA FALSE 6.00 38 NA NA NA FALSE NA NA 31.98 1 168300462 HCC1395_HCC1395T 96 0.157 111 17,4 41,7 63,11 NA 0/1 NA NA NA NA 38,58,5,10 C/A PANCANCER NA FALSE TBX19_p.Q236K chr1:168300462:168300463:C:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 171704133 171704134 C G 38 130 0.292307692307692 MODIFIER VAMP4 ENSG00000117533 G 3_prime_UTR_variant Transcript ENST00000236192 protein_coding 8/8 ENST00000236192.12:c.*373G>C NA 1004 -1 SNV HGNC HGNC:12645 YES NM_003762.5 1 P3 CCDS1298.1 ENSP00000236192 O75379.195 Q6IAZ3.152 UPI00000015F3 O75379-1 1 NA NA PASS SITE 59,143|13,25 NA NA 1 93 32,20 183,142 60,60 29 1.91 NA 23.78 NA FALSE 6.00 71 NA NA NA FALSE NA NA 95.75 1 171704133 HCC1395_HCC1395T 92 0.274 130 17,6 30,16 73,27 NA 0/1 NA NA NA NA 23,69,13,25 C/G PANCANCER NA FALSE VAMP4 chr1:171704133:171704134:C:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 172309527 172309528 C G 376 546 0.688644688644689 MODIFIER DNM3 ENSG00000197959 G intron_variant Transcript ENST00000355305 protein_coding 17/20 ENST00000355305.9:c.1911+688C>G NA 1 SNV HGNC HGNC:29125 5 A1 CCDS86032.1 ENSP00000347457 Q9UQ16.195 UPI0000458803 Q9UQ16-1 1 NA NA PASS SITE 207,277|150,226 NA NA 1 93 20,20 160,165 60,60 33 2.33 NA 62.31 NA FALSE 6.00 93 NA NA NA FALSE NA NA 1062.69 1 172309527 HCC1395_HCC1395T 170 0.696 546 38,94 65,131 111,255 NA 0/1 NA NA NA NA 67,103,150,226 C/G PANCANCER NA FALSE DNM3 chr1:172309527:172309528:C:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 173911069 173911070 C T 12 44 0.272727272727273 MODIFIER SERPINC1 ENSG00000117601 T intron_variant Transcript ENST00000367698 protein_coding 3/6 ENST00000367698.4:c.625-178G>A NA -1 SNV HGNC HGNC:775 YES NM_000488.4 1 P1 CCDS1313.1 ENSP00000356671 P01008.259 A0A024R944.50 UPI000002C0C1 1 1 NA NA PASS SITE 10,45|3,9 NA NA 1 59 39,38 176,193 60,60 13 1.33 NA 6.02 NA FALSE 6.00 36 NA NA NA FALSE NA NA 34.36 1 173911069 HCC1395_HCC1395T 32 0.270 44 13,2 12,6 26,9 NA 0/1 NA NA NA NA 6,26,3,9 C/T PANCANCER NA FALSE SERPINC1 chr1:173911069:173911070:C:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 176711958 176711959 A G 35 219 0.159817351598174 MODERATE PAPPA2 ENSG00000116183 G missense_variant Transcript ENST00000367662 protein_coding 12/23 ENST00000367662.5:c.3775A>G ENSP00000356634.3:p.K1259E ENSP00000356634.3 p.K1259E 4935 3775 1259 K/E Aaa/Gaa rs1439300319 1 SNV HGNC HGNC:14615 YES NM_020318.3 1 P1 CCDS41438.1 ENSP00000356634 Q9BXP8.179 UPI000004A835 Q9BXP8-1 1 tolerated(1) benign(0.003) PANTHER:PTHR46130&AlphaFold_DB_import:AF-Q9BXP8-F1 6.574e-06 2.414e-05 0 0 0 0 0 0 0 0 0 2.414e-05 gnomADg_AFR 1 NA NA PASS SITE 111,178|14,21 NA NA 1 93 20,20 159,185 60,60 22 1.86 NA 20.77 NA FALSE 4.61 86 NA NA NA FALSE NA NA 73.89 1 176711958 HCC1395_HCC1395T 184 0.162 219 46,12 63,10 123,23 NA 0/1 NA NA NA NA 71,113,14,21 A/G PANCANCER NA FALSE PAPPA2_p.K1259E chr1:176711958:176711959:A:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 179105846 179105847 C T 10 19 0.526315789473684 MODIFIER ABL2 ENSG00000143322 T 3_prime_UTR_variant Transcript ENST00000344730 protein_coding 13/13 ENST00000344730.8:c.*1872G>A NA 5099 -1 SNV HGNC HGNC:77 1 A1 CCDS44282.1 ENSP00000339209 P42684.235 UPI0000458861 P42684-10 1 1 NA NA PASS SITE 12,14|3,7 NA NA 1 41 38,35 204,209 60,60 27 1.15 NA 3.91 NA FALSE 6.00 67 NA NA NA FALSE NA NA 30.92 1 179105846 HCC1395_HCC1395T 9 0.500 19 2,4 7,5 9,9 NA 0/1 NA NA NA NA 5,4,3,7 C/T PANCANCER NA FALSE ABL2 chr1:179105846:179105847:C:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 179109010 179109011 T C 60 212 0.283018867924528 MODIFIER ABL2 ENSG00000143322 C intron_variant Transcript ENST00000344730 protein_coding 12/12 ENST00000344730.8:c.2015-112A>G NA COSV61012846 -1 SNV HGNC HGNC:77 1 A1 CCDS44282.1 ENSP00000339209 P42684.235 UPI0000458861 P42684-10 1 1 1 1 NA NA PASS SITE 100,197|22,38 NA NA 1 93 20,20 149,159 60,60 30 1.99 NA 28.59 NA FALSE 6.00 93 NA NA NA FALSE NA NA 153.01 1 179109010 HCC1395_HCC1395T 152 0.286 212 33,14 61,21 104,41 NA 0/1 NA NA NA NA 48,104,22,38 T/C PANCANCER NA FALSE ABL2 chr1:179109010:179109011:T:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 179813632 179813634 GA AC 14 36 0.388888888888889 MODIFIER FAM163A ENSG00000143340 AC intron_variant Transcript ENST00000341785 protein_coding 4/4 ENST00000341785.5:c.94-147_94-146delinsAC NA 1 substitution HGNC HGNC:28274 YES NM_173509.3 1 P1 CCDS1333.1 ENSP00000354891 Q96GL9.130 UPI000006ED82 1 NA NA PASS SITE 25,15|9,5 NA NA 1 44 20,36 150,205 60,60 39 1.19 NA 4.21 NA FALSE 6.00 67 NA NA NA FALSE NA NA 52.23 1 179813632 HCC1395_HCC1395T 22 0.448 36 6,5 8,7 15,12 NA 0/1 NA NA NA NA 14,8,9,5 GA/AC PANCANCER NA FALSE FAM163A chr1:179813632:179813634:GA:AC indel 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 183235431 183235432 C G 73 198 0.368686868686869 MODIFIER LAMC2 ENSG00000058085 G intron_variant Transcript ENST00000264144 protein_coding 15/22 ENST00000264144.5:c.2301-144C>G NA rs1363163281 1 SNV HGNC HGNC:6493 YES NM_005562.3 1 P1 CCDS1352.1 ENSP00000264144 Q13753.212 UPI000013D4CA Q13753-1 1 6.568e-06 0 0 0 0 0.0001923 0 0 0 0 0 0.0001923 gnomADg_EAS 1 NA NA PASS SITE 161,123|41,32 NA NA 1 93 20,20 154,156 60,60 32 2.02 NA 31.31 NA FALSE 6.00 93 NA NA NA FALSE NA NA 175.36 1 183235431 HCC1395_HCC1395T 125 0.360 198 34,20 42,23 81,45 NA 0/1 NA NA NA NA 69,56,41,32 C/G PANCANCER NA FALSE LAMC2 chr1:183235431:183235432:C:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 183880711 183880712 A C 80 190 0.421052631578947 MODERATE RGL1 ENSG00000143344 C missense_variant Transcript ENST00000304685 protein_coding 6/19 ENST00000304685.8:c.626A>C ENSP00000303192.3:p.Y209S ENSP00000303192.3 p.Y209S 1075 626 209 Y/S tAt/tCt COSV58993692 1 SNV HGNC HGNC:30281 1 CCDS1359.1 ENSP00000303192 Q9NZL6.183 UPI000002B24C Q9NZL6-2 deleterious(0) probably_damaging(0.992) Gene3D:1.20.870.10&AlphaFold_DB_import:AF-Q9NZL6-F1&PROSITE_profiles:PS50212&PANTHER:PTHR23113&SMART:SM00229&Superfamily:SSF48366&CDD:cd06224 1 1 1 NA NA PASS SITE 148,114|42,38 NA NA 1 93 20,20 160,153 60,60 38 2.02 NA 30.40 NA FALSE 6.00 93 NA NA NA FALSE NA NA 198.19 1 183880711 HCC1395_HCC1395T 110 0.400 190 24,21 49,30 77,51 NA 0/1 NA NA NA NA 59,51,42,38 A/C PANCANCER NA FALSE RGL1_p.Y209S chr1:183880711:183880712:A:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 196995756 196995757 A G 32 105 0.304761904761905 MODERATE CFHR5 ENSG00000134389 G missense_variant Transcript ENST00000256785 protein_coding 5/10 ENST00000256785.5:c.647A>G ENSP00000256785.4:p.N216S ENSP00000256785.4 p.N216S 756 647 216 N/S aAt/aGt rs147488267&COSV56830119 1 SNV HGNC HGNC:24668 YES NM_030787.4 1 P1 CCDS1387.1 ENSP00000256785 Q9BXR6.162 UPI0000043814 1 tolerated(0.08) Gene3D:2.10.70.10&AlphaFold_DB_import:AF-Q9BXR6-F1&Pfam:PF00084&PROSITE_profiles:PS50923&PANTHER:PTHR45785&SMART:SM00032&Superfamily:SSF57535&CDD:cd00033 6.77e-05 6.154e-05 0 0 0 0 4.406e-05 0 0.0003594 3.287e-05 2.414e-05 0 0 0 0 0 0 2.941e-05 0 0.0004146 0.0004146 gnomADg_SAS uncertain_significance 0&1 1&1 1 NA NA PASS SITE 96,43|21,11 NA NA 1 93 20,20 170,181 60,60 36 1.70 NA 14.70 NA FALSE 4.61 58 NA NA NA FALSE NA NA 74.74 1 196995756 HCC1395_HCC1395T 73 0.294 105 15,6 36,14 52,21 NA 0/1 NA NA NA NA 50,23,21,11 A/G PANCANCER NA FALSE CFHR5_p.N216S chr1:196995756:196995757:A:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 200029019 200029020 C G 278 390 0.712820512820513 MODIFIER NR5A2 ENSG00000116833 G intron_variant Transcript ENST00000236914 protein_coding 1/6 ENST00000236914.7:c.64+1108C>G NA 1 SNV HGNC HGNC:7984 1 A1 CCDS1400.1 ENSP00000236914 O00482.213 F1D8R9.77 UPI000002AF8E O00482-2 1 NA NA PASS SITE 273,128|193,85 NA NA 1 93 20,20 168,167 60,60 30 2.32 NA 62.01 NA FALSE 6.00 93 NA NA NA FALSE NA NA 829.87 1 200029019 HCC1395_HCC1395T 112 0.706 390 30,81 51,114 82,198 NA 0/1 NA NA NA NA 79,33,193,85 C/G PANCANCER NA FALSE NR5A2 chr1:200029019:200029020:C:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 200858296 200858297 TATGTGTTATCAG T 36 120 0.3 MODIFIER CAMSAP2 ENSG00000118200 - 3_prime_UTR_variant Transcript ENST00000236925 protein_coding 18/18 ENST00000236925.8:c.*238_*249del NA 4757-4768 1 deletion HGNC HGNC:29188 1 CCDS72998.1 ENSP00000236925 Q08AD1.137 UPI0000160246 Q08AD1-1 1 NA NA PASS SITE 37,137|2,34 NA NA 1 93 33,38 187,211 60,60 24 1.86 NA 20.99 NA FALSE 6.00 93 NA NA NA FALSE NA NA 131.90 1 200858296 HCC1395_HCC1395T 84 0.328 120 12,5 18,8 71,34 NA 0/1 NA NA NA NA 13,71,2,34 TATGTGTTATCAG/T PANCANCER NA FALSE CAMSAP2 chr1:200858296:200858297:TATGTGTTATCAG:T indel 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 201000898 201000899 G A 3 8 0.375 MODIFIER KIF21B ENSG00000116852 A intron_variant Transcript ENST00000332129 protein_coding 9/33 ENST00000332129.6:c.1403-118C>T NA -1 SNV HGNC HGNC:29442 1 CCDS30965.1 ENSP00000328494 O75037.189 UPI00005E272D O75037-2 1 NA NA PASS SITE 0,17|1,2 NA NA 1 38 40,20 212,136 60,60 7 1.11 NA 3.61 NA FALSE 6.00 8 NA NA NA FALSE NA NA 6.45 1 201000898 HCC1395_HCC1395T 5 0.330 8 2,0 3,2 5,2 NA 0/1 NA NA NA NA 0,5,1,2 G/A PANCANCER NA FALSE KIF21B chr1:201000898:201000899:G:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 202746102 202746103 A G 9 19 0.473684210526316 MODIFIER KDM5B ENSG00000117139 G intron_variant Transcript ENST00000235790 protein_coding 15/25 ENST00000235790.9:c.1724+40T>C NA -1 cds_end_NF SNV HGNC HGNC:18039 2 ENSP00000235790 B3KV94.122 UPI0000EE3E33 1 1 NA NA PASS SITE 13,16|2,7 NA NA 1 51 34,39 188,238 60,60 46 1.24 NA 4.81 NA FALSE 6.00 24 NA NA NA FALSE NA NA 28.06 1 202746102 HCC1395_HCC1395T 10 0.450 19 2,1 7,4 10,8 NA 0/1 NA NA NA NA 7,3,2,7 A/G PANCANCER NA FALSE KDM5B chr1:202746102:202746103:A:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 203347718 203347719 G C 34 107 0.317757009345794 MODERATE FMOD ENSG00000122176 C missense_variant Transcript ENST00000354955 protein_coding 2/3 ENST00000354955.5:c.553C>G ENSP00000347041.4:p.H185D ENSP00000347041.4 p.H185D 650 553 185 H/D Cac/Gac COSV61609880 -1 SNV HGNC HGNC:3774 YES NM_002023.5 1 P1 CCDS30976.1 ENSP00000347041 Q06828.193 A0A024R971.60 UPI00000746A2 deleterious(0.01) possibly_damaging(0.535) PDB-ENSP_mappings:5mx0.A&PDB-ENSP_mappings:5mx0.B&PROSITE_profiles:PS51450&PANTHER:PTHR45712&Gene3D:3.80.10.10&Pfam:PF13855&SMART:SM00369&SMART:SM00364&Superfamily:SSF52058&AlphaFold_DB_import:AF-Q06828-F1 1 1 1 NA NA PASS SITE 74,91|15,19 NA NA 1 93 20,20 162,172 60,60 28 1.80 NA 18.66 NA FALSE 6.00 59 NA NA NA FALSE NA NA 83.85 1 203347718 HCC1395_HCC1395T 73 0.335 107 21,4 27,18 50,25 NA 0/1 NA NA NA NA 30,43,15,19 G/C PANCANCER NA FALSE FMOD_p.H185D chr1:203347718:203347719:G:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 203712146 203712147 C G 31 110 0.281818181818182 LOW ATP2B4 ENSG00000058668 G splice_region_variant&intron_variant Transcript ENST00000341360 protein_coding 13/21 ENST00000341360.7:c.2211+7C>G NA 1 SNV HGNC HGNC:817 1 A1 CCDS30977.1 ENSP00000340930 P23634.224 UPI000002A460 P23634-2 1 NA NA PASS SITE 39,104|9,22 NA NA 1 93 20,20 187,192 60,60 25 1.67 NA 13.55 NA FALSE 6.00 93 NA NA NA FALSE NA NA 78.65 1 203712146 HCC1395_HCC1395T 79 0.271 110 26,10 33,11 61,22 NA 0/1 NA NA NA NA 19,60,9,22 C/G PANCANCER NA FALSE ATP2B4 chr1:203712146:203712147:C:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 203741500 203741501 C G 51 70 0.728571428571429 MODIFIER ATP2B4 ENSG00000058668 G 3_prime_UTR_variant Transcript ENST00000341360 protein_coding 22/22 ENST00000341360.7:c.*1929C>G NA 6294 1 SNV HGNC HGNC:817 1 A1 CCDS30977.1 ENSP00000340930 P23634.224 UPI000002A460 P23634-2 1 NA NA PASS SITE 29,27|26,25 NA NA 1 93 26,38 192,186 60,60 30 1.46 NA 8.13 NA FALSE 6.00 93 NA NA NA FALSE NA NA 166.61 1 203741500 HCC1395_HCC1395T 19 0.720 70 6,14 9,25 15,40 NA 0/1 NA NA NA NA 9,10,26,25 C/G PANCANCER NA FALSE ATP2B4 chr1:203741500:203741501:C:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 204469485 204469486 A G 25 88 0.284090909090909 MODIFIER PIK3C2B ENSG00000133056 G upstream_gene_variant Transcript ENST00000367184 protein_coding NA 2139 -1 cds_end_NF SNV HGNC HGNC:8972 5 ENSP00000356152 Q5SWA0.105 UPI0000470232 1 NA NA PASS SITE 64,86|9,16 NA NA 1 93 20,20 182,156 60,60 22 1.80 NA 18.27 NA FALSE 6.00 82 NA NA NA FALSE NA NA 62.38 1 204469485 HCC1395_HCC1395T 63 0.273 88 16,8 30,9 47,17 NA 0/1 NA NA NA NA 26,37,9,16 A/G PANCANCER NA FALSE PIK3C2B chr1:204469485:204469486:A:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 204986103 204986104 C G 52 96 0.541666666666667 MODIFIER NFASC ENSG00000163531 G intron_variant Transcript ENST00000339876 protein_coding 21/29 ENST00000339876.11:c.2471-1315C>G NA COSV58363672&COSV58372322 1 SNV HGNC HGNC:29866 YES NM_001005388.3 5 CCDS53460.1 ENSP00000344786 O94856.194 UPI0000237208 O94856-9 1 1&1 1&1 1 NA NA PASS SITE 68,100|19,33 NA NA 1 93 20,20 155,158 60,60 36 1.90 NA 23.48 NA FALSE 6.00 93 NA NA NA FALSE NA NA 143.25 1 204986103 HCC1395_HCC1395T 44 0.556 96 8,13 17,15 28,35 NA 0/1 NA NA NA NA 17,27,19,33 C/G PANCANCER NA FALSE NFASC chr1:204986103:204986104:C:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 205612985 205612986 G C 189 315 0.6 MODIFIER ELK4 ENSG00000158711 C 3_prime_UTR_variant Transcript ENST00000357992 protein_coding 5/5 ENST00000357992.9:c.*3561C>G NA 5246 -1 SNV HGNC HGNC:3326 YES NM_001973.4 1 P1 CCDS1456.1 ENSP00000350681 P28324.201 A0A024R985.15 UPI0000129E67 P28324-1 1 1 NA NA PASS SITE 235,150|126,63 NA NA 1 93 20,20 161,164 60,60 39 2.29 NA 56.65 NA FALSE 6.00 93 NA NA NA FALSE NA NA 503.81 1 205612985 HCC1395_HCC1395T 126 0.619 315 33,41 44,92 90,145 NA 0/1 NA NA NA NA 77,49,126,63 G/C PANCANCER NA FALSE ELK4 chr1:205612985:205612986:G:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 205813151 205813152 G T 65 118 0.550847457627119 MODIFIER SLC41A1 ENSG00000133065 T 5_prime_UTR_variant Transcript ENST00000367137 protein_coding 1/11 ENST00000367137.4:c.-990C>A NA 48 -1 SNV HGNC HGNC:19429 YES NM_173854.6 1 P1 CCDS30988.1 ENSP00000356105 Q8IVJ1.139 B2RMP2.108 UPI000013E1E6 1 1 NA NA PASS SITE 61,140|22,43 NA NA 1 93 20,20 169,170 60,60 20 2.03 NA 31.60 NA FALSE 6.00 93 NA NA NA FALSE NA NA 181.63 1 205813151 HCC1395_HCC1395T 53 0.535 118 1,11 14,11 41,47 NA 0/1 NA NA NA NA 15,38,22,43 G/T PANCANCER NA FALSE SLC41A1 chr1:205813151:205813152:G:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 205918780 205918781 T G 9 16 0.5625 MODIFIER SLC26A9 ENSG00000174502 G intron_variant Transcript ENST00000340781 protein_coding 18/20 ENST00000340781.8:c.2256+60A>C NA -1 SNV HGNC HGNC:14469 1 CCDS30989.1 ENSP00000341682 Q7LBE3.152 UPI000013DF98 Q7LBE3-2 1 1 NA NA PASS SITE 26,3|9,0 NA NA 1 62 36,34 183,236 60,60 46 1.35 NA 6.32 NA FALSE 6.00 80 NA NA NA FALSE NA NA 29.69 1 205918780 HCC1395_HCC1395T 7 0.625 16 0,3 5,6 5,9 NA 0/1 NA NA NA NA 5,2,9,0 T/G PANCANCER NA FALSE SLC26A9 chr1:205918780:205918781:T:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 206474453 206474454 C G 75 218 0.344036697247706 LOW IKBKE ENSG00000263528 G synonymous_variant Transcript ENST00000578328 protein_coding 4/21 ENST00000578328.6:c.210C>G ENSP00000473833.1:p.L70= ENSP00000473833.1 p.L70= 536 210 70 L ctC/ctG rs56388356 1 SNV HGNC HGNC:14552 1 CCDS73019.1 ENSP00000473833 A0A075B7B4.54 UPI0000E060E6 PROSITE_profiles:PS50011&PANTHER:PTHR22969&Gene3D:3.30.200.20&Pfam:PF00069&SMART:SM00220&Superfamily:SSF56112&AlphaFold_DB_import:AF-A0A075B7B4-F1 1 NA NA PASS SITE 197,173|39,36 NA NA 1 93 20,20 149,144 60,60 31 2.17 NA 43.60 NA FALSE 6.00 93 NA NA NA FALSE NA NA 190.32 1 206474453 HCC1395_HCC1395T 143 0.370 218 31,22 51,26 89,52 NA 0/1 NA NA NA NA 78,65,39,36 C/G PANCANCER NA FALSE IKBKE_p.L70= chr1:206474453:206474454:C:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 207071385 207071386 G A 34 98 0.346938775510204 MODIFIER PFKFB2 ENSG00000123836 A intron_variant Transcript ENST00000367079 protein_coding 13/14 ENST00000367079.3:c.1286-124G>A NA rs1038840489 1 SNV HGNC HGNC:8873 1 P1 CCDS31003.1 ENSP00000356046 O60825.206 UPI000002A942 O60825-2 1.314e-05 4.828e-05 0 0 0 0 0 0 0 0 0 4.828e-05 gnomADg_AFR 1 NA NA PASS SITE 67,77|18,16 NA NA 1 93 20,20 164,172 60,60 37 1.76 NA 16.86 NA FALSE 6.00 72 NA NA NA FALSE NA NA 85.06 1 207071385 HCC1395_HCC1395T 64 0.348 98 15,8 27,15 44,23 NA 0/1 NA NA NA NA 32,32,18,16 G/A PANCANCER NA FALSE PFKFB2 chr1:207071385:207071386:G:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 212791835 212791836 ATCCGGCTGGAAACTCAGGACGCTGCAGCTGAAACGT A 43 151 0.28476821192053 MODIFIER TATDN3 ENSG00000203705 - upstream_gene_variant Transcript ENST00000366973 protein_coding NA 13 1 deletion HGNC HGNC:27010 1 A1 CCDS41465.1 ENSP00000355940 Q17R31.135 UPI0000141612 Q17R31-2 1 NA NA PASS SITE 188,159|27,16 NA NA 1 93 20,35 155,188 60,60 32 2.20 NA 45.85 NA FALSE 6.00 93 NA NA NA FALSE NA NA 160.88 1 212791835 HCC1395_HCC1395T 108 0.334 151 20,16 28,13 75,36 NA 0/1 NA NA NA NA 64,44,27,16 ATCCGGCTGGAAACTCAGGACGCTGCAGCTGAAACGT/A PANCANCER NA FALSE TATDN3 chr1:212791835:212791836:ATCCGGCTGGAAACTCAGGACGCTGCAGCTGAAACGT:A indel 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 216418729 216418730 G C 12 80 0.15 MODIFIER USH2A ENSG00000042781 C intron_variant Transcript ENST00000307340 protein_coding 2/71 ENST00000307340.8:c.486-50C>G NA -1 SNV HGNC HGNC:12601 YES NM_206933.4 1 P1 CCDS31025.1 ENSP00000305941 O75445.185 UPI000034E5B6 O75445-1 1 1 NA NA PASS SITE 38,85|4,8 NA NA 1 93 20,28 168,152 60,60 23 1.63 NA 12.29 NA FALSE 6.00 57 NA NA NA FALSE NA NA 27.71 1 216418729 HCC1395_HCC1395T 68 0.169 80 16,4 30,3 48,9 NA 0/1 NA NA NA NA 22,46,4,8 G/C PANCANCER NA FALSE USH2A chr1:216418729:216418730:G:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 217668967 217668968 G T 7 13 0.538461538461538 MODIFIER SPATA17 ENSG00000162814 T intron_variant Transcript ENST00000366933 protein_coding 3/10 ENST00000366933.5:c.241-66G>T NA COSV65126142 1 SNV HGNC HGNC:25184 YES NM_138796.4 1 P1 CCDS1519.1 ENSP00000355900 Q96L03.139 UPI00000717C2 1 1 1 NA NA PASS SITE 15,13|4,3 NA NA 1 59 40,37 234,173 60,60 35 1.34 NA 6.02 NA FALSE 6.00 24 NA NA NA FALSE NA NA 22.29 1 217668967 HCC1395_HCC1395T 6 0.539 13 0,4 3,1 5,6 NA 0/1 NA NA NA NA 3,3,4,3 G/T PANCANCER NA FALSE SPATA17 chr1:217668967:217668968:G:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 220690313 220690314 C T 91 255 0.356862745098039 MODIFIER C1orf115 ENSG00000162817 T upstream_gene_variant Transcript ENST00000294889 protein_coding NA 50 1 SNV HGNC HGNC:25873 YES NM_024709.5 1 P1 CCDS1524.1 ENSP00000294889 Q9H7X2.122 UPI0000073CC0 1 NA NA PASS SITE 229,200|49,42 NA NA 1 93 20,31 164,179 60,60 27 2.29 NA 56.89 NA FALSE 6.00 93 NA NA NA FALSE NA NA 243.60 1 220690313 HCC1395_HCC1395T 164 0.363 255 53,30 64,36 122,69 NA 0/1 NA NA NA NA 94,70,49,42 C/T PANCANCER NA FALSE C1orf115 chr1:220690313:220690314:C:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 222584064 222584065 G A 16 52 0.307692307692308 MODIFIER TAF1A ENSG00000143498 A intron_variant Transcript ENST00000350027 protein_coding 3/11 ENST00000350027.8:c.291+64C>T NA -1 SNV HGNC HGNC:11532 2 P1 CCDS1531.1 ENSP00000339976 Q15573.172 UPI000006F49B Q15573-1 1 1 NA NA PASS SITE 53,16|14,2 NA NA 1 88 36,34 181,167 60,60 11 1.47 NA 8.37 NA FALSE 6.00 73 NA NA NA FALSE NA NA 44.39 1 222584064 HCC1395_HCC1395T 36 0.366 52 12,6 13,8 25,14 NA 0/1 NA NA NA NA 25,11,14,2 G/A PANCANCER NA FALSE TAF1A chr1:222584064:222584065:G:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 223264672 223264673 G C 54 178 0.303370786516854 MODERATE SUSD4 ENSG00000143502 C missense_variant Transcript ENST00000343846 protein_coding 4/8 ENST00000343846.7:c.682C>G ENSP00000344219.3:p.L228V ENSP00000344219.3 p.L228V 1316 682 228 L/V Ctt/Gtt -1 SNV HGNC HGNC:25470 2 P1 CCDS41471.1 ENSP00000344219 Q5VX71.136 UPI0000205CB5 Q5VX71-1 deleterious(0.01) possibly_damaging(0.876) Gene3D:2.10.70.10&AlphaFold_DB_import:AF-Q5VX71-F1&Pfam:PF00084&PROSITE_profiles:PS50923&PANTHER:PTHR47007&SMART:SM00032&Superfamily:SSF57535&CDD:cd00033 1 NA NA PASS SITE 120,129|28,26 NA NA 1 93 20,20 163,158 60,60 35 1.95 NA 25.89 NA FALSE 6.00 93 NA NA NA FALSE NA NA 133.60 1 223264672 HCC1395_HCC1395T 124 0.328 178 29,13 46,21 81,39 NA 0/1 NA NA NA NA 58,66,28,26 G/C PANCANCER NA FALSE SUSD4_p.L228V chr1:223264672:223264673:G:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 225402193 225402194 G A 68 161 0.422360248447205 MODIFIER LBR ENSG00000143815 A 3_prime_UTR_variant Transcript ENST00000272163 protein_coding 14/14 ENST00000272163.9:c.*1110C>T NA 3057 -1 SNV HGNC HGNC:6518 YES NM_002296.4 1 P1 CCDS1545.1 ENSP00000272163 Q14739.211 UPI000012E256 1 1 NA NA PASS SITE 102,166|27,41 NA NA 1 93 20,20 174,171 60,60 30 2.06 NA 34.26 NA FALSE 6.00 93 NA NA NA FALSE NA NA 187.18 1 225402193 HCC1395_HCC1395T 93 0.439 161 22,14 34,28 63,49 NA 0/1 NA NA NA NA 33,60,27,41 G/A PANCANCER NA FALSE LBR chr1:225402193:225402194:G:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 226737201 226737202 G A 35 92 0.380434782608696 LOW ITPKB ENSG00000143772 A synonymous_variant Transcript ENST00000272117 protein_coding 2/8 ENST00000272117.8:c.258C>T ENSP00000272117.3:p.S86= ENSP00000272117.3 p.S86= 499 258 86 S agC/agT -1 SNV HGNC HGNC:6179 1 P1 CCDS1555.1 ENSP00000272117 P27987.193 UPI000013D92B P27987-1 Low_complexity_(Seg):seg&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-P27987-F1 1 NA NA PASS SITE 89,82|18,17 NA NA 1 93 26,20 184,155 60,60 28 1.94 NA 25.58 NA FALSE 6.00 76 NA NA NA FALSE NA NA 81.09 1 226737201 HCC1395_HCC1395T 57 0.333 92 14,8 18,10 45,22 NA 0/1 NA NA NA NA 30,27,18,17 G/A PANCANCER NA FALSE ITPKB_p.S86= chr1:226737201:226737202:G:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 227646449 227646450 G A 81 163 0.496932515337423 MODIFIER ZNF678 ENSG00000181450 A intron_variant Transcript ENST00000343776 protein_coding 1/3 ENST00000343776.10:c.-163-95G>A NA 1 SNV HGNC HGNC:28652 YES NM_001367909.1 1 P1 CCDS1560.1 ENSP00000344828 Q5SXM1.150 UPI000019862A 1 NA NA PASS SITE 140,49|59,24 NA NA 1 93 34,20 173,158 60,60 20 -1.066e+00 NA 19.20 NA FALSE 6.00 93 NA NA NA FALSE NA NA 224.22 1 227646449 HCC1395_HCC1395T 82 0.469 163 13,22 53,37 67,59 NA 0/1 NA NA NA NA 61,21,58,23 G/A PANCANCER NA FALSE ZNF678 chr1:227646449:227646450:G:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 228182162 228182163 C G 80 192 0.416666666666667 MODIFIER IBA57 ENSG00000181873 G 3_prime_UTR_variant Transcript ENST00000366711 protein_coding 3/3 ENST00000366711.4:c.*6649C>G NA 7733 1 SNV HGNC HGNC:27302 YES NM_001010867.4 2 P1 CCDS31046.1 ENSP00000355672 Q5T440.134 UPI0000160A21 1 1 NA NA PASS SITE 145,119|39,41 NA NA 1 93 20,20 157,155 60,60 35 1.99 NA 29.15 NA FALSE 6.00 87 NA NA NA FALSE NA NA 194.90 1 228182162 HCC1395_HCC1395T 112 0.419 192 24,12 40,32 70,50 NA 0/1 NA NA NA NA 61,51,39,41 C/G PANCANCER NA FALSE IBA57 chr1:228182162:228182163:C:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 228307554 228307555 G A 13 69 0.188405797101449 MODIFIER OBSCN ENSG00000154358 A intron_variant Transcript ENST00000284548 protein_coding 46/80 ENST00000284548.16:c.12466+23G>A NA rs1012788555 1 SNV HGNC HGNC:15719 2 CCDS1570.2 ENSP00000284548 Q5VST9.195 UPI0000425971 Q5VST9-3 1 NA NA PASS SITE 56,68|5,8 NA NA 1 93 20,26 165,156 60,60 34 1.72 NA 14.45 NA FALSE 6.00 44 NA NA NA FALSE NA NA 31.44 1 228307554 HCC1395_HCC1395T 56 0.196 69 13,6 26,3 40,9 NA 0/1 NA NA NA NA 25,31,5,8 G/A PANCANCER NA FALSE OBSCN chr1:228307554:228307555:G:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 229638354 229638355 C T 40 92 0.434782608695652 MODIFIER URB2 ENSG00000135763 T intron_variant Transcript ENST00000258243 protein_coding 4/9 ENST00000258243.7:c.3634+107C>T NA 1 SNV HGNC HGNC:28967 YES NM_014777.4 1 P1 CCDS31052.1 ENSP00000258243 Q14146.155 UPI000013CFBD 1 NA NA PASS SITE 26,100|5,35 NA NA 1 93 39,35 178,176 60,60 11 1.80 NA 18.31 NA FALSE 6.00 93 NA NA NA FALSE NA NA 118.79 1 229638354 HCC1395_HCC1395T 52 0.450 92 22,13 16,19 43,35 NA 0/1 NA NA NA NA 9,43,5,35 C/T PANCANCER NA FALSE URB2 chr1:229638354:229638355:C:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 231220790 231220791 C T 17 56 0.303571428571429 MODIFIER C1orf131 ENSG00000143633 T downstream_gene_variant Transcript ENST00000318906 protein_coding NA 2973 -1 SNV HGNC HGNC:25332 1 ENSP00000321341 Q5TBH9.123 UPI0000140466 1 NA NA PASS SITE 56,39|11,6 NA NA 1 93 20,20 165,162 60,60 25 1.59 NA 11.14 NA FALSE 6.00 71 NA NA NA FALSE NA NA 42.21 1 231220790 HCC1395_HCC1395T 39 0.329 56 14,5 13,6 27,13 NA 0/1 NA NA NA NA 24,15,11,6 C/T PANCANCER NA FALSE C1orf131 chr1:231220790:231220791:C:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 231221014 231221015 ACCAGACACCCAGAGCC A 10 41 0.24390243902439 MODIFIER C1orf131 ENSG00000143633 - downstream_gene_variant Transcript ENST00000318906 protein_coding NA 2733 -1 deletion HGNC HGNC:25332 1 ENSP00000321341 Q5TBH9.123 UPI0000140466 1 NA NA PASS SITE 42,45|5,5 NA NA 1 93 20,28 174,199 60,60 24 1.60 NA 11.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 34.95 1 231221014 HCC1395_HCC1395T 31 0.258 41 4,4 10,2 25,8 NA 0/1 NA NA NA NA 13,18,5,5 ACCAGACACCCAGAGCC/A PANCANCER NA FALSE C1orf131 chr1:231221014:231221015:ACCAGACACCCAGAGCC:A indel 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 231273931 231273932 G T 43 81 0.530864197530864 HIGH GNPAT ENSG00000116906 T stop_gained Transcript ENST00000366647 protein_coding 12/16 ENST00000366647.9:c.1612G>T ENSP00000355607.4:p.E538* ENSP00000355607.4 p.E538* 1779 1612 538 E/* Gaa/Taa COSV64154572 1 SNV HGNC HGNC:4416 YES NM_014236.4 1 P1 CCDS1592.1 ENSP00000355607 O15228.197 UPI0000000A2A O15228-1 1 PANTHER:PTHR12563&PIRSF:PIRSF000437&Pfam:PF19277&PIRSF:PIRSF500063&AlphaFold_DB_import:AF-O15228-F1 1 1 1 NA NA PASS SITE 71,37|29,14 NA NA 1 93 20,20 178,182 60,60 24 1.71 NA 15.05 NA FALSE 6.00 93 NA NA NA FALSE NA NA 117.88 1 231273931 HCC1395_HCC1395T 38 0.535 81 7,14 19,16 26,30 NA 0/1 NA NA NA NA 25,13,29,14 G/T PANCANCER NA FALSE GNPAT_p.E538* chr1:231273931:231273932:G:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 231528839 231528840 A T 177 299 0.591973244147157 MODIFIER TSNAX ENSG00000116918 T intron_variant Transcript ENST00000366639 protein_coding 1/5 ENST00000366639.9:c.16+13A>T NA 1 SNV HGNC HGNC:12380 YES NM_005999.3 1 P1 CCDS1596.1 ENSP00000355599 Q99598.185 A0A024R3V8.51 UPI0000137768 1 NA NA PASS SITE 194,153|95,82 NA NA 1 93 20,20 159,147 60,60 37 2.19 NA 45.65 NA FALSE 6.00 93 NA NA NA FALSE NA NA 458.19 1 231528839 HCC1395_HCC1395T 122 0.572 299 35,53 47,59 85,114 NA 0/1 NA NA NA NA 70,52,95,82 A/T PANCANCER NA FALSE TSNAX chr1:231528839:231528840:A:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 232038284 232038285 C G 17 30 0.566666666666667 MODIFIER DISC1 ENSG00000162946 G 3_prime_UTR_variant Transcript ENST00000366637 protein_coding 13/13 ENST00000366637.8:c.*1453C>G NA 4005 1 SNV HGNC HGNC:2888 5 P2 CCDS86058.1 ENSP00000355597 Q9NRI5.183 UPI00004EC290 Q9NRI5-2 1 1 NA NA PASS SITE 17,21|6,11 NA NA 1 54 38,20 186,174 60,60 30 1.30 NA 5.72 NA FALSE 6.00 85 NA NA NA FALSE NA NA 46.00 1 232038284 HCC1395_HCC1395T 13 0.500 30 3,7 8,4 12,12 NA 0/1 NA NA NA NA 6,7,6,11 C/G PANCANCER NA FALSE DISC1 chr1:232038284:232038285:C:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 232805682 232805683 C T 42 148 0.283783783783784 MODERATE MAP10 ENSG00000212916 T missense_variant Transcript ENST00000418460 protein_coding 1/1 ENST00000418460.4:c.233C>T ENSP00000403208.2:p.P78L ENSP00000403208.2 p.P78L 267 233 78 P/L cCc/cTc 1 SNV HGNC HGNC:29265 YES NM_019090.3 P1 CCDS44334.2 ENSP00000403208 Q9P2G4.133 UPI0000001C5A tolerated(0.06) possibly_damaging(0.782) Low_complexity_(Seg):seg&PANTHER:PTHR21831&AlphaFold_DB_import:AF-Q9P2G4-F1 1 NA NA PASS SITE 123,162|15,27 NA NA 1 93 20,35 166,176 60,60 33 2.11 NA 38.18 NA FALSE 6.00 79 NA NA NA FALSE NA NA 109.59 1 232805682 HCC1395_HCC1395T 106 0.305 148 37,10 35,19 78,34 NA 0/1 NA NA NA NA 45,61,15,27 C/T PANCANCER NA FALSE MAP10_p.P78L chr1:232805682:232805683:C:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 235464815 235464816 G C 7 13 0.538461538461538 MODIFIER B3GALNT2 ENSG00000162885 C downstream_gene_variant Transcript ENST00000313984 protein_coding NA 81 -1 SNV HGNC HGNC:28596 1 CCDS60453.1 ENSP00000315678 Q8NCR0.154 UPI0000470B12 Q8NCR0-2 1 1 NA NA PASS SITE 14,0|7,0 NA NA 1 23 40,39 247,277 60,60 16 0.954 NA 2.41 NA FALSE 6.00 78 NA NA NA FALSE NA NA 25.68 1 235464815 HCC1395_HCC1395T 6 0.533 13 2,3 4,4 6,7 NA 0/1 NA NA NA NA 6,0,7,0 G/C PANCANCER NA FALSE B3GALNT2 chr1:235464815:235464816:G:C SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 235766274 235766275 ATTCCTGAAAAAATAAAAAAAACTCTCT A 13 22 0.590909090909091 HIGH LYST ENSG00000143669 - splice_acceptor_variant&coding_sequence_variant&intron_variant Transcript ENST00000389793 protein_coding 21/53 20/52 ENST00000389793.7:c.5923-24_5925del NA ?-6086 ?-5925 ?-1975 -1 deletion HGNC HGNC:1968 YES NM_000081.4 5 P1 CCDS31062.1 ENSP00000374443 Q99698.201 UPI000020509E Q99698-1 1 1 NA NA PASS SITE 4,19|2,11 NA NA 1 11 33,35 173,199 60,60 27 1.11 NA 2.96 NA FALSE 6.00 93 NA NA NA FALSE NA NA 52.30 1 235766274 HCC1395_HCC1395T 9 0.575 22 1,1 2,5 8,11 NA 0/1 NA NA NA NA 1,8,2,11 ATTCCTGAAAAAATAAAAAAAACTCTCT/A PANCANCER NA FALSE LYST chr1:235766274:235766275:ATTCCTGAAAAAATAAAAAAAACTCTCT:A indel 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 245083509 245083510 A G 18 36 0.5 MODIFIER EFCAB2 ENSG00000203666 G intron_variant&non_coding_transcript_variant Transcript ENST00000366521 protein_coding_CDS_not_defined 6/7 ENST00000366521.7:n.481+25A>G NA rs760237391 1 SNV HGNC HGNC:28166 2 8.361e-06 0 0 0 5.701e-05 0 0 0 3.487e-05 5.701e-05 gnomADe_EAS 1 NA NA PASS SITE 17,32|7,11 NA NA 1 70 34,20 163,146 60,60 20 1.41 NA 7.22 NA FALSE 6.00 31 NA NA NA FALSE NA NA 46.17 1 245083509 HCC1395_HCC1395T 18 0.448 36 2,2 11,10 15,12 NA 0/1 NA NA NA NA 5,13,7,11 A/G PANCANCER NA FALSE EFCAB2 chr1:245083509:245083510:A:G SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 245915779 245915780 T A 6 8 0.75 MODIFIER SMYD3 ENSG00000185420 A intron_variant&non_coding_transcript_variant Transcript ENST00000366516 retained_intron 2/6 ENST00000366516.5:n.1058-139A>T NA -1 SNV HGNC HGNC:15513 1 1 NA NA PASS SITE 0,10|0,6 NA NA 1 27 34,38 239,235 60,60 37 0.992 NA 2.41 NA FALSE 6.00 40 NA NA NA FALSE NA NA 22.59 1 245915779 HCC1395_HCC1395T 2 0.700 8 1,1 1,5 2,6 NA 0/1 NA NA NA NA 0,2,0,6 T/A PANCANCER NA FALSE SMYD3 chr1:245915779:245915780:T:A SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr1 248239030 248239031 C T 162 331 0.489425981873112 LOW OR2M4 ENSG00000171180 T synonymous_variant Transcript ENST00000641868 protein_coding 2/2 ENST00000641868.1:c.102C>T ENSP00000492992.1:p.I34= ENSP00000492992.1 p.I34= 285 102 34 I atC/atT rs375886519&COSV60707946 1 SNV HGNC HGNC:8270 YES NM_017504.2 P1 CCDS31108.1 ENSP00000492992 Q96R27.158 A0A126GV73.45 UPI000004B233 Gene3D:1.20.1070.10&AlphaFold_DB_import:AF-Q96R27-F1&Pfam:PF13853&Prints:PR00237&PANTHER:PTHR26453&SMART:SM01381&Superfamily:SSF81321&Transmembrane_helices:TMhelix&CDD:cd15421 3.977e-06 6.152e-05 0 0 0 0 0 0 0 6.152e-05 gnomADe_AFR 0&1 0&1 1 NA NA PASS SITE 200,227|75,87 NA NA 1 93 20,20 154,164 60,60 32 2.25 NA 51.77 NA FALSE 6.00 93 NA NA NA FALSE NA NA 424.99 1 248239030 HCC1395_HCC1395T 169 0.489 331 49,44 52,58 112,107 NA 0/1 NA NA NA NA 79,90,75,87 C/T PANCANCER NA FALSE OR2M4_p.I34= chr1:248239030:248239031:C:T SNV 2:1 chr1:145744615:248916508:2:1:1 TRUE NA 0.96 +chr2 669670 669671 C T 44 141 0.312056737588652 MODERATE TMEM18 ENSG00000151353 T missense_variant Transcript ENST00000281017 protein_coding 5/5 ENST00000281017.8:c.333G>A ENSP00000281017.3:p.M111I ENSP00000281017.3 p.M111I 394 333 111 M/I atG/atA -1 SNV HGNC HGNC:25257 YES NM_152834.4 1 P1 CCDS33141.1 ENSP00000281017 Q96B42.126 UPI0000208A7D Q96B42-1 tolerated(0.15) benign(0.023) AlphaFold_DB_import:AF-Q96B42-F1&Pfam:PF14770&Transmembrane_helices:TMhelix 12 NA NA PASS SITE 118,102|21,23 NA NA 1 93 20,32 173,199 60,60 26 1.65 NA 25.79 NA FALSE 6.00 74 NA NA NA FALSE NA NA 111.28 12 669670 HCC1395_HCC1395T 97 0.348 141 23,10 41,24 66,35 NA 0/1 NA NA NA NA 50,47,21,23 C/T PANCANCER NA FALSE TMEM18_p.M111I chr2:669670:669671:C:T SNV 3:0 chr2:40569:10123930:3:0:1 NA NA 0.96 +chr2 3641446 3641447 G A 17 30 0.566666666666667 MODIFIER COLEC11 ENSG00000118004 A intron_variant Transcript ENST00000236693 protein_coding 6/7 ENST00000236693.11:c.319+1115G>A NA 1 SNV HGNC HGNC:17213 1 CCDS1650.1 ENSP00000236693 Q9BWP8.175 UPI000013C9EF Q9BWP8-9 1 12 NA NA PASS SITE 12,36|3,14 NA NA 1 81 35,38 166,196 60,60 22 1.47 NA 8.43 NA FALSE 6.00 30 NA NA NA FALSE NA NA 54.80 12 3641446 HCC1395_HCC1395T 13 0.600 30 6,2 3,12 9,14 NA 0/1 NA NA NA NA 4,9,3,14 G/A PANCANCER NA FALSE COLEC11 chr2:3641446:3641447:G:A SNV 3:0 chr2:40569:10123930:3:0:1 NA NA 0.96 +chr2 7068190 7068191 TCAGTGAGTAAGGTTTTCTTTAACAGGGTGATGC T 45 144 0.3125 MODIFIER ENSG00000223884 - intron_variant&non_coding_transcript_variant Transcript ENST00000415520 lncRNA 2/2 ENST00000415520.5:n.343-5309_343-5277del NA -1 deletion 4 12 NA NA PASS SITE 103,129|10,35 NA NA 1 93 20,34 175,198 60,60 35 1.97 NA 27.02 NA FALSE 6.00 93 NA NA NA FALSE NA NA 173.59 12 7068190 HCC1395_HCC1395T 99 0.373 144 17,4 26,13 65,38 NA 0/1 NA NA NA NA 42,57,10,35 TCAGTGAGTAAGGTTTTCTTTAACAGGGTGATGC/T PANCANCER NA FALSE chr2:7068190:7068191:TCAGTGAGTAAGGTTTTCTTTAACAGGGTGATGC:T indel 3:0 chr2:40569:10123930:3:0:1 NA NA 0.96 +chr2 7109626 7109627 G A 21 174 0.120689655172414 MODIFIER A regulatory_region_variant RegulatoryFeature ENSR00001027135 enhancer NA SNV 12 NA NA PASS SITE 119,183|7,14 NA NA 1 93 20,33 162,202 60,60 34 2.00 NA 29.45 NA FALSE 6.00 63 NA NA NA FALSE NA NA 49.18 12 7109626 HCC1395_HCC1395T 153 0.145 174 44,6 45,9 99,16 NA 0/1 NA NA NA NA 64,89,7,14 G/A PANCANCER NA FALSE chr2:7109626:7109627:G:A SNV 3:0 chr2:40569:10123930:3:0:1 NA NA 0.96 +chr2 11344357 11344358 G A 31 31 1 MODIFIER ROCK2 ENSG00000134318 A upstream_gene_variant Transcript ENST00000261535 nonsense_mediated_decay NA 216 -1 SNV HGNC HGNC:10252 5 ENSP00000261535 D6REE7.79 UPI000173A3F4 12 NA NA PASS SITE 29,45|11,20 NA NA 1 93 20,20 152,155 60,60 16 1.72 NA 15.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 93.16 12 11344357 HCC1395_HCC1395T 0 0.957 31 0,7 0,8 0,21 NA 0/1 NA NA NA NA 0,0,11,20 G/A PANCANCER NA FALSE ROCK2 chr2:11344357:11344358:G:A SNV 2:0 chr2:10192413:25379441:2:0:1 TRUE NA 0.96 +chr2 15474346 15474347 G A 11 21 0.523809523809524 MODIFIER NBAS ENSG00000151779 A intron_variant Transcript ENST00000281513 protein_coding 14/51 ENST00000281513.10:c.1342-22C>T NA -1 SNV HGNC HGNC:15625 YES NM_015909.4 1 P1 CCDS1685.1 ENSP00000281513 A2RRP1.126 UPI00001AEA68 A2RRP1-1 1 12 NA NA PASS SITE 14,32|3,8 NA NA 1 75 20,20 152,138 60,60 23 1.45 NA 7.83 NA FALSE 6.00 45 NA NA NA FALSE NA NA 30.43 12 15474346 HCC1395_HCC1395T 10 0.500 21 3,4 3,2 8,8 NA 0/1 NA NA NA NA 2,8,3,8 G/A PANCANCER NA FALSE NBAS chr2:15474346:15474347:G:A SNV 2:0 chr2:10192413:25379441:2:0:1 TRUE NA 0.96 +chr2 19975745 19975746 C G 42 96 0.4375 MODIFIER WDR35 ENSG00000118965 G intron_variant Transcript ENST00000281405 protein_coding 5/26 ENST00000281405.9:c.437-82G>C NA -1 SNV HGNC HGNC:29250 YES NM_020779.4 1 P3 CCDS1695.1 ENSP00000281405 Q9P2L0.181 UPI00001AF317 Q9P2L0-2 1 12 NA NA PASS SITE 41,122|10,32 NA NA 1 93 35,38 184,174 60,60 26 1.93 NA 25.28 NA FALSE 6.00 93 NA NA NA FALSE NA NA 128.26 12 19975745 HCC1395_HCC1395T 54 0.450 96 14,10 25,19 42,34 NA 0/1 NA NA NA NA 14,40,10,32 C/G PANCANCER NA FALSE WDR35 chr2:19975745:19975746:C:G SNV 2:0 chr2:10192413:25379441:2:0:1 TRUE NA 0.96 +chr2 25233971 25233972 G A 91 164 0.554878048780488 MODIFIER DNMT3A ENSG00000119772 A 3_prime_UTR_variant Transcript ENST00000264709 protein_coding 23/23 ENST00000264709.7:c.*308C>T NA 3385 -1 SNV HGNC HGNC:2978 1 P3 CCDS33157.1 ENSP00000264709 Q9Y6K1.196 UPI000000DA70 Q9Y6K1-1 1 12 NA NA PASS SITE 103,158|39,52 NA NA 1 93 20,20 166,163 60,60 31 2.13 NA 39.37 NA FALSE 6.00 93 NA NA NA FALSE NA NA 231.97 12 25233971 HCC1395_HCC1395T 73 0.568 164 20,24 25,28 47,62 NA 0/1 NA NA NA NA 32,41,39,52 G/A PANCANCER TRUE FALSE DNMT3A chr2:25233971:25233972:G:A SNV 2:0 chr2:10192413:25379441:2:0:1 TRUE NA 0.96 +chr2 26430884 26430885 A G 59 59 1 MODIFIER DRC1 ENSG00000157856 G intron_variant Transcript ENST00000288710 protein_coding 6/16 ENST00000288710.7:c.765+12A>G NA 1 SNV HGNC HGNC:24245 YES NM_145038.5 2 P1 CCDS1723.1 ENSP00000288710 Q96MC2.136 UPI000013DF36 1 12 NA NA PASS SITE 13,45|15,44 NA NA 1 93 35,35 171,186 60,60 27 1.68 NA 13.84 NA FALSE 6.00 93 NA NA NA FALSE NA NA 201.22 12 26430884 HCC1395_HCC1395T 0 0.980 59 0,12 0,28 0,46 NA 0/1 NA NA NA NA 0,0,15,44 A/G PANCANCER NA FALSE DRC1 chr2:26430884:26430885:A:G SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 26458128 26458129 A G 150 150 1 MODIFIER OTOF ENSG00000115155 G 3_prime_UTR_variant Transcript ENST00000272371 protein_coding 47/47 ENST00000272371.7:c.*110T>C NA 6289 COSV55512748 -1 SNV HGNC HGNC:8515 YES NM_194248.3 1 A1 CCDS1725.1 ENSP00000272371 Q9HC10.188 UPI000013D94D Q9HC10-1 1 1 1 12 NA NA PASS SITE 73,92|62,88 NA NA 1 93 20,20 162,165 60,60 34 2.04 NA 32.16 NA FALSE 6.00 93 NA NA NA FALSE NA NA 444.18 12 26458128 HCC1395_HCC1395T 0 0.990 150 0,52 0,39 0,100 NA 0/1 NA NA NA NA 0,0,62,88 A/G PANCANCER NA FALSE OTOF chr2:26458128:26458129:A:G SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 26489403 26489404 A G 10 39 0.256410256410256 MODIFIER OTOF ENSG00000115155 G intron_variant Transcript ENST00000272371 protein_coding 10/46 ENST00000272371.7:c.961-108T>C NA -1 SNV HGNC HGNC:8515 YES NM_194248.3 1 A1 CCDS1725.1 ENSP00000272371 Q9HC10.188 UPI000013D94D Q9HC10-1 1 12 NA NA PASS SITE 18,56|3,7 NA NA 1 93 34,20 161,175 60,60 28 1.56 NA 10.54 NA FALSE 6.00 15 NA NA NA FALSE NA NA 24.62 12 26489403 HCC1395_HCC1395T 29 0.258 39 8,1 11,4 22,7 NA 0/1 NA NA NA NA 8,21,3,7 A/G PANCANCER NA FALSE OTOF chr2:26489403:26489404:A:G SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 28549024 28549025 G A 6 7 0.857142857142857 MODIFIER PLB1 ENSG00000163803 A intron_variant Transcript ENST00000327757 protein_coding 15/57 ENST00000327757.10:c.1008+93G>A NA 1 SNV HGNC HGNC:30041 YES NM_153021.5 1 P1 CCDS33168.1 ENSP00000330442 Q6P1J6.147 UPI0000D6117C Q6P1J6-1 12 NA NA PASS SITE 0,10|0,6 NA NA 1 35 39,39 254,275 60,60 42 1.000 NA 2.71 NA FALSE 6.00 34 NA NA NA FALSE NA NA 23.84 12 28549024 HCC1395_HCC1395T 1 0.781 7 0,1 1,5 1,6 NA 0/1 NA NA NA NA 0,1,0,6 G/A PANCANCER NA FALSE PLB1 chr2:28549024:28549025:G:A SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 29033589 29033590 C T 5 27 0.185185185185185 MODIFIER TOGARAM2 ENSG00000189350 T intron_variant Transcript ENST00000379558 protein_coding 16/19 ENST00000379558.5:c.2225+26C>T NA 1 SNV HGNC HGNC:33715 YES NM_199280.4 5 P1 CCDS1769.2 ENSP00000368876 Q6ZUX3.134 UPI00014F7B81 Q6ZUX3-1 12 NA NA PASS SITE 3,43|0,5 NA NA 1 80 39,39 205,244 60,60 11 1.35 NA 6.32 NA FALSE 6.00 36 NA NA NA FALSE NA NA 15.53 12 29033589 HCC1395_HCC1395T 22 0.207 27 5,2 15,3 22,5 NA 0/1 NA NA NA NA 0,22,0,5 C/T PANCANCER NA FALSE TOGARAM2 chr2:29033589:29033590:C:T SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 29045496 29045497 T C 100 297 0.336700336700337 MODIFIER TOGARAM2 ENSG00000189350 C intron_variant Transcript ENST00000379558 protein_coding 19/19 ENST00000379558.5:c.2722+86T>C NA rs1349711774 1 SNV HGNC HGNC:33715 YES NM_199280.4 5 P1 CCDS1769.2 ENSP00000368876 Q6ZUX3.134 UPI00014F7B81 Q6ZUX3-1 9.218e-06 0 0 0 0 0 2.032e-05 0 0 2.032e-05 gnomADe_NFE 12 NA NA PASS SITE 218,214|48,52 NA NA 1 93 20,20 159,164 60,60 32 2.19 NA 45.10 NA FALSE 6.00 93 NA NA NA FALSE NA NA 250.33 12 29045496 HCC1395_HCC1395T 197 0.352 297 39,23 82,41 126,68 NA 0/1 NA NA NA NA 99,98,48,52 T/C PANCANCER NA FALSE TOGARAM2 chr2:29045496:29045497:T:C SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 31366061 31366062 G C 320 321 0.996884735202492 MODERATE XDH ENSG00000158125 C missense_variant Transcript ENST00000379416 protein_coding 22/36 ENST00000379416.4:c.2371C>G ENSP00000368727.3:p.R791G ENSP00000368727.3 p.R791G 2447 2371 791 R/G Cga/Gga rs775646772&COSV65149715&COSV65151558 -1 SNV HGNC HGNC:12805 YES NM_000379.4 1 P1 CCDS1775.1 ENSP00000368727 P47989.216 UPI0000036BC9 1 deleterious(0) probably_damaging(0.976) PDB-ENSP_mappings:2ckj.A&PDB-ENSP_mappings:2ckj.B&PDB-ENSP_mappings:2ckj.C&PDB-ENSP_mappings:2ckj.D&PDB-ENSP_mappings:2e1q.A&PDB-ENSP_mappings:2e1q.B&PDB-ENSP_mappings:2e1q.C&PDB-ENSP_mappings:2e1q.D&Gene3D:3.30.365.10&Gene3D:3.30.365.10&AlphaFold_DB_import:AF-P47989-F1&Pfam:PF02738&PIRSF:PIRSF000127&PANTHER:PTHR45444&Superfamily:SSF56003 1.193e-05 0 8.673e-05 0 0 0 0 0 0 8.673e-05 gnomADe_AMR 0&1&1 0&1&1 12 NA NA PASS SITE 157,119|176,144 NA NA 1 93 20,20 157,163 60,60 35 2.24 NA 51.77 NA FALSE 6.00 93 NA NA NA FALSE NA NA 965.92 12 31366061 HCC1395_HCC1395T 1 0.991 321 1,101 0,98 1,207 NA 0/1 NA NA NA NA 1,0,176,144 G/C PANCANCER NA FALSE XDH_p.R791G chr2:31366061:31366062:G:C SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 32063572 32063573 G C 16 51 0.313725490196078 MODIFIER SPAST ENSG00000021574 C 5_prime_UTR_variant Transcript ENST00000315285 protein_coding 1/17 ENST00000315285.9:c.-260G>C NA 17 rs1249692851 1 SNV HGNC HGNC:11233 YES NM_014946.4 1 P4 CCDS1778.1 ENSP00000320885 Q9UBP0.205 E5KRP5.94 UPI0000038A6B Q9UBP0-1 1 12 NA NA PASS SITE 73,46|10,6 NA NA 1 93 20,20 165,155 60,60 16 1.77 NA 16.81 NA FALSE 4.61 80 NA NA NA FALSE NA NA 35.97 12 32063572 HCC1395_HCC1395T 35 0.323 51 8,6 13,4 22,10 NA 0/1 NA NA NA NA 21,14,10,6 G/C PANCANCER NA FALSE SPAST chr2:32063572:32063573:G:C SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 36805792 36805793 C G 35 35 1 MODIFIER VIT ENSG00000205221 G intron_variant Transcript ENST00000379241 protein_coding 12/13 ENST00000379241.7:c.1278+128C>G NA 1 SNV HGNC HGNC:12697 1 A2 CCDS54349.1 ENSP00000368543 Q6UXI7.127 UPI0000371A40 Q6UXI7-2 12 NA NA PASS SITE 11,23|10,25 NA NA 1 93 20,20 155,192 60,60 28 1.39 NA 6.92 NA FALSE 6.00 93 NA NA NA FALSE NA NA 118.36 12 36805792 HCC1395_HCC1395T 0 0.965 35 0,7 0,17 0,26 NA 0/1 NA NA NA NA 0,0,10,25 C/G PANCANCER NA FALSE VIT chr2:36805792:36805793:C:G SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 36846676 36846677 C G 28 118 0.23728813559322 MODIFIER STRN ENSG00000115808 G 3_prime_UTR_variant Transcript ENST00000263918 protein_coding 18/18 ENST00000263918.9:c.*2780G>C NA 5196 -1 SNV HGNC HGNC:11424 YES NM_003162.4 1 P1 CCDS1784.1 ENSP00000263918 O43815.200 UPI000013D48A O43815-1 1 12 NA NA PASS SITE 127,106|17,11 NA NA 1 93 32,38 189,182 60,60 22 2.06 NA 33.41 NA FALSE 6.00 88 NA NA NA TRUE NA NA 72.11 12 36846676 HCC1395_HCC1395T 90 0.240 118 22,7 38,10 71,22 NA 0/1 NA NA NA NA 50,40,17,11 C/G PANCANCER NA FALSE STRN chr2:36846676:36846677:C:G SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 37952221 37952222 T A 44 193 0.227979274611399 MODIFIER RMDN2 ENSG00000115841 A intron_variant Transcript ENST00000234195 protein_coding 2/10 ENST00000234195.7:c.986+20T>A NA 1 SNV HGNC HGNC:26567 2 CCDS1792.1 ENSP00000234195 A0A0C4DFM4.47 UPI000006E974 12 NA NA PASS SITE 206,171|26,18 NA NA 1 93 20,20 166,171 60,60 31 2.20 NA 47.46 NA FALSE 6.00 93 NA NA NA FALSE NA NA 103.61 12 37952221 HCC1395_HCC1395T 149 0.236 193 40,16 59,14 106,32 NA 0/1 NA NA NA NA 77,72,26,18 T/A PANCANCER NA FALSE RMDN2 chr2:37952221:37952222:T:A SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 44285717 44285718 G A 154 154 1 MODIFIER SLC3A1 ENSG00000138079 A intron_variant Transcript ENST00000260649 protein_coding 3/9 ENST00000260649.11:c.766-315G>A NA 1 SNV HGNC HGNC:11025 YES NM_000341.4 1 P1 CCDS1819.1 ENSP00000260649 Q07837.215 A0A0S2Z4E1.45 UPI000013D0F2 Q07837-1 1 12 NA NA PASS SITE 82,61|74,80 NA NA 1 93 20,20 166,173 60,60 27 2.01 NA 29.80 NA FALSE 6.00 93 NA NA NA FALSE NA NA 454.84 12 44285717 HCC1395_HCC1395T 0 0.990 154 0,31 0,63 0,101 NA 0/1 NA NA NA NA 0,0,74,80 G/A PANCANCER NA FALSE SLC3A1 chr2:44285717:44285718:G:A SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 44942972 44942973 G A 77 215 0.358139534883721 MODIFIER SIX3 ENSG00000138083 A intron_variant Transcript ENST00000260653 protein_coding 1/1 ENST00000260653.5:c.806+62G>A NA 1 SNV HGNC HGNC:10889 YES NM_005413.4 1 P1 CCDS1821.1 ENSP00000260653 O95343.180 UPI00001359C4 1 12 NA NA PASS SITE 83,213|21,56 NA NA 2 93 20,20 171,175 60,60 23 2.09 NA 35.51 NA FALSE 6.00 44 NA NA NA FALSE NA NA 200.94 12 44942972 HCC1395_HCC1395T 138 0.361 215 19,5 29,17 103,58 NA 0/1 NA NA NA NA 39,99,21,56 G/A PANCANCER NA FALSE SIX3 chr2:44942972:44942973:G:A SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 44943000 44943001 G T 34 108 0.314814814814815 MODIFIER SIX3 ENSG00000138083 T intron_variant Transcript ENST00000260653 protein_coding 1/1 ENST00000260653.5:c.806+90G>T NA 1 SNV HGNC HGNC:10889 YES NM_005413.4 1 P1 CCDS1821.1 ENSP00000260653 O95343.180 UPI00001359C4 1 12 NA NA PASS SITE 25,124|6,28 NA NA 2 93 38,34 189,190 60,60 23 1.86 NA 21.02 NA FALSE 6.00 15 NA NA NA FALSE NA NA 88.44 12 44943000 HCC1395_HCC1395T 74 0.329 108 7,0 12,6 60,29 NA 0/1 NA NA NA NA 15,59,6,28 G/T PANCANCER NA FALSE SIX3 chr2:44943000:44943001:G:T SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 45005499 45005500 G A 20 51 0.392156862745098 MODIFIER SIX2 ENSG00000170577 A 3_prime_UTR_variant Transcript ENST00000303077 protein_coding 2/2 ENST00000303077.7:c.*671C>T NA 1889 -1 SNV HGNC HGNC:10888 YES NM_016932.5 1 P1 CCDS1822.1 ENSP00000304502 Q9NPC8.165 UPI00001359C0 1 12 NA NA PASS SITE 44,49|10,10 NA NA 1 93 20,20 156,156 60,60 28 1.60 NA 11.44 NA FALSE 6.00 74 NA NA NA FALSE NA NA 49.99 12 45005499 HCC1395_HCC1395T 31 0.412 51 7,6 11,7 19,13 NA 0/1 NA NA NA NA 14,17,10,10 G/A PANCANCER NA FALSE SIX2 chr2:45005499:45005500:G:A SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 45006212 45006213 G A 168 546 0.307692307692308 LOW SIX2 ENSG00000170577 A synonymous_variant Transcript ENST00000303077 protein_coding 2/2 ENST00000303077.7:c.834C>T ENSP00000304502.6:p.I278= ENSP00000304502.6 p.I278= 1176 834 278 I atC/atT rs1437494866 -1 SNV HGNC HGNC:10888 YES NM_016932.5 1 P1 CCDS1822.1 ENSP00000304502 Q9NPC8.165 UPI00001359C0 1 AlphaFold_DB_import:AF-Q9NPC8-F1&PANTHER:PTHR10390&MobiDB_lite:mobidb-lite 3.995e-06 0 0 0 5.437e-05 0 0 0 0 1.314e-05 0 0 0.0001308 0 0 0 0 0 0 0 0.0001308 gnomADg_AMR 12 NA NA PASS SITE 411,353|94,74 NA NA 1 93 20,20 155,157 60,60 35 2.40 NA 73.70 NA FALSE 4.61 93 NA NA NA FALSE NA NA 377.95 12 45006212 HCC1395_HCC1395T 378 0.301 546 117,46 113,57 245,105 NA 0/1 NA NA NA NA 202,176,94,74 G/A PANCANCER NA FALSE SIX2_p.I278= chr2:45006212:45006213:G:A SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 45413085 45413086 G T 22 27 0.814814814814815 MODIFIER SRBD1 ENSG00000068784 T intron_variant Transcript ENST00000263736 protein_coding 19/20 ENST00000263736.5:c.2513+29C>A NA -1 SNV HGNC HGNC:25521 YES NM_018079.5 2 P1 CCDS1823.1 ENSP00000263736 Q8N5C6.153 UPI000004CC06 Q8N5C6-1 12 NA NA PASS SITE 22,3|17,5 NA NA 1 60 39,32 213,174 60,60 18 1.28 NA 5.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 65.78 12 45413085 HCC1395_HCC1395T 5 0.751 27 2,8 3,9 5,17 NA 0/1 NA NA NA NA 5,0,17,5 G/T PANCANCER NA FALSE SRBD1 chr2:45413085:45413086:G:T SNV 3:0 chr2:25531366:45419904:3:0:1 NA NA 0.96 +chr2 46384706 46384707 C G 28 222 0.126126126126126 MODIFIER EPAS1 ENSG00000116016 G 3_prime_UTR_variant Transcript ENST00000263734 protein_coding 16/16 ENST00000263734.5:c.*46C>G NA 3164 1 SNV HGNC HGNC:3374 YES NM_001430.5 1 P1 CCDS1825.1 ENSP00000263734 Q99814.224 UPI000013D44F 1 12 NA NA PASS SITE 163,182|13,15 NA NA 1 93 36,31 183,167 60,60 27 2.07 NA 34.57 NA FALSE 6.00 76 NA NA NA FALSE NA NA 62.95 12 46384706 HCC1395_HCC1395T 194 0.128 222 44,7 108,14 155,22 NA 0/1 NA NA NA NA 95,99,13,15 C/G PANCANCER TRUE FALSE EPAS1 chr2:46384706:46384707:C:G SNV 2:1 chr2:45546677:63443140:2:1:1 TRUE NA 0.96 +chr2 46905211 46905212 G C 200 291 0.687285223367698 MODIFIER MCFD2 ENSG00000180398 C 3_prime_UTR_variant Transcript ENST00000319466 protein_coding 4/4 ENST00000319466.9:c.*252C>G NA 783 -1 SNV HGNC HGNC:18451 YES NM_139279.6 1 P1 CCDS33192.1 ENSP00000317271 Q8NI22.167 UPI000005275E Q8NI22-1 1 12 NA NA PASS SITE 200,92|153,47 NA NA 1 93 20,35 171,175 60,60 31 2.16 NA 42.69 NA FALSE 6.00 93 NA NA NA FALSE NA NA 623.02 12 46905211 HCC1395_HCC1395T 91 0.673 291 34,50 37,103 75,156 NA 0/1 NA NA NA NA 65,26,153,47 G/C PANCANCER NA FALSE MCFD2 chr2:46905211:46905212:G:C SNV 2:1 chr2:45546677:63443140:2:1:1 TRUE NA 0.96 +chr2 47806320 47806321 G A 74 233 0.317596566523605 MODERATE MSH6 ENSG00000116062 A missense_variant Transcript ENST00000234420 protein_coding 8/10 ENST00000234420.11:c.3763G>A ENSP00000234420.5:p.D1255N ENSP00000234420.5 p.D1255N 3852 3763 1255 D/N Gat/Aat rs1336339961 1 SNV HGNC HGNC:7329 YES NM_000179.3 1 P2 CCDS1836.1 ENSP00000234420 P52701.244 UPI00000405F8 P52701-1 1 deleterious(0.01) PDB-ENSP_mappings:2o8b.B&PDB-ENSP_mappings:2o8c.B&PDB-ENSP_mappings:2o8d.B&PDB-ENSP_mappings:2o8e.B&PDB-ENSP_mappings:2o8f.B&Gene3D:3.40.50.300&AlphaFold_DB_import:AF-P52701-F1&Pfam:PF00488&PIRSF:PIRSF037677&PANTHER:PTHR11361&SMART:SM00534&Superfamily:SSF52540 uncertain_significance 1 12 NA NA PASS SITE 146,145|40,34 NA NA 1 93 20,20 171,167 60,60 29 1.94 NA 25.83 NA FALSE 6.00 93 NA NA NA FALSE NA NA 189.87 12 47806320 HCC1395_HCC1395T 159 0.317 233 37,20 67,29 111,51 NA 0/1 NA NA NA NA 79,80,40,34 G/A PANCANCER NA FALSE MSH6_p.D1255N chr2:47806320:47806321:G:A SNV 2:1 chr2:45546677:63443140:2:1:1 TRUE NA 0.96 +chr2 48723384 48723385 AG A 18 65 0.276923076923077 MODIFIER LHCGR ENSG00000138039 - intron_variant Transcript ENST00000294954 protein_coding 6/10 ENST00000294954.12:c.536+71del NA -1 deletion HGNC HGNC:6585 YES NM_000233.4 1 P4 CCDS1842.1 ENSP00000294954 P22888.227 UPI000013E1E1 P22888-1 1 12 NA NA PASS SITE 65,30|11,7 NA NA 1 76 20,20 154,150 60,60 20 1.50 NA 9.03 NA FALSE 6.00 93 NA NA NA FALSE NA NA 36.00 12 48723384 HCC1395_HCC1395T 47 0.245 65 14,2 24,9 39,12 NA 0/1 NA NA NA NA 37,10,11,7 AG/A PANCANCER NA FALSE LHCGR chr2:48723384:48723385:AG:A indel 2:1 chr2:45546677:63443140:2:1:1 TRUE NA 0.96 +chr2 49020159 49020160 C T 25 90 0.277777777777778 MODERATE FSHR ENSG00000170820 T missense_variant&splice_region_variant Transcript ENST00000304421 protein_coding 3/9 ENST00000304421.8:c.226G>A ENSP00000306780.4:p.E76K ENSP00000306780.4 p.E76K 290 226 76 E/K Gag/Aag COSV105165207&COSV58633546 -1 SNV HGNC HGNC:3969 1 CCDS1844.2 ENSP00000306780 P23945.229 UPI0000E49B12 1 tolerated(0.07) benign(0.407) PDB-ENSP_mappings:1xwd.C&PDB-ENSP_mappings:1xwd.F&Gene3D:3.80.10.10&PDB-ENSP_mappings:4ay9.X&PDB-ENSP_mappings:4ay9.Y&PDB-ENSP_mappings:4ay9.Z&PDB-ENSP_mappings:4mqw.X&PDB-ENSP_mappings:4mqw.Y&PDB-ENSP_mappings:4mqw.Z&AlphaFold_DB_import:AF-P23945-F1&Pfam:PF13306&PANTHER:PTHR24372&Superfamily:SSF52058 1&1 1&1 12 NA NA PASS SITE 36,85|6,19 NA NA 1 93 33,34 170,161 60,60 28 1.65 NA 12.64 NA FALSE 6.00 57 NA NA NA FALSE NA NA 65.64 12 49020159 HCC1395_HCC1395T 65 0.279 90 20,5 23,12 51,19 NA 0/1 NA NA NA NA 18,47,6,19 C/T PANCANCER NA FALSE FSHR_p.E76K chr2:49020159:49020160:C:T SNV 2:1 chr2:45546677:63443140:2:1:1 TRUE NA 0.96 +chr2 53808402 53808403 A C 28 185 0.151351351351351 MODERATE ERLEC1 ENSG00000068912 C missense_variant Transcript ENST00000185150 protein_coding 9/14 ENST00000185150.9:c.983A>C ENSP00000185150.4:p.K328T ENSP00000185150.4 p.K328T 1150 983 328 K/T aAa/aCa rs200669336 1 SNV HGNC HGNC:25222 YES NM_015701.5 1 P2 CCDS1848.1 ENSP00000185150 Q96DZ1.174 V9HWD3.48 UPI00000373C1 Q96DZ1-1 tolerated(0.13) benign(0.007) AlphaFold_DB_import:AF-Q96DZ1-F1&PANTHER:PTHR15414 0.0002 0 0 0.001 0 0 1.194e-05 6.152e-05 0 0 5.437e-05 4.62e-05 0 0 0 1.971e-05 4.827e-05 0 0 0 0.0001924 0 0 0 0 0 0.001 EAS 12 NA NA PASS SITE 130,143|15,13 NA NA 1 93 20,20 168,142 60,60 36 1.91 NA 23.78 NA FALSE 6.00 93 NA NA NA FALSE NA NA 63.10 12 53808402 HCC1395_HCC1395T 157 0.152 185 39,7 56,10 105,18 NA 0/1 NA NA NA NA 75,82,15,13 A/C PANCANCER NA FALSE ERLEC1_p.K328T chr2:53808402:53808403:A:C SNV 2:1 chr2:45546677:63443140:2:1:1 TRUE NA 0.96 +chr2 53901385 53901386 G C 45 119 0.378151260504202 MODIFIER PSME4 ENSG00000068878 C 3_prime_UTR_variant&NMD_transcript_variant Transcript ENST00000389993 nonsense_mediated_decay 27/46 ENST00000389993.7:c.*1383C>G NA 3155 COSV66364490 -1 SNV HGNC HGNC:20635 1 ENSP00000374643 F8WBH5.57 UPI000173A53A 1 1 12 NA NA PASS SITE 96,64|26,19 NA NA 1 93 20,20 149,163 60,60 28 1.74 NA 16.21 NA FALSE 6.00 93 NA NA NA FALSE NA NA 117.68 12 53901385 HCC1395_HCC1395T 74 0.401 119 16,11 29,16 47,31 NA 0/1 NA NA NA NA 45,29,26,19 G/C PANCANCER NA FALSE PSME4 chr2:53901385:53901386:G:C SNV 2:1 chr2:45546677:63443140:2:1:1 TRUE NA 0.96 +chr2 61348285 61348286 C G 157 451 0.348115299334812 MODERATE USP34 ENSG00000115464 G missense_variant Transcript ENST00000398571 protein_coding 15/80 ENST00000398571.7:c.1870G>C ENSP00000381577.2:p.D624H ENSP00000381577.2 p.D624H 2265 1870 624 D/H Gat/Cat COSV68400312 -1 SNV HGNC HGNC:20066 YES NM_014709.4 5 P1 CCDS42686.1 ENSP00000381577 Q70CQ2.151 UPI0000410E09 Q70CQ2-1 deleterious_low_confidence(0) benign(0.097) MobiDB_lite:mobidb-lite 1 1 12 NA NA PASS SITE 309,301|83,74 NA NA 1 93 20,20 164,156 60,60 32 2.35 NA 64.97 NA FALSE 6.00 93 NA NA NA FALSE NA NA 384.69 12 61348285 HCC1395_HCC1395T 294 0.339 451 71,42 116,54 199,102 NA 0/1 NA NA NA NA 150,144,83,74 C/G PANCANCER NA FALSE USP34_p.D624H chr2:61348285:61348286:C:G SNV 2:1 chr2:45546677:63443140:2:1:1 TRUE NA 0.96 +chr2 61872914 61872915 G A 20 32 0.625 MODIFIER CCT4 ENSG00000115484 A intron_variant Transcript ENST00000394440 protein_coding 10/13 ENST00000394440.8:c.1125+88C>T NA rs1443297943 -1 SNV HGNC HGNC:1617 YES NM_006430.4 1 P1 CCDS33206.1 ENSP00000377958 P50991.207 UPI00000362DF P50991-1 6.576e-06 0 0 0 0 0 0 0 1.47e-05 0 0 1.47e-05 gnomADg_NFE 12 NA NA PASS SITE 36,3|18,2 NA NA 1 77 39,35 196,200 60,60 22 1.43 NA 7.82 NA FALSE 6.00 93 NA NA NA FALSE NA NA 63.93 12 61872914 HCC1395_HCC1395T 12 0.613 32 9,8 2,10 11,18 NA 0/1 NA NA NA NA 11,1,18,2 G/A PANCANCER NA FALSE CCT4 chr2:61872914:61872915:G:A SNV 2:1 chr2:45546677:63443140:2:1:1 TRUE NA 0.96 +chr2 63942506 63942507 C G 24 26 0.923076923076923 MODERATE VPS54 ENSG00000143952 G missense_variant Transcript ENST00000272322 protein_coding 11/23 ENST00000272322.9:c.1357G>C ENSP00000272322.4:p.D453H ENSP00000272322.4 p.D453H 1868 1357 453 D/H Gat/Cat -1 SNV HGNC HGNC:18652 YES NM_016516.3 5 P1 CCDS33208.1 ENSP00000272322 Q9P1Q0.154 UPI0000053408 Q9P1Q0-1 tolerated(0.07) benign(0) PANTHER:PTHR12965&AlphaFold_DB_import:AF-Q9P1Q0-F1 12 NA NA PASS SITE 17,12|13,11 NA NA 1 70 20,20 138,144 60,60 30 1.23 NA 4.81 NA FALSE 6.00 71 NA NA NA FALSE NA NA 60.81 12 63942506 HCC1395_HCC1395T 2 0.875 26 1,3 0,10 1,13 NA 0/1 NA NA NA NA 1,1,13,11 C/G PANCANCER NA FALSE VPS54_p.D453H chr2:63942506:63942507:C:G SNV 2:0 chr2:63622357:84423583:2:0:1 TRUE NA 0.96 +chr2 69781792 69781793 G A 8 8 1 MODIFIER ANXA4 ENSG00000196975 A intron_variant Transcript ENST00000394295 protein_coding 2/12 ENST00000394295.6:c.9+218G>A NA 1 SNV HGNC HGNC:542 YES NM_001153.5 1 P1 CCDS1894.1 ENSP00000377833 P09525.219 UPI000013D51A P09525-3 12 NA NA PASS SITE 0,11|1,7 NA NA 1 49 39,38 243,229 60,60 24 1.08 NA 3.26 NA FALSE 6.00 54 NA NA NA FALSE NA NA 32.67 12 69781792 HCC1395_HCC1395T 0 0.889 8 0,1 0,5 0,7 NA 0/1 NA NA NA NA 0,0,1,7 G/A PANCANCER NA FALSE ANXA4 chr2:69781792:69781793:G:A SNV 2:0 chr2:63622357:84423583:2:0:1 TRUE NA 0.96 +chr2 71611504 71611505 C G 63 63 1 MODERATE DYSF ENSG00000135636 G missense_variant Transcript ENST00000258104 protein_coding 38/55 ENST00000258104.8:c.4045C>G ENSP00000258104.3:p.L1349V ENSP00000258104.3 p.L1349V 4483 4045 1349 L/V Ctg/Gtg COSV50644282 1 SNV HGNC HGNC:3097 NM_003494.4 1 A1 CCDS1918.1 ENSP00000258104 O75923.201 UPI0000129A56 O75923-1 1 deleterious_low_confidence(0) AlphaFold_DB_import:AF-O75923-F1&Pfam:PF00168&PROSITE_profiles:PS50004&PANTHER:PTHR12546&SMART:SM00239&Superfamily:SSF49562 1 1 12 NA NA PASS SITE 48,57|29,34 NA NA 1 93 20,20 163,193 60,60 31 1.88 NA 21.93 NA FALSE 6.00 93 NA NA NA FALSE NA NA 209.49 12 71611504 HCC1395_HCC1395T 0 0.980 63 0,20 0,25 0,47 NA 0/1 NA NA NA NA 0,0,29,34 C/G PANCANCER NA FALSE DYSF_p.L1349V chr2:71611504:71611505:C:G SNV 2:0 chr2:63622357:84423583:2:0:1 TRUE NA 0.96 +chr2 72887695 72887696 G A 43 98 0.438775510204082 MODERATE SPR ENSG00000116096 A missense_variant Transcript ENST00000234454 protein_coding 1/3 ENST00000234454.6:c.263G>A ENSP00000234454.5:p.R88Q ENSP00000234454.5 p.R88Q 288 263 88 R/Q cGg/cAg rs979284301 1 SNV HGNC HGNC:11257 YES NM_003124.5 1 P1 CCDS1920.1 ENSP00000234454 P35270.210 UPI000004C79D 1 tolerated(0.6) benign(0.015) PDB-ENSP_mappings:1z6z.A&PDB-ENSP_mappings:1z6z.B&PDB-ENSP_mappings:1z6z.C&PDB-ENSP_mappings:1z6z.D&PDB-ENSP_mappings:1z6z.E&PDB-ENSP_mappings:1z6z.F&Gene3D:3.40.50.720&PDB-ENSP_mappings:4hwk.A&PDB-ENSP_mappings:4hwk.B&PDB-ENSP_mappings:4hwk.C&PDB-ENSP_mappings:4hwk.D&PDB-ENSP_mappings:4j7u.A&PDB-ENSP_mappings:4j7u.B&PDB-ENSP_mappings:4j7u.C&PDB-ENSP_mappings:4j7u.D&PDB-ENSP_mappings:4j7x.A&PDB-ENSP_mappings:4j7x.B&PDB-ENSP_mappings:4j7x.F&PDB-ENSP_mappings:4j7x.J&PDB-ENSP_mappings:4xwy.A&PDB-ENSP_mappings:4xwy.B&PDB-ENSP_mappings:4xwy.C&PDB-ENSP_mappings:4xwy.D&PDB-ENSP_mappings:4z3k.A&PDB-ENSP_mappings:4z3k.B&PDB-ENSP_mappings:4z3k.C&PDB-ENSP_mappings:4z3k.D&PDB-ENSP_mappings:6i6c.A&PDB-ENSP_mappings:6i6c.B&PDB-ENSP_mappings:6i6f.A&PDB-ENSP_mappings:6i6f.B&PDB-ENSP_mappings:6i6p.A&PDB-ENSP_mappings:6i6p.B&PDB-ENSP_mappings:6i6t.A&PDB-ENSP_mappings:6i6t.B&PDB-ENSP_mappings:6i6v.A&PDB-ENSP_mappings:6i6v.B&PDB-ENSP_mappings:6i79.A&PDB-ENSP_mappings:6i79.B&PDB-ENSP_mappings:6usn.A&PDB-ENSP_mappings:6usn.B&PDB-ENSP_mappings:6usn.C&PDB-ENSP_mappings:6usn.D&PDB-ENSP_mappings:7dsf.A&PDB-ENSP_mappings:7dsf.B&AlphaFold_DB_import:AF-P35270-F1&Pfam:PF00106&PANTHER:PTHR44085&Superfamily:SSF51735&TIGRFAM:TIGR01500&CDD:cd05367 9.974e-06 0 0 0 0 0 0 0 5.005e-05 2.628e-05 2.411e-05 0 0 0 0 0 0 0 0 0.0006209 0.0006209 gnomADg_SAS uncertain_significance 1 12 NA NA PASS SITE 106,106|20,23 NA NA 1 93 20,20 155,146 60,60 40 2.01 NA 30.05 NA FALSE 6.00 82 NA NA NA FALSE NA NA 109.95 12 72887695 HCC1395_HCC1395T 55 0.461 98 9,17 23,9 34,29 NA 0/1 NA NA NA NA 27,28,20,23 G/A PANCANCER NA FALSE SPR_p.R88Q chr2:72887695:72887696:G:A SNV 2:0 chr2:63622357:84423583:2:0:1 TRUE NA 0.96 +chr2 73112794 73112795 GC G 25 67 0.373134328358209 MODIFIER RAB11FIP5 ENSG00000135631 - 5_prime_UTR_variant Transcript ENST00000258098 protein_coding 1/5 ENST00000258098.6:c.-18del NA 224 -1 deletion HGNC HGNC:24845 1 P1 CCDS1923.1 ENSP00000258098 Q9BXF6.173 UPI000007079C 12 NA NA PASS SITE 93,95|13,12 NA NA 1 93 20,39 152,181 60,60 31 1.97 NA 27.37 NA FALSE 6.00 93 NA NA NA FALSE NA NA 62.18 12 73112794 HCC1395_HCC1395T 42 0.447 67 15,9 8,8 25,20 NA 0/1 NA NA NA NA 20,22,13,12 GC/G PANCANCER NA FALSE RAB11FIP5 chr2:73112794:73112795:GC:G indel 2:0 chr2:63622357:84423583:2:0:1 TRUE NA 0.96 +chr2 73672842 73672843 G C 278 279 0.996415770609319 MODIFIER ALMS1P1 ENSG00000163016 C non_coding_transcript_exon_variant Transcript ENST00000428767 transcribed_unprocessed_pseudogene 3/6 ENST00000428767.1:n.343G>C NA 343 1 SNV HGNC HGNC:29586 YES 12 NA NA PASS SITE 210,108|182,96 NA NA 1 93 20,20 168,169 60,60 31 2.36 NA 67.07 NA FALSE 6.00 93 NA NA NA FALSE NA NA 864.91 12 73672842 HCC1395_HCC1395T 1 0.992 279 0,51 1,131 1,192 NA 0/1 NA NA NA NA 0,1,182,96 G/C PANCANCER NA FALSE ALMS1P1 chr2:73672842:73672843:G:C SNV 2:0 chr2:63622357:84423583:2:0:1 TRUE NA 0.96 +chr2 74557535 74557536 C T 46 470 0.0978723404255319 MODIFIER DOK1 ENSG00000115325 T 3_prime_UTR_variant Transcript ENST00000233668 protein_coding 5/5 ENST00000233668.10:c.*421C>T NA 1902 1 SNV HGNC HGNC:2990 YES NM_001381.5 1 P1 CCDS1954.1 ENSP00000233668 Q99704.195 UPI00001296A9 Q99704-1 12 NA NA PASS SITE 399,490|22,24 NA NA 1 93 20,20 163,167 60,60 32 2.48 NA 89.95 NA FALSE 6.00 83 NA NA NA FALSE NA NA 89.22 12 74557535 HCC1395_HCC1395T 424 0.100 470 111,11 141,17 278,30 NA 0/1 NA NA NA NA 188,236,22,24 C/T PANCANCER NA FALSE DOK1 chr2:74557535:74557536:C:T SNV 2:0 chr2:63622357:84423583:2:0:1 TRUE NA 0.96 +chr2 74969235 74969236 A T 33 66 0.5 MODIFIER POLE4 ENSG00000115350 T intron_variant&non_coding_transcript_variant Transcript ENST00000233699 protein_coding_CDS_not_defined 4/4 ENST00000233699.8:n.280-174A>T NA 1 SNV HGNC HGNC:18755 3 12 NA NA PASS SITE 72,18|27,6 NA NA 1 93 32,36 180,194 60,60 13 1.69 NA 14.14 NA FALSE 6.00 93 NA NA NA FALSE NA NA 100.38 12 74969235 HCC1395_HCC1395T 33 0.519 66 8,13 17,14 25,27 NA 0/1 NA NA NA NA 25,8,27,6 A/T PANCANCER NA FALSE POLE4 chr2:74969235:74969236:A:T SNV 2:0 chr2:63622357:84423583:2:0:1 TRUE NA 0.96 +chr2 75672097 75672098 C G 9 9 1 MODIFIER GCFC2 ENSG00000005436 G intron_variant Transcript ENST00000321027 protein_coding 13/16 ENST00000321027.8:c.1890-81G>C NA -1 SNV HGNC HGNC:1317 YES NM_003203.5 1 P1 CCDS1961.1 ENSP00000318690 P16383.195 UPI000013C96B P16383-1 12 NA NA PASS SITE 1,8|0,9 NA NA 1 45 39,39 208,218 60,60 29 1.000 NA 2.71 NA FALSE 6.00 93 NA NA NA FALSE NA NA 36.99 12 75672097 HCC1395_HCC1395T 0 0.909 9 0,6 0,3 0,9 NA 0/1 NA NA NA NA 0,0,0,9 C/G PANCANCER NA FALSE GCFC2 chr2:75672097:75672098:C:G SNV 2:0 chr2:63622357:84423583:2:0:1 TRUE NA 0.96 +chr2 82857185 82857186 T A 11 29 0.379310344827586 MODIFIER DHFRP3 ENSG00000168129 A non_coding_transcript_exon_variant Transcript ENST00000455595 processed_pseudogene 1/1 ENST00000455595.1:n.360T>A NA 360 1 SNV HGNC HGNC:52354 YES 12 NA NA PASS SITE 15,35|4,7 NA NA 1 76 28,37 196,226 60,60 26 1.41 NA 7.48 NA FALSE 6.00 61 NA NA NA FALSE NA NA 38.54 12 82857185 HCC1395_HCC1395T 18 0.461 29 8,7 5,3 13,11 NA 0/1 NA NA NA NA 8,10,4,7 T/A PANCANCER NA FALSE DHFRP3 chr2:82857185:82857186:T:A SNV 2:0 chr2:63622357:84423583:2:0:1 TRUE NA 0.96 +chr2 86025443 86025444 C G 43 65 0.661538461538462 MODIFIER POLR1A ENSG00000068654 G 3_prime_UTR_variant Transcript ENST00000263857 protein_coding 34/34 ENST00000263857.11:c.*1980G>C NA 7253 -1 SNV HGNC HGNC:17264 YES NM_015425.6 1 P2 CCDS42706.1 ENSP00000263857 O95602.198 UPI0000D7DB86 1 12 NA NA PASS SITE 35,41|23,20 NA NA 2 93 20,20 173,152 60,60 22 1.59 NA 11.14 NA FALSE 6.00 93 NA NA NA FALSE NA NA 121.95 12 86025443 HCC1395_HCC1395T 22 0.653 65 6,12 10,17 16,31 NA 0/1 NA NA NA NA 10,12,23,20 C/G PANCANCER NA FALSE POLR1A chr2:86025443:86025444:C:G SNV 2:1 chr2:84544443:102452374:2:1:1 TRUE NA 0.96 +chr2 86025467 86025468 C G 42 63 0.666666666666667 MODIFIER POLR1A ENSG00000068654 G 3_prime_UTR_variant Transcript ENST00000263857 protein_coding 34/34 ENST00000263857.11:c.*1956G>C NA 7229 -1 SNV HGNC HGNC:17264 YES NM_015425.6 1 P2 CCDS42706.1 ENSP00000263857 O95602.198 UPI0000D7DB86 1 12 NA NA PASS SITE 37,39|23,19 NA NA 2 93 20,20 167,155 60,60 36 1.61 NA 11.74 NA FALSE 6.00 93 NA NA NA FALSE NA NA 120.65 12 86025467 HCC1395_HCC1395T 21 0.653 63 6,12 7,14 15,29 NA 0/1 NA NA NA NA 11,10,23,19 C/G PANCANCER NA FALSE POLR1A chr2:86025467:86025468:C:G SNV 2:1 chr2:84544443:102452374:2:1:1 TRUE NA 0.96 +chr2 88735662 88735663 C A 88 199 0.442211055276382 LOW RPIA ENSG00000153574 A splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000283646 protein_coding 5/8 ENST00000283646.5:c.528-7C>A NA COSV99376018 1 SNV HGNC HGNC:10297 YES NM_144563.3 1 P1 CCDS2004.2 ENSP00000283646 P49247.194 UPI0000037A98 1 1 1 12 NA NA PASS SITE 135,140|43,45 NA NA 1 93 20,20 156,164 60,60 33 2.01 NA 30.70 NA FALSE 6.00 87 NA NA NA FALSE NA NA 207.91 12 88735662 HCC1395_HCC1395T 111 0.448 199 23,17 39,35 69,56 NA 0/1 NA NA NA NA 55,56,43,45 C/A PANCANCER NA FALSE RPIA chr2:88735662:88735663:C:A SNV 2:1 chr2:84544443:102452374:2:1:1 TRUE NA 0.96 +chr2 94874876 94874877 T A 259 619 0.418416801292407 MODERATE TEKT4 ENSG00000163060 A missense_variant Transcript ENST00000295201 protein_coding 4/6 ENST00000295201.5:c.814T>A ENSP00000295201.4:p.C272S ENSP00000295201.4 p.C272S 964 814 272 C/S Tgc/Agc COSV54629254 1 SNV HGNC HGNC:31012 YES NM_144705.4 1 P1 CCDS2005.1 ENSP00000295201 Q8WW24.147 A0A384MEB7.23 UPI00000730A8 tolerated(0.47) benign(0.005) PDB-ENSP_mappings:7ung.D0&PDB-ENSP_mappings:7ung.D1&PDB-ENSP_mappings:7ung.D2&PDB-ENSP_mappings:7ung.D3&PDB-ENSP_mappings:7ung.D5&PDB-ENSP_mappings:7ung.D6&PDB-ENSP_mappings:7ung.D7&PDB-ENSP_mappings:7ung.D8&AlphaFold_DB_import:AF-Q8WW24-F1&Pfam:PF03148&PANTHER:PTHR19960 1 1 12 NA NA PASS SITE 440,496|132,127 NA NA 1 93 20,20 150,157 60,60 35 2.55 NA 104.75 NA FALSE 6.00 93 NA NA NA FALSE NA NA 634.39 12 94874876 HCC1395_HCC1395T 360 0.414 619 109,63 104,90 230,162 NA 0/1 NA NA NA NA 176,184,132,127 T/A PANCANCER NA FALSE TEKT4_p.C272S chr2:94874876:94874877:T:A SNV 2:1 chr2:84544443:102452374:2:1:1 TRUE NA 0.96 +chr2 96145043 96145044 G C 42 306 0.137254901960784 MODERATE DUSP2 ENSG00000158050 C missense_variant Transcript ENST00000288943 protein_coding 1/4 ENST00000288943.5:c.312C>G ENSP00000288943.4:p.D104E ENSP00000288943.4 p.D104E 398 312 104 D/E gaC/gaG -1 SNV HGNC HGNC:3068 YES NM_004418.4 1 P1 CCDS2016.1 ENSP00000288943 Q05923.203 UPI000012995D tolerated(0.33) Gene3D:3.40.250.10&AlphaFold_DB_import:AF-Q05923-F1&Pfam:PF00581&PIRSF:PIRSF000939&PROSITE_profiles:PS50206&PANTHER:PTHR10159&SMART:SM00450&Superfamily:SSF52821&CDD:cd01446 12 NA NA PASS SITE 195,286|17,25 NA NA 1 93 20,33 162,159 60,60 34 2.17 NA 43.60 NA FALSE 6.00 87 NA NA NA FALSE NA NA 101.87 12 96145043 HCC1395_HCC1395T 264 0.150 306 58,8 79,13 175,30 NA 0/1 NA NA NA NA 106,158,17,25 G/C PANCANCER NA FALSE DUSP2_p.D104E chr2:96145043:96145044:G:C SNV 2:1 chr2:84544443:102452374:2:1:1 TRUE NA 0.96 +chr2 96689377 96689378 G T 36 48 0.75 HIGH FER1L5 ENSG00000249715 T splice_donor_variant&non_coding_transcript_variant Transcript ENST00000457909 retained_intron 8/34 ENST00000457909.2:n.984+1G>T NA rs555193102 1 SNV HGNC HGNC:19044 2 0.0002 0 0 0 0 0.001 6.575e-06 0 0 0 0 0 0 0 0 0 0.0002076 0.001 SAS 12 NA NA PASS SITE 27,46|14,22 NA NA 1 93 20,20 168,170 60,60 26 1.63 NA 12.34 NA FALSE 6.00 93 NA NA NA FALSE NA NA 95.81 12 96689377 HCC1395_HCC1395T 12 0.706 48 3,9 5,13 9,23 NA 0/1 NA NA NA NA 4,8,14,22 G/T PANCANCER NA FALSE FER1L5 chr2:96689377:96689378:G:T SNV 2:1 chr2:84544443:102452374:2:1:1 TRUE NA 0.96 +chr2 96738168 96738169 C A 86 187 0.459893048128342 MODIFIER LMAN2L ENSG00000114988 A intron_variant Transcript ENST00000264963 protein_coding 1/7 ENST00000264963.9:c.188-101G>T NA -1 SNV HGNC HGNC:19263 YES NM_030805.4 1 P1 CCDS2023.1 ENSP00000264963 Q9H0V9.186 UPI000003777C Q9H0V9-1 1 12 NA NA PASS SITE 102,130|35,51 NA NA 1 93 20,20 156,169 60,60 36 1.93 NA 24.94 NA FALSE 6.00 93 NA NA NA FALSE NA NA 209.71 12 96738168 HCC1395_HCC1395T 101 0.457 187 26,23 37,32 70,59 NA 0/1 NA NA NA NA 44,57,35,51 C/A PANCANCER NA FALSE LMAN2L chr2:96738168:96738169:C:A SNV 2:1 chr2:84544443:102452374:2:1:1 TRUE NA 0.96 +chr2 97211773 97211774 C T 35 255 0.137254901960784 MODIFIER ANKRD36 ENSG00000135976 T intron_variant Transcript ENST00000420699 protein_coding 58/75 ENST00000420699.9:c.3469+32C>T NA rs1259609142 1 SNV HGNC HGNC:24079 YES NM_001354587.1 5 P1 CCDS92815.1 ENSP00000391950 A6QL64.109 UPI000387C901 A6QL64-1 5.906e-06 0 0 0 0 0 1.441e-05 0 0 6.589e-06 0 0 0 0 0 0 0 1.472e-05 0 0 1.472e-05 gnomADg_NFE 12 NA NA PASS SITE 132,265|10,25 NA NA 1 93 20,20 162,163 60,60 33 2.10 NA 36.97 NA FALSE 6.00 44 NA NA NA FALSE NA NA 82.25 12 97211773 HCC1395_HCC1395T 220 0.142 255 56,4 36,9 156,25 NA 0/1 NA NA NA NA 69,151,10,25 C/T PANCANCER NA FALSE ANKRD36 chr2:97211773:97211774:C:T SNV 2:1 chr2:84544443:102452374:2:1:1 TRUE NA 0.96 +chr2 101308570 101308571 C T 324 529 0.612476370510397 MODERATE RNF149 ENSG00000163162 T missense_variant Transcript ENST00000295317 protein_coding 1/7 ENST00000295317.4:c.19G>A ENSP00000295317.3:p.E7K ENSP00000295317.3 p.E7K 132 19 7 E/K Gaa/Aaa rs763258401&COSV54865879 -1 SNV HGNC HGNC:23137 YES NM_173647.4 1 P1 CCDS2051.1 ENSP00000295317 Q8NC42.156 UPI0000366F4A tolerated_low_confidence(0.64) benign(0) AlphaFold_DB_import:AF-Q8NC42-F1&Cleavage_site_(Signalp):SignalP-noTM 5.954e-06 0 0 0 0 0 0 0.0002309 0 0.0002309 gnomADe_OTH 0&1 0&1 12 NA NA PASS SITE 273,376|127,197 NA NA 1 93 20,25 165,173 60,60 26 2.51 NA 94.50 NA FALSE 6.00 93 NA NA NA FALSE NA NA 954.76 12 101308570 HCC1395_HCC1395T 205 0.626 529 65,91 62,118 145,243 NA 0/1 NA NA NA NA 88,117,127,197 C/T PANCANCER NA FALSE RNF149_p.E7K chr2:101308570:101308571:C:T SNV 2:1 chr2:84544443:102452374:2:1:1 TRUE NA 0.96 +chr2 110116048 110116049 G C 80 80 1 MODIFIER MALL ENSG00000144063 C upstream_gene_variant Transcript ENST00000272462 protein_coding NA 226 -1 SNV HGNC HGNC:6818 YES NM_005434.5 1 P1 CCDS2085.1 ENSP00000272462 Q13021.153 UPI0000126897 12 NA NA PASS SITE 78,60|43,37 NA NA 1 93 20,20 156,158 60,60 35 1.96 NA 27.09 NA FALSE 6.00 93 NA NA NA FALSE NA NA 241.50 12 110116048 HCC1395_HCC1395T 0 0.981 80 0,25 0,24 0,52 NA 0/1 NA NA NA NA 0,0,43,37 G/C PANCANCER NA FALSE MALL chr2:110116048:110116049:G:C SNV 1:0 chr2:102473582:113961874:1:0:1 NA NA 0.96 +chr2 110933497 110933498 G A 96 96 1 MODERATE ACOXL ENSG00000153093 A missense_variant Transcript ENST00000389811 protein_coding 12/19 ENST00000389811.8:c.914G>A ENSP00000374461.4:p.G305E ENSP00000374461.4 p.G305E 1138 914 305 G/E gGg/gAg COSV67738808 1 SNV HGNC HGNC:25621 5 CCDS42730.1 ENSP00000374461 Q9NUZ1.163 UPI0000E5A27A Q9NUZ1-1 tolerated(0.08) benign(0.027) Gene3D:1.20.140.10&AlphaFold_DB_import:AF-Q9NUZ1-F1&Pfam:PF00441&PANTHER:PTHR10909&Superfamily:SSF47203 1 1 12 NA NA PASS SITE 112,117|41,55 NA NA 1 93 20,20 149,149 60,60 34 2.15 NA 42.05 NA FALSE 6.00 93 NA NA NA FALSE NA NA 273.99 12 110933497 HCC1395_HCC1395T 0 0.983 96 0,18 0,38 0,58 NA 0/1 NA NA NA NA 0,0,41,55 G/A PANCANCER NA FALSE ACOXL_p.G305E chr2:110933497:110933498:G:A SNV 1:0 chr2:102473582:113961874:1:0:1 NA NA 0.96 +chr2 112584781 112584782 C T 19 19 1 MODIFIER POLR1B ENSG00000125630 T downstream_gene_variant Transcript ENST00000263331 protein_coding NA rs1289561150 4963 1 SNV HGNC HGNC:20454 YES NM_019014.6 2 P1 CCDS2097.1 ENSP00000263331 Q9H9Y6.194 UPI00001B6B03 Q9H9Y6-1 1 6.572e-06 0 0 0 0 0 0 0 1.47e-05 0 0 1.47e-05 gnomADg_NFE 12 NA NA PASS SITE 30,55|9,10 NA NA 1 93 20,20 148,150 60,60 30 1.76 NA 16.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 52.46 12 112584781 HCC1395_HCC1395T 0 0.925 19 0,6 0,4 0,11 NA 0/1 NA NA NA NA 0,0,9,10 C/T PANCANCER NA FALSE POLR1B chr2:112584781:112584782:C:T SNV 1:0 chr2:102473582:113961874:1:0:1 NA NA 0.96 +chr2 126902118 126902119 C T 14 104 0.134615384615385 MODIFIER TEX51 ENSG00000237524 T downstream_gene_variant Transcript ENST00000436605 protein_coding NA 21 1 cds_start_NF SNV HGNC HGNC:52387 2 ENSP00000490892 A0A1B0GWE4.19 UPI0002466C76 12 NA NA PASS SITE 61,112|5,9 NA NA 1 93 20,32 166,160 60,60 40 1.74 NA 15.95 NA FALSE 6.00 53 NA NA NA FALSE NA NA 35.94 12 126902118 HCC1395_HCC1395T 90 0.152 104 29,4 31,6 66,11 NA 0/1 NA NA NA NA 29,61,5,9 C/T PANCANCER NA FALSE TEX51 chr2:126902118:126902119:C:T SNV 2:0 chr2:115526092:159956738:2:0:1 TRUE NA 0.96 +chr2 135715801 135715802 T C 31 31 1 MODIFIER R3HDM1 ENSG00000048991 C intron_variant Transcript ENST00000264160 protein_coding 23/25 ENST00000264160.8:c.2776+107T>C NA 1 SNV HGNC HGNC:9757 1 P4 CCDS2177.1 ENSP00000264160 Q15032.168 UPI000007456C Q15032-1 12 NA NA PASS SITE 5,19|3,28 NA NA 1 93 27,32 173,203 60,60 25 1.30 NA 5.67 NA FALSE 6.00 93 NA NA NA FALSE NA NA 106.70 12 135715801 HCC1395_HCC1395T 0 0.968 31 0,13 0,9 0,28 NA 0/1 NA NA NA NA 0,0,3,28 T/C PANCANCER NA FALSE R3HDM1 chr2:135715801:135715802:T:C SNV 2:0 chr2:115526092:159956738:2:0:1 TRUE NA 0.96 +chr2 137479708 137479709 T G 62 62 1 MODIFIER THSD7B ENSG00000144229 G intron_variant Transcript ENST00000409968 protein_coding 15/27 ENST00000409968.6:c.3138+28685T>G NA 1 SNV HGNC HGNC:29348 YES NM_001316349.2 5 P1 CCDS82515.1 ENSP00000387145 Q9C0I4.120 UPI00018816B7 12 NA NA PASS SITE 15,48|17,45 NA NA 1 93 35,30 189,187 60,60 19 1.71 NA 15.26 NA FALSE 6.00 93 NA NA NA FALSE NA NA 208.27 12 137479708 HCC1395_HCC1395T 0 0.980 62 0,17 0,25 0,48 NA 0/1 NA NA NA NA 0,0,17,45 T/G PANCANCER NA FALSE THSD7B chr2:137479708:137479709:T:G SNV 2:0 chr2:115526092:159956738:2:0:1 TRUE NA 0.96 +chr2 157736941 157736942 C T 26 232 0.112068965517241 MODIFIER ACVR1 ENSG00000115170 T 3_prime_UTR_variant Transcript ENST00000263640 protein_coding 11/11 ENST00000263640.7:c.*590G>A NA 2550 -1 SNV HGNC HGNC:171 1 P4 CCDS2206.1 ENSP00000263640 Q04771.216 D3DPA4.112 UPI000000163F 1 12 NA NA PASS SITE 199,212|12,14 NA NA 1 93 20,20 160,147 60,60 36 2.10 NA 37.63 NA FALSE 6.00 41 NA NA NA FALSE NA NA 45.92 12 157736941 HCC1395_HCC1395T 206 0.106 232 45,4 69,10 125,14 NA 0/1 NA NA NA NA 102,104,12,14 C/T PANCANCER TRUE FALSE ACVR1 chr2:157736941:157736942:C:T SNV 2:0 chr2:115526092:159956738:2:0:1 TRUE NA 0.96 +chr2 159555875 159555876 G T 353 353 1 LOW BAZ2B ENSG00000123636 T splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000392782 protein_coding 1/35 ENST00000392782.5:c.-45-10C>A NA -1 SNV HGNC HGNC:963 1 CCDS74594.1 ENSP00000376533 Q9UIF8.205 UPI0000E5A28F Q9UIF8-5 12 NA NA PASS SITE 116,132|171,182 NA NA 1 93 20,20 158,162 60,60 33 2.19 NA 46.05 NA FALSE 6.00 93 NA NA NA FALSE NA NA 955.40 12 159555875 HCC1395_HCC1395T 0 0.995 353 0,90 0,108 0,211 NA 0/1 NA NA NA NA 0,0,171,182 G/T PANCANCER NA FALSE BAZ2B chr2:159555875:159555876:G:T SNV 2:0 chr2:115526092:159956738:2:0:1 TRUE NA 0.96 +chr2 160107762 160107763 T A 82 357 0.2296918767507 MODERATE ITGB6 ENSG00000115221 A missense_variant Transcript ENST00000283249 protein_coding 14/15 ENST00000283249.7:c.2185A>T ENSP00000283249.2:p.I729F ENSP00000283249.2 p.I729F 2394 2185 729 I/F Atc/Ttc -1 SNV HGNC HGNC:6161 YES NM_000888.5 1 P1 CCDS2212.1 ENSP00000283249 P18564.217 UPI000012DA13 P18564-1 1 deleterious(0.01) possibly_damaging(0.803) Gene3D:1.20.5.100&PDB-ENSP_mappings:4um8.B&PDB-ENSP_mappings:4um8.D&AlphaFold_DB_import:AF-P18564-F1&PIRSF:PIRSF002512&Prints:PR01186&PANTHER:PTHR10082&Transmembrane_helices:TMhelix 12 NA NA PASS SITE 189,268|35,47 NA NA 1 93 20,20 157,157 60,60 33 2.09 NA 36.67 NA FALSE 6.00 93 NA NA NA FALSE NA NA 189.52 12 160107762 HCC1395_HCC1395T 275 0.223 357 83,22 82,25 191,54 NA 0/1 NA NA NA NA 112,163,35,47 T/A PANCANCER NA FALSE ITGB6_p.I729F chr2:160107762:160107763:T:A SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 166197758 166197759 G C 124 523 0.237093690248566 MODIFIER SCN9A ENSG00000169432 C 3_prime_UTR_variant Transcript ENST00000303354 protein_coding 27/27 ENST00000303354.11:c.*914C>G NA 7129 -1 SNV HGNC HGNC:10597 5 P1 CCDS92892.1 ENSP00000304748 Q15858.202 UPI0001881757 Q15858-1 1 12 NA NA PASS SITE 238,459|44,80 NA NA 1 93 20,20 168,171 60,60 41 2.32 NA 62.26 NA FALSE 6.00 93 NA NA NA FALSE NA NA 306.59 12 166197758 HCC1395_HCC1395T 399 0.234 523 91,27 166,48 284,86 NA 0/1 NA NA NA NA 131,268,44,80 G/C PANCANCER NA FALSE SCN9A chr2:166197758:166197759:G:C SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 169181679 169181680 C A 12 29 0.413793103448276 MODIFIER LRP2 ENSG00000081479 A intron_variant&non_coding_transcript_variant Transcript ENST00000461418 protein_coding_CDS_not_defined 2/3 ENST00000461418.1:n.200-61G>T NA -1 SNV HGNC HGNC:6694 4 1 12 NA NA PASS SITE 1,26|2,10 NA NA 1 32 41,37 233,201 60,60 14 1.06 NA 3.01 NA FALSE 6.00 68 NA NA NA FALSE NA NA 35.01 12 169181679 HCC1395_HCC1395T 17 0.392 29 8,5 6,4 16,10 NA 0/1 NA NA NA NA 1,16,2,10 C/A PANCANCER NA FALSE LRP2 chr2:169181679:169181680:C:A SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 169188223 169188224 C A 24 171 0.140350877192982 MODERATE LRP2 ENSG00000081479 A missense_variant Transcript ENST00000649046 protein_coding 49/79 ENST00000649046.1:c.9075G>T ENSP00000496870.1:p.R3025S ENSP00000496870.1 p.R3025S 9210 9075 3025 R/S agG/agT rs778200506 -1 SNV HGNC HGNC:6694 YES NM_004525.3 P1 CCDS2232.1 ENSP00000496870 P98164.215 UPI0000141BA5 1 benign(0.398) CDD:cd00112&Pfam:PF00057&Gene3D:4.10.400.10&SMART:SM00192&Superfamily:SSF57424&PROSITE_profiles:PS50068 3.98e-06 0 0 0 5.439e-05 0 0 0 0 5.439e-05 gnomADe_EAS 12 NA NA PASS SITE 74,156|8,17 NA NA 1 93 20,20 173,199 60,60 23 1.76 NA 17.02 NA FALSE 6.00 29 NA NA NA FALSE NA NA 48.36 12 169188223 HCC1395_HCC1395T 147 0.135 171 46,4 52,11 108,16 NA 0/1 NA NA NA NA 46,101,8,16 C/A PANCANCER NA FALSE LRP2_p.R3025S chr2:169188223:169188224:C:A SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 169270904 169270905 C A 13 37 0.351351351351351 MODIFIER LRP2 ENSG00000081479 A intron_variant Transcript ENST00000443831 protein_coding 14/22 ENST00000443831.1:c.1909+2023G>T NA -1 SNV HGNC HGNC:6694 2 ENSP00000409813 E9PC35.79 UPI000198C5D9 1 12 NA NA PASS SITE 39,9|9,4 NA NA 1 58 37,20 161,162 60,60 21 1.31 NA 5.72 NA FALSE 6.00 64 NA NA NA FALSE NA NA 30.77 12 169270904 HCC1395_HCC1395T 24 0.322 37 8,5 12,4 20,9 NA 0/1 NA NA NA NA 20,4,9,4 C/A PANCANCER NA FALSE LRP2 chr2:169270904:169270905:C:A SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 169641207 169641208 ATTATATTTTTTTAATGAAGTTTAGAAAAAAAGCTG A 152 210 0.723809523809524 MODIFIER PPIG ENSG00000138398 - 3_prime_UTR_variant Transcript ENST00000260970 protein_coding 14/14 ENST00000260970.8:c.*3687_*3721del NA 6159-6193 1 deletion HGNC HGNC:14650 YES NM_004792.3 1 P1 CCDS2235.1 ENSP00000260970 Q13427.193 UPI000013D124 Q13427-1 2 12 NA NA PASS SITE 51,121|26,126 NA NA 1 93 20,36 189,198 60,60 29 1.94 NA 23.15 NA FALSE 6.00 93 NA NA NA FALSE NA NA 640.06 12 169641207 HCC1395_HCC1395T 58 0.719 210 7,17 10,36 44,112 NA 0/1 NA NA NA NA 16,42,26,126 ATTATATTTTTTTAATGAAGTTTAGAAAAAAAGCTG/A PANCANCER NA FALSE PPIG chr2:169641207:169641208:ATTATATTTTTTTAATGAAGTTTAGAAAAAAAGCTG:A indel 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 169645788 169645789 G T 7 10 0.7 MODIFIER PPIG ENSG00000138398 T downstream_gene_variant Transcript ENST00000260970 protein_coding NA 4382 1 SNV HGNC HGNC:14650 YES NM_004792.3 1 P1 CCDS2235.1 ENSP00000260970 Q13427.193 UPI000013D124 Q13427-1 12 NA NA PASS SITE 11,2|6,1 NA NA 2 31 40,37 213,210 60,60 8 1.04 NA 3.01 NA FALSE 6.00 54 NA NA NA FALSE NA NA 27.01 12 169645788 HCC1395_HCC1395T 3 0.700 10 1,2 1,4 2,6 NA 0|1 0|1 169645788_G_T NA 169645788 2,1,6,1 G|T PANCANCER NA FALSE PPIG chr2:169645788:169645789:G:T SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 169645793 169645794 T A 7 10 0.7 MODIFIER PPIG ENSG00000138398 A downstream_gene_variant Transcript ENST00000260970 protein_coding NA 4387 1 SNV HGNC HGNC:14650 YES NM_004792.3 1 P1 CCDS2235.1 ENSP00000260970 Q13427.193 UPI000013D124 Q13427-1 12 NA NA PASS SITE 12,3|7,0 NA NA 2 34 35,37 213,210 60,60 11 0.813 NA 3.31 NA FALSE 6.00 63 NA NA NA FALSE NA NA 22.74 12 169645793 HCC1395_HCC1395T 3 0.750 10 1,4 1,3 2,8 NA 0|1 0|1 169645788_G_T NA 169645788 2,1,7,0 T|A PANCANCER NA FALSE PPIG chr2:169645793:169645794:T:A SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 169735201 169735202 A G 36 274 0.131386861313869 MODERATE KLHL23 ENSG00000213160 G missense_variant Transcript ENST00000272797 protein_coding 4/6 ENST00000272797.8:c.187A>G ENSP00000272797.4:p.K63E ENSP00000272797.4 p.K63E 525 187 63 K/E Aag/Gag 1 SNV HGNC HGNC:27506 2 P1 ENSP00000272797 Q8NBE8.152 UPI000006D999 deleterious(0.01) benign(0.413) Gene3D:3.30.710.10&AlphaFold_DB_import:AF-Q8NBE8-F1&Pfam:PF00651&PIRSF:PIRSF037037&PROSITE_profiles:PS50097&PANTHER:PTHR24412&SMART:SM00225&Superfamily:SSF54695&CDD:cd18252 12 NA NA PASS SITE 148,247|13,23 NA NA 1 93 20,20 163,171 60,60 31 2.07 NA 34.57 NA FALSE 6.00 54 NA NA NA FALSE NA NA 85.59 12 169735201 HCC1395_HCC1395T 238 0.139 274 54,7 91,19 166,26 NA 0/1 NA NA NA NA 84,154,13,23 A/G PANCANCER NA FALSE KLHL23_p.K63E chr2:169735201:169735202:A:G SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 172065717 172065718 T A 230 352 0.653409090909091 LOW METAP1D ENSG00000172878 A synonymous_variant Transcript ENST00000315796 protein_coding 4/10 ENST00000315796.5:c.462T>A ENSP00000315152.4:p.S154= ENSP00000315152.4 p.S154= 479 462 154 S tcT/tcA 1 SNV HGNC HGNC:32583 YES NM_199227.3 1 P1 CCDS2246.1 ENSP00000315152 Q6UB28.142 UPI00001AF10C HAMAP:MF_01974&CDD:cd01086&PANTHER:PTHR43330&Pfam:PF00557&TIGRFAM:TIGR00500&Gene3D:3.90.230.10&Superfamily:SSF55920&Prints:PR00599&AlphaFold_DB_import:AF-Q6UB28-F1 12 NA NA PASS SITE 115,162|96,134 NA NA 1 93 20,20 157,160 60,60 29 2.01 NA 30.06 NA FALSE 6.00 93 NA NA NA FALSE NA NA 623.76 12 172065717 HCC1395_HCC1395T 122 0.647 352 28,53 48,88 81,149 NA 0/1 NA NA NA NA 52,70,96,134 T/A PANCANCER NA FALSE METAP1D_p.S154= chr2:172065717:172065718:T:A SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 172087561 172087562 A G 90 279 0.32258064516129 MODIFIER DLX1 ENSG00000144355 G intron_variant Transcript ENST00000341900 protein_coding 1/1 ENST00000341900.6:c.314-442A>G NA rs772516917 1 SNV HGNC HGNC:2914 1 CCDS33328.1 ENSP00000341786 P56177.183 UPI00001A3E8C P56177-2 7.804e-06 0 0 0 9.58e-05 0 0 0 0 6.568e-06 0 0 0 0 0.0001922 0 0 0 0 0 0.0001922 gnomADg_EAS 12 NA NA PASS SITE 217,153|55,35 NA NA 1 93 20,20 166,158 60,60 25 2.09 NA 35.82 NA FALSE 6.00 93 NA NA NA FALSE NA NA 205.78 12 172087561 HCC1395_HCC1395T 189 0.313 279 63,28 64,29 130,59 NA 0/1 NA NA NA NA 114,75,55,35 A/G PANCANCER NA FALSE DLX1 chr2:172087561:172087562:A:G SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 172917794 172917795 T C 32 219 0.146118721461187 LOW RAPGEF4 ENSG00000091428 C splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000397081 protein_coding 4/30 ENST00000397081.8:c.445-8T>C NA 1 SNV HGNC HGNC:16626 YES NM_007023.4 1 P1 CCDS42775.1 ENSP00000380271 Q8WZA2.175 UPI000006D4C7 Q8WZA2-1 12 NA NA PASS SITE 182,135|21,11 NA NA 1 93 20,20 160,151 60,60 35 1.91 NA 23.78 NA FALSE 6.00 35 NA NA NA FALSE NA NA 71.83 12 172917794 HCC1395_HCC1395T 187 0.144 219 39,5 86,16 130,21 NA 0/1 NA NA NA NA 112,75,21,11 T/C PANCANCER NA FALSE RAPGEF4 chr2:172917794:172917795:T:C SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 172988912 172988913 A G 34 51 0.666666666666667 MODIFIER RAPGEF4 ENSG00000091428 G intron_variant Transcript ENST00000397081 protein_coding 14/30 ENST00000397081.8:c.1374+73A>G NA 1 SNV HGNC HGNC:16626 YES NM_007023.4 1 P1 CCDS42775.1 ENSP00000380271 Q8WZA2.175 UPI000006D4C7 Q8WZA2-1 12 NA NA PASS SITE 15,45|7,27 NA NA 1 93 20,38 176,169 60,60 24 1.54 NA 9.93 NA FALSE 6.00 82 NA NA NA FALSE NA NA 109.33 12 172988912 HCC1395_HCC1395T 17 0.683 51 4,14 6,7 12,27 NA 0/1 NA NA NA NA 5,12,7,27 A/G PANCANCER NA FALSE RAPGEF4 chr2:172988912:172988913:A:G SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 175093192 175093193 C G 71 263 0.269961977186312 MODERATE ATF2 ENSG00000115966 G missense_variant Transcript ENST00000264110 protein_coding 12/14 ENST00000264110.7:c.1054G>C ENSP00000264110.2:p.D352H ENSP00000264110.2 p.D352H 1350 1054 352 D/H Gat/Cat COSV51376871 -1 SNV HGNC HGNC:784 YES NM_001880.4 1 CCDS2262.1 ENSP00000264110 P15336.228 UPI000013D4BE P15336-1 deleterious(0) probably_damaging(0.962) AlphaFold_DB_import:AF-P15336-F1&PIRSF:PIRSF003153&PROSITE_profiles:PS50217&PANTHER:PTHR19304&SMART:SM00338&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite 1 1 12 NA NA PASS SITE 139,184|31,40 NA NA 1 93 20,20 161,157 60,60 35 1.93 NA 25.28 NA FALSE 6.00 93 NA NA NA FALSE NA NA 174.74 12 175093192 HCC1395_HCC1395T 192 0.274 263 54,16 62,28 129,48 NA 0/1 NA NA NA NA 83,109,31,40 C/G PANCANCER NA FALSE ATF2_p.D352H chr2:175093192:175093193:C:G SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 178116159 178116160 G A 6 10 0.6 MODIFIER RBM45 ENSG00000155636 A intron_variant Transcript ENST00000286070 protein_coding 1/9 ENST00000286070.10:c.301-103G>A NA 1 SNV HGNC HGNC:24468 YES NM_152945.4 1 P1 CCDS33335.1 ENSP00000286070 Q8IUH3.166 UPI00001AEAD8 Q8IUH3-3 12 NA NA PASS SITE 18,2|6,0 NA NA 1 43 38,39 191,224 60,60 35 1.18 NA 4.21 NA FALSE 6.00 43 NA NA NA FALSE NA NA 22.98 12 178116159 HCC1395_HCC1395T 4 0.584 10 3,2 1,4 4,6 NA 0/1 NA NA NA NA 4,0,6,0 G/A PANCANCER NA FALSE RBM45 chr2:178116159:178116160:G:A SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 182981198 182981199 G A 22 127 0.173228346456693 MODIFIER NCKAP1 ENSG00000061676 A intron_variant Transcript ENST00000360982 protein_coding 14/31 ENST00000360982.2:c.1359+46C>T NA -1 SNV HGNC HGNC:7666 1 CCDS2288.1 ENSP00000354251 Q9Y2A7.188 UPI00001693F2 Q9Y2A7-2 1 12 NA NA PASS SITE 107,57|15,7 NA NA 1 93 20,20 160,167 60,60 23 1.64 NA 12.64 NA FALSE 6.00 64 NA NA NA FALSE NA NA 50.77 12 182981198 HCC1395_HCC1395T 105 0.195 127 25,6 43,9 69,16 NA 0/1 NA NA NA NA 66,39,15,7 G/A PANCANCER NA FALSE NCKAP1 chr2:182981198:182981199:G:A SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 183003036 183003037 A G 7 21 0.333333333333333 LOW NCKAP1 ENSG00000061676 G splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000360982 protein_coding 4/31 ENST00000360982.2:c.331-6T>C NA -1 SNV HGNC HGNC:7666 1 CCDS2288.1 ENSP00000354251 Q9Y2A7.188 UPI00001693F2 Q9Y2A7-2 1 12 NA NA PASS SITE 2,21|2,5 NA NA 1 28 36,20 183,136 60,60 11 1.02 NA 2.71 NA FALSE 6.00 38 NA NA NA FALSE NA NA 14.34 12 183003036 HCC1395_HCC1395T 14 0.298 21 4,2 7,3 13,5 NA 0/1 NA NA NA NA 1,13,2,5 A/G PANCANCER NA FALSE NCKAP1 chr2:183003036:183003037:A:G SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 183095803 183095804 C T 29 152 0.190789473684211 MODIFIER DUSP19 ENSG00000162999 T 3_prime_UTR_variant Transcript ENST00000342619 protein_coding 3/3 ENST00000342619.10:c.*145C>T NA 1021 1 SNV HGNC HGNC:18894 1 CCDS46469.1 ENSP00000343905 Q8WTR2.166 UPI000002A867 Q8WTR2-2 12 NA NA PASS SITE 56,177|3,26 NA NA 1 93 30,38 174,202 60,60 15 1.90 NA 23.13 NA FALSE 6.00 86 NA NA NA FALSE NA NA 84.45 12 183095803 HCC1395_HCC1395T 123 0.209 152 27,9 49,12 101,26 NA 0/1 NA NA NA NA 22,101,3,26 C/T PANCANCER NA FALSE DUSP19 chr2:183095803:183095804:C:T SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 189561579 189561580 C T 18 117 0.153846153846154 MODIFIER SLC40A1 ENSG00000138449 T 3_prime_UTR_variant Transcript ENST00000261024 protein_coding 8/8 ENST00000261024.7:c.*299G>A NA 2341 -1 SNV HGNC HGNC:10909 YES NM_014585.6 1 P1 CCDS2299.1 ENSP00000261024 Q9NP59.183 UPI0000034CC2 1 12 NA NA PASS SITE 114,81|15,3 NA NA 1 93 20,38 181,234 60,60 30 1.81 NA 18.91 NA FALSE 6.00 63 NA NA NA FALSE NA NA 48.89 12 189561579 HCC1395_HCC1395T 99 0.196 117 23,6 37,9 65,15 NA 0/1 NA NA NA NA 56,43,15,3 C/T PANCANCER NA FALSE SLC40A1 chr2:189561579:189561580:C:T SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 190982494 190982495 G C 100 158 0.632911392405063 MODERATE STAT1 ENSG00000115415 C missense_variant Transcript ENST00000361099 protein_coding 18/25 ENST00000361099.8:c.1471C>G ENSP00000354394.4:p.P491A ENSP00000354394.4 p.P491A 1780 1471 491 P/A Cca/Gca COSV63117719 -1 SNV HGNC HGNC:11362 YES NM_007315.4 1 P4 CCDS2309.1 ENSP00000354394 P42224.251 UPI00000473FB P42224-1 1 deleterious_low_confidence(0.02) probably_damaging(0.955) PDB-ENSP_mappings:1bf5.A&PDB-ENSP_mappings:1yvl.A&PDB-ENSP_mappings:1yvl.B&PDB-ENSP_mappings:7nuf.A&PDB-ENSP_mappings:8d3f.A&PANTHER:PTHR11801&Gene3D:1.10.238.10&Superfamily:SSF49417&AlphaFold_DB_import:AF-P42224-F1 1 1 12 NA NA PASS SITE 71,86|51,49 NA NA 1 93 20,20 171,165 60,60 28 1.85 NA 21.02 NA FALSE 6.00 93 NA NA NA FALSE NA NA 288.38 12 190982494 HCC1395_HCC1395T 58 0.646 158 10,24 20,39 37,68 NA 0/1 NA NA NA NA 24,34,51,49 G/C PANCANCER NA FALSE STAT1_p.P491A chr2:190982494:190982495:G:C SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 192177574 192177575 A G 18 23 0.782608695652174 MODIFIER TMEFF2 ENSG00000144339 G intron_variant Transcript ENST00000272771 protein_coding 4/9 ENST00000272771.10:c.439+2094T>C NA -1 SNV HGNC HGNC:11867 YES NM_016192.4 1 P1 CCDS2314.1 ENSP00000272771 Q9UIK5.173 UPI0000048F19 Q9UIK5-1 12 NA NA PASS SITE 14,29|5,13 NA NA 1 93 34,25 200,219 60,60 23 1.23 NA 9.63 NA FALSE 6.00 68 NA NA NA FALSE NA NA 49.01 12 192177574 HCC1395_HCC1395T 5 0.751 23 2,4 2,9 4,14 NA 0/1 NA NA NA NA 2,3,5,13 A/G PANCANCER NA FALSE TMEFF2 chr2:192177574:192177575:A:G SNV 3:1 chr2:159969442:192177984:3:1:1 NA NA 0.96 +chr2 196026941 196026942 C G 15 33 0.454545454545455 HIGH DNAH7 ENSG00000118997 G splice_acceptor_variant Transcript ENST00000312428 protein_coding 6/64 ENST00000312428.11:c.487-1G>C NA -1 SNV HGNC HGNC:18661 YES NM_018897.3 1 P1 CCDS42794.1 ENSP00000311273 Q8WXX0.154 UPI0000141B95 Q8WXX0-1 12 NA NA PASS SITE 17,50|4,11 NA NA 1 93 20,20 151,147 60,60 16 1.55 NA 10.23 NA FALSE 6.00 47 NA NA NA FALSE NA NA 41.47 12 196026941 HCC1395_HCC1395T 18 0.416 33 4,2 9,7 16,11 NA 0/1 NA NA NA NA 2,16,4,11 C/G PANCANCER NA FALSE DNAH7 chr2:196026941:196026942:C:G SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 197500318 197500319 CCGCT C 74 160 0.4625 MODIFIER HSPE1 ENSG00000115541 - upstream_gene_variant Transcript ENST00000233893 protein_coding NA 57 1 deletion HGNC HGNC:5269 YES NM_002157.3 1 P1 CCDS2320.1 ENSP00000233893 P61604.166 A0A384N6A4.21 UPI0000001C17 12 NA NA PASS SITE 123,139|35,39 NA NA 2 93 34,34 187,193 60,60 27 2.22 NA 45.53 NA FALSE 6.00 93 NA NA NA FALSE NA NA 286.90 12 197500318 HCC1395_HCC1395T 86 0.481 160 20,14 21,28 70,64 NA 0|1 0|1 197500318_CCGCT_C NA 197500318 34,52,35,39 CCGCT|C PANCANCER NA FALSE HSPE1 chr2:197500318:197500319:CCGCT:C indel 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 197500324 197500325 GGGCGAGCGCGC G 74 169 0.437869822485207 MODIFIER HSPE1 ENSG00000115541 - upstream_gene_variant Transcript ENST00000233893 protein_coding NA 44 1 deletion HGNC HGNC:5269 YES NM_002157.3 1 P1 CCDS2320.1 ENSP00000233893 P61604.166 A0A384N6A4.21 UPI0000001C17 12 NA NA PASS SITE 148,150|35,39 NA NA 2 93 39,39 187,193 60,60 27 2.24 NA 51.18 NA FALSE 6.00 93 NA NA NA FALSE NA NA 284.56 12 197500324 HCC1395_HCC1395T 95 0.453 169 21,13 22,27 78,64 NA 0|1 0|1 197500318_CCGCT_C NA 197500318 42,53,35,39 GGGCGAGCGCGC|G PANCANCER NA FALSE HSPE1 chr2:197500324:197500325:GGGCGAGCGCGC:G indel 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 200620711 200620712 G C 36 79 0.455696202531646 MODERATE AOX1 ENSG00000138356 C missense_variant Transcript ENST00000374700 protein_coding 17/35 ENST00000374700.7:c.1766G>C ENSP00000363832.2:p.G589A ENSP00000363832.2 p.G589A 1861 1766 589 G/A gGt/gCt 1 SNV HGNC HGNC:553 YES NM_001159.4 1 P1 CCDS33360.1 ENSP00000363832 Q06278.208 UPI0000071863 tolerated_low_confidence(0.32) benign(0.022) PDB-ENSP_mappings:4uhw.A&PDB-ENSP_mappings:4uhx.A&PDB-ENSP_mappings:5epg.A&PDB-ENSP_mappings:6q6q.A&PDB-ENSP_mappings:7opn.A&PDB-ENSP_mappings:7opn.B&PDB-ENSP_mappings:7orc.A&PDB-ENSP_mappings:7orc.B&PANTHER:PTHR45444&PIRSF:PIRSF000127&TIGRFAM:TIGR02969&Superfamily:SSF54665&AlphaFold_DB_import:AF-Q06278-F1 12 NA NA PASS SITE 67,55|21,15 NA NA 1 93 20,20 149,147 60,60 35 1.69 NA 14.45 NA FALSE 6.00 75 NA NA NA FALSE NA NA 86.01 12 200620711 HCC1395_HCC1395T 43 0.450 79 7,6 21,14 28,23 NA 0/1 NA NA NA NA 25,18,21,15 G/C PANCANCER NA FALSE AOX1_p.G589A chr2:200620711:200620712:G:C SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 200816181 200816182 C A 25 81 0.308641975308642 MODIFIER BZW1 ENSG00000082153 A upstream_gene_variant Transcript ENST00000359893 protein_coding NA 2145 1 cds_start_NF SNV HGNC HGNC:18380 3 ENSP00000395673 H0Y503.61 UPI0001881958 12 NA NA PASS SITE 75,59|13,12 NA NA 1 93 20,20 166,164 60,60 30 1.70 NA 14.75 NA FALSE 6.00 49 NA NA NA FALSE NA NA 58.70 12 200816181 HCC1395_HCC1395T 56 0.333 81 11,5 20,10 33,16 NA 0/1 NA NA NA NA 30,26,13,12 C/A PANCANCER NA FALSE BZW1 chr2:200816181:200816182:C:A SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 200889230 200889231 T G 24 54 0.444444444444444 MODIFIER PPIL3 ENSG00000240344 G 5_prime_UTR_variant Transcript ENST00000286175 protein_coding 1/7 ENST00000286175.12:c.-345A>C NA 40 rs571518940 -1 SNV HGNC HGNC:9262 1 CCDS2332.1 ENSP00000286175 Q9H2H8.171 A0A0S2Z5A8.44 UPI000006E160 Q9H2H8-2 0.0002 0.0008 0 0 0 0 0.0002103 0.0007483 0 6.546e-05 0 0 0 0 0 0 0 0.0008 AFR 12 NA NA PASS SITE 66,57|15,9 NA NA 1 93 20,20 164,174 60,60 27 1.80 NA 18.36 NA FALSE 3.65 81 NA NA NA FALSE NA NA 62.41 12 200889230 HCC1395_HCC1395T 30 0.458 54 7,5 13,11 21,18 NA 0/1 NA NA NA NA 17,13,15,9 T/G PANCANCER NA FALSE PPIL3 chr2:200889230:200889231:T:G SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 201330523 201330524 C G 53 102 0.519607843137255 HIGH FLACC1 ENSG00000155749 G splice_acceptor_variant Transcript ENST00000286190 protein_coding 7/13 ENST00000286190.9:c.623-1G>C NA COSV53788183 -1 SNV HGNC HGNC:14439 1 CCDS2346.1 ENSP00000286190 Q96Q35.153 UPI00001AEADD Q96Q35-1 1 1 12 NA NA PASS SITE 68,56|28,25 NA NA 1 93 34,20 171,176 60,60 27 1.77 NA 17.15 NA FALSE 6.00 93 NA NA NA FALSE NA NA 142.22 12 201330523 HCC1395_HCC1395T 49 0.486 102 14,11 22,26 40,38 NA 0/1 NA NA NA NA 29,20,28,25 C/G PANCANCER NA FALSE FLACC1 chr2:201330523:201330524:C:G SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 201835740 201835741 A C 54 127 0.425196850393701 MODERATE CDK15 ENSG00000138395 C missense_variant Transcript ENST00000260967 protein_coding 8/14 ENST00000260967.6:c.675A>C ENSP00000260967.2:p.E225D ENSP00000260967.2 p.E225D 878 675 225 E/D gaA/gaC COSV53640349 1 SNV HGNC HGNC:14434 1 CCDS2350.1 ENSP00000260967 Q96Q40.182 UPI0000125024 Q96Q40-4 tolerated_low_confidence(1) benign(0.013) PROSITE_profiles:PS50011&CDD:cd07870&PANTHER:PTHR24056&Pfam:PF00069&Gene3D:1.10.510.10&SMART:SM00220&Superfamily:SSF56112&AlphaFold_DB_import:AF-Q96Q40-F1 1 1 12 NA NA PASS SITE 67,106|22,32 NA NA 1 93 20,20 152,153 60,60 42 1.79 NA 18.06 NA FALSE 6.00 93 NA NA NA FALSE NA NA 131.31 12 201835740 HCC1395_HCC1395T 73 0.400 127 14,8 33,19 50,33 NA 0/1 NA NA NA NA 26,47,22,32 A/C PANCANCER NA FALSE CDK15_p.E225D chr2:201835740:201835741:A:C SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 206791577 206791578 C G 3 10 0.3 MODIFIER FASTKD2 ENSG00000118246 G intron_variant Transcript ENST00000236980 protein_coding 11/11 ENST00000236980.10:c.2014-106C>G NA rs1296576943 1 SNV HGNC HGNC:29160 1 P1 CCDS2371.1 ENSP00000236980 Q9NYY8.162 A0A024R3X5.13 UPI0000073E9F Q9NYY8-1 1 6.573e-06 0 0 6.548e-05 0 0 0 0 0 0 0 6.548e-05 gnomADg_AMR 12 NA NA PASS SITE 33,2|3,0 NA NA 1 80 39,40 196,186 60,60 23 1.45 NA 7.83 NA FALSE 6.00 32 NA NA NA FALSE NA NA 10.11 12 206791577 HCC1395_HCC1395T 7 0.335 10 2,3 4,0 7,3 NA 0/1 NA NA NA NA 7,0,3,0 C/G PANCANCER NA FALSE FASTKD2 chr2:206791577:206791578:C:G SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 206960746 206960747 G A 30 66 0.454545454545455 MODIFIER CPO ENSG00000144410 A intron_variant Transcript ENST00000272852 protein_coding 5/8 ENST00000272852.4:c.484-106G>A NA 1 SNV HGNC HGNC:21011 YES NM_173077.3 1 P1 CCDS2372.1 ENSP00000272852 Q8IVL8.140 UPI0000047AEF 12 NA NA PASS SITE 68,21|20,10 NA NA 1 93 34,34 180,190 60,60 36 1.65 NA 12.94 NA FALSE 6.00 68 NA NA NA FALSE NA NA 86.29 12 206960746 HCC1395_HCC1395T 36 0.488 66 13,7 12,15 25,24 NA 0/1 NA NA NA NA 25,11,20,10 G/A PANCANCER NA FALSE CPO chr2:206960746:206960747:G:A SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 206960999 206961000 G C 8 20 0.4 MODIFIER CPO ENSG00000144410 C intron_variant Transcript ENST00000272852 protein_coding 6/8 ENST00000272852.4:c.574+57G>C NA 1 SNV HGNC HGNC:21011 YES NM_173077.3 1 P1 CCDS2372.1 ENSP00000272852 Q8IVL8.140 UPI0000047AEF 12 NA NA PASS SITE 4,30|1,7 NA NA 1 60 39,38 190,230 60,60 14 1.32 NA 6.02 NA FALSE 6.00 73 NA NA NA FALSE NA NA 25.40 12 206960999 HCC1395_HCC1395T 12 0.421 20 2,3 8,4 10,7 NA 0/1 NA NA NA NA 2,10,1,7 G/C PANCANCER NA FALSE CPO chr2:206960999:206961000:G:C SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 207080246 207080247 T C 3 6 0.5 MODIFIER KLF7 ENSG00000118263 C 3_prime_UTR_variant Transcript ENST00000309446 protein_coding 4/4 ENST00000309446.11:c.*967A>G NA 2256 -1 SNV HGNC HGNC:6350 YES NM_003709.4 1 P1 CCDS2373.1 ENSP00000309570 O75840.173 A0A024R3X8.47 UPI0000042958 O75840-1 1 12 NA NA PASS SITE 7,16|1,2 NA NA 1 45 34,20 147,135 60,60 54 1.20 NA 4.51 NA FALSE 6.00 21 NA NA NA FALSE NA NA 6.12 12 207080246 HCC1395_HCC1395T 3 0.429 6 0,0 3,2 3,2 NA 0/1 NA NA NA NA 1,2,1,2 T/C PANCANCER NA FALSE KLF7 chr2:207080246:207080247:T:C SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 207088424 207088425 C G 50 91 0.549450549450549 MODIFIER KLF7 ENSG00000118263 G intron_variant Transcript ENST00000309446 protein_coding 3/3 ENST00000309446.11:c.857+34G>C NA -1 SNV HGNC HGNC:6350 YES NM_003709.4 1 P1 CCDS2373.1 ENSP00000309570 O75840.173 A0A024R3X8.47 UPI0000042958 O75840-1 1 12 NA NA PASS SITE 62,71|25,25 NA NA 1 93 20,20 166,184 60,60 28 1.81 NA 18.96 NA FALSE 6.00 93 NA NA NA FALSE NA NA 147.93 12 207088424 HCC1395_HCC1395T 41 0.571 91 7,20 15,16 27,36 NA 0/1 NA NA NA NA 18,23,25,25 C/G PANCANCER NA FALSE KLF7 chr2:207088424:207088425:C:G SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 208181449 208181450 C T 6 12 0.5 MODIFIER C2orf80 ENSG00000188674 T intron_variant Transcript ENST00000341287 protein_coding 4/8 ENST00000341287.9:c.207-144G>A NA rs916347172 -1 SNV HGNC HGNC:34352 YES NM_001099334.3 1 P1 CCDS42809.1 ENSP00000343171 Q0P641.95 UPI00001D7E1A 1.315e-05 4.833e-05 0 0 0 0 0 0 0 0 0 4.833e-05 gnomADg_AFR 12 NA NA PASS SITE 0,14|0,6 NA NA 1 23 40,36 246,217 60,60 20 0.954 NA 2.41 NA FALSE 6.00 32 NA NA NA FALSE NA NA 17.13 12 208181449 HCC1395_HCC1395T 6 0.500 12 1,1 4,4 6,6 NA 0/1 NA NA NA NA 0,6,0,6 C/T PANCANCER NA FALSE C2orf80 chr2:208181449:208181450:C:T SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 210658789 210658790 C A 75 149 0.503355704697987 MODIFIER CPS1 ENSG00000021826 A intron_variant Transcript ENST00000233072 protein_coding 31/37 ENST00000233072.10:c.3756+101C>A NA 1 SNV HGNC HGNC:2323 YES NM_001875.5 1 P1 CCDS2393.1 ENSP00000233072 P31327.243 A0A024R454.49 UPI000000D7EC P31327-1 1 12 NA NA PASS SITE 111,128|35,40 NA NA 1 93 20,20 162,162 60,60 34 2.04 NA 32.46 NA FALSE 6.00 93 NA NA NA FALSE NA NA 189.25 12 210658789 HCC1395_HCC1395T 74 0.506 149 18,17 28,27 48,49 NA 0/1 NA NA NA NA 31,43,35,40 C/A PANCANCER NA FALSE CPS1 chr2:210658789:210658790:C:A SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 216428742 216428743 C G 78 178 0.438202247191011 MODERATE SMARCAL1 ENSG00000138375 G missense_variant Transcript ENST00000357276 protein_coding 7/18 ENST00000357276.9:c.1294C>G ENSP00000349823.4:p.L432V ENSP00000349823.4 p.L432V 1554 1294 432 L/V Ctc/Gtc COSV61924305 1 SNV HGNC HGNC:11102 YES NM_014140.4 2 P1 CCDS2403.1 ENSP00000349823 Q9NZC9.175 UPI000000DA30 1 tolerated(0.06) benign(0.23) PANTHER:PTHR45766&Gene3D:3.40.50.10810&SMART:SM00487&Superfamily:SSF52540&AlphaFold_DB_import:AF-Q9NZC9-F1 1 1 12 NA NA PASS SITE 166,173|39,39 NA NA 1 93 20,20 150,157 60,60 38 2.17 NA 43.95 NA FALSE 6.00 93 NA NA NA FALSE NA NA 189.31 12 216428742 HCC1395_HCC1395T 100 0.450 178 27,24 27,19 61,50 NA 0/1 NA NA NA NA 51,49,39,39 C/G PANCANCER NA FALSE SMARCAL1_p.L432V chr2:216428742:216428743:C:G SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 218234831 218234832 G C 55 141 0.390070921985816 MODIFIER ARPC2 ENSG00000163466 C intron_variant Transcript ENST00000295685 protein_coding 4/9 ENST00000295685.14:c.268+434G>C NA 1 SNV HGNC HGNC:705 1 P1 CCDS2410.1 ENSP00000295685 O15144.188 Q53R19.133 UPI0000125D3D 12 NA NA PASS SITE 134,93|34,21 NA NA 1 93 20,20 164,169 60,60 34 1.98 NA 28.29 NA FALSE 6.00 93 NA NA NA FALSE NA NA 140.14 12 218234831 HCC1395_HCC1395T 86 0.394 141 18,11 36,25 56,36 NA 0/1 NA NA NA NA 50,36,34,21 G/C PANCANCER NA FALSE ARPC2 chr2:218234831:218234832:G:C SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 218594451 218594452 GTCTTGAGGACCTGGGCTCCCTCTGCTA G 30 65 0.461538461538462 MODIFIER CNOT9 ENSG00000144580 - 3_prime_UTR_variant Transcript ENST00000273064 protein_coding 8/8 ENST00000273064.11:c.*176_*202del NA 1192-1218 1 deletion HGNC HGNC:10445 YES NM_005444.3 1 P1 CCDS33379.1 ENSP00000273064 Q92600.183 D5MQE1.68 UPI0000052E10 Q92600-1 12 NA NA PASS SITE 71,67|14,16 NA NA 1 93 20,26 166,199 60,60 37 1.83 NA 19.79 NA FALSE 6.00 93 NA NA NA FALSE NA NA 118.92 12 218594451 HCC1395_HCC1395T 35 0.471 65 7,5 7,12 26,23 NA 0/1 NA NA NA NA 16,19,14,16 GTCTTGAGGACCTGGGCTCCCTCTGCTA/G PANCANCER NA FALSE CNOT9 chr2:218594451:218594452:GTCTTGAGGACCTGGGCTCCCTCTGCTA:G indel 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 218991946 218991947 G C 44 99 0.444444444444444 MODIFIER CRYBA2 ENSG00000163499 C intron_variant Transcript ENST00000295728 protein_coding 2/3 ENST00000295728.7:c.303+156C>G NA -1 SNV HGNC HGNC:2395 YES NM_057093.2 1 P1 CCDS2429.1 ENSP00000295728 P53672.164 A0A024R429.58 UPI0000000C76 1 12 NA NA PASS SITE 97,62|26,18 NA NA 1 93 20,20 157,159 60,60 30 1.86 NA 21.32 NA FALSE 6.00 93 NA NA NA FALSE NA NA 110.57 12 218991946 HCC1395_HCC1395T 55 0.431 99 15,13 21,14 36,27 NA 0/1 NA NA NA NA 35,20,26,18 G/C PANCANCER NA FALSE CRYBA2 chr2:218991946:218991947:G:C SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 219208260 219208261 G C 32 233 0.137339055793991 MODIFIER ABCB6 ENSG00000115657 C downstream_gene_variant Transcript ENST00000265316 protein_coding NA COSV54699249 1512 -1 SNV HGNC HGNC:47 YES NM_005689.4 1 P1 CCDS2436.1 ENSP00000265316 Q9NP58.205 UPI000004C4BA Q9NP58-1 1 1 1 12 NA NA PASS SITE 219,194|16,16 NA NA 1 93 20,20 157,179 60,60 29 2.14 NA 41.23 NA FALSE 6.00 72 NA NA NA FALSE NA NA 67.34 12 219208260 HCC1395_HCC1395T 201 0.134 233 62,6 60,12 135,20 NA 0/1 NA NA NA NA 105,96,16,16 G/C PANCANCER NA FALSE ABCB6 chr2:219208260:219208261:G:C SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 219471925 219471926 A G 46 86 0.534883720930233 MODERATE SPEG ENSG00000072195 G missense_variant Transcript ENST00000312358 protein_coding 14/41 ENST00000312358.12:c.3773A>G ENSP00000311684.7:p.Y1258C ENSP00000311684.7 p.Y1258C 3908 3773 1258 Y/C tAc/tGc 1 SNV HGNC HGNC:16901 YES NM_005876.5 5 P1 CCDS42824.1 ENSP00000311684 Q15772.195 UPI000066D99E Q15772-5 1 deleterious(0) probably_damaging(0.997) PROSITE_profiles:PS50835&PANTHER:PTHR47633&Gene3D:2.60.40.10&Pfam:PF07679&SMART:SM00408&SMART:SM00409&Superfamily:SSF48726 12 NA NA PASS SITE 71,55|26,20 NA NA 1 93 20,20 157,163 60,60 34 1.77 NA 16.81 NA FALSE 6.00 93 NA NA NA FALSE NA NA 120.70 12 219471925 HCC1395_HCC1395T 40 0.525 86 13,14 13,13 27,30 NA 0/1 NA NA NA NA 23,17,26,20 A/G PANCANCER NA FALSE SPEG_p.Y1258C chr2:219471925:219471926:A:G SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 222689428 222689429 G T 40 373 0.107238605898123 MODERATE MOGAT1 ENSG00000124003 T missense_variant Transcript ENST00000446656 protein_coding 3/6 ENST00000446656.4:c.437G>T ENSP00000406674.3:p.W146L ENSP00000406674.3 p.W146L 565 437 146 W/L tGg/tTg COSV71479866 1 SNV HGNC HGNC:18210 YES NM_058165.3 5 P1 CCDS46524.1 ENSP00000406674 Q96PD6.132 UPI000013D50F tolerated(0.05) benign(0.106) AlphaFold_DB_import:AF-Q96PD6-F1&Pfam:PF03982&PANTHER:PTHR12317&CDD:cd07987 1 1 12 NA NA PASS SITE 277,326|18,22 NA NA 1 93 20,20 153,139 60,60 39 2.24 NA 51.11 NA FALSE 6.00 75 NA NA NA FALSE NA NA 71.99 12 222689428 HCC1395_HCC1395T 333 0.105 373 79,9 118,14 211,24 NA 0/1 NA NA NA NA 156,177,18,22 G/T PANCANCER NA FALSE MOGAT1_p.W146L chr2:222689428:222689429:G:T SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 223053486 223053487 TG T 49 111 0.441441441441441 MODIFIER KCNE4 ENSG00000152049 - 3_prime_UTR_variant Transcript ENST00000281830 protein_coding 2/2 ENST00000281830.4:c.*148del NA 765 COSV56055302 1 deletion HGNC HGNC:6244 YES NM_080671.4 1 P1 CCDS2456.3 ENSP00000281830 Q8WWG9.155 A5H1P5.105 UPI000013DCA0 4 1 1 12 NA NA PASS SITE 78,99|22,28 NA NA 2 93 20,33 161,187 60,60 33 1.86 NA 22.30 NA FALSE 6.00 93 5,4 G NA TRUE NA 93 93.08 12 223053486 HCC1395_HCC1395T 62 0.461 111 5,10 24,18 42,36 NA 0/1 NA NA NA NA 27,35,21,28 TG/T PANCANCER NA FALSE KCNE4 chr2:223053486:223053487:TG:T indel 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 223053494 223053495 TAGGCTCAGCCGGAACCAGCACCTCCA T 47 116 0.405172413793103 MODIFIER KCNE4 ENSG00000152049 - 3_prime_UTR_variant Transcript ENST00000281830 protein_coding 2/2 ENST00000281830.4:c.*155_*180del NA 773-798 1 deletion HGNC HGNC:6244 YES NM_080671.4 1 P1 CCDS2456.3 ENSP00000281830 Q8WWG9.155 A5H1P5.105 UPI000013DCA0 3 12 NA NA PASS SITE 89,110|23,25 NA NA 2 93 20,35 162,189 60,60 32 -6.074e-01 NA 21.72 NA FALSE 6.00 93 NA NA NA FALSE NA NA 187.46 12 223053494 HCC1395_HCC1395T 69 0.437 116 6,9 25,16 46,35 NA 0/1 NA NA NA NA 31,38,22,25 TAGGCTCAGCCGGAACCAGCACCTCCA/T PANCANCER NA FALSE KCNE4 chr2:223053494:223053495:TAGGCTCAGCCGGAACCAGCACCTCCA:T indel 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 224770651 224770652 G A 113 222 0.509009009009009 LOW DOCK10 ENSG00000135905 A splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000258390 protein_coding 53/55 ENST00000258390.12:c.6205-6C>T NA -1 SNV HGNC HGNC:23479 YES NM_014689.3 5 P3 CCDS46528.1 ENSP00000258390 Q96BY6.178 UPI000021D2A7 Q96BY6-1 12 NA NA PASS SITE 154,163|55,58 NA NA 1 93 20,20 153,169 60,60 36 2.13 NA 39.43 NA FALSE 6.00 93 NA NA NA FALSE NA NA 277.78 12 224770651 HCC1395_HCC1395T 109 0.493 222 22,22 44,44 72,70 NA 0/1 NA NA NA NA 53,56,55,58 G/A PANCANCER NA FALSE DOCK10 chr2:224770651:224770652:G:A SNV 1:1 chr2:192192011:225408774:1:1:1 NA NA 0.96 +chr2 227702681 227702682 C G 49 161 0.304347826086957 MODIFIER SLC19A3 ENSG00000135917 G intron_variant Transcript ENST00000258403 protein_coding 1/5 ENST00000258403.8:c.-2-361G>C NA -1 SNV HGNC HGNC:16266 1 P1 CCDS2468.1 ENSP00000258403 Q9BZV2.162 UPI000004DAE9 1 12 NA NA PASS SITE 162,39|36,13 NA NA 1 93 37,38 194,171 60,60 25 1.88 NA 21.97 NA FALSE 6.00 83 NA NA NA FALSE NA NA 141.65 12 227702681 HCC1395_HCC1395T 112 0.298 161 38,11 54,28 93,39 NA 0/1 NA NA NA NA 91,21,36,13 C/G PANCANCER NA FALSE SLC19A3 chr2:227702681:227702682:C:G SNV 3:1 chr2:225408973:231461706:3:1:1 NA NA 0.96 +chr2 227893863 227893864 C T 72 244 0.295081967213115 MODERATE DAW1 ENSG00000123977 T missense_variant Transcript ENST00000309931 protein_coding 5/13 ENST00000309931.3:c.386C>T ENSP00000311899.2:p.T129M ENSP00000311899.2 p.T129M 445 386 129 T/M aCg/aTg rs113776284&COSV59368404 1 SNV HGNC HGNC:26383 YES NM_178821.3 1 P1 CCDS2470.1 ENSP00000311899 Q8N136.155 A0A140VKH6.32 UPI000006EAC6 Q8N136-1 1 deleterious(0.03) probably_damaging(0.952) Gene3D:2.130.10.10&PDB-ENSP_mappings:5nnz.A&PDB-ENSP_mappings:5nnz.B&AlphaFold_DB_import:AF-Q8N136-F1&Pfam:PF00400&PROSITE_profiles:PS50082&PANTHER:PTHR22847&SMART:SM00320&Superfamily:SSF50978&CDD:cd00200 0.0002 0 0 0 0 0.001 3.585e-05 0.0001231 0 0 0 0 2.643e-05 0 0.0001308 3.945e-05 2.414e-05 0 0 0 0 0 0 5.88e-05 0 0.0002071 0.001 SAS 0&1 0&1 12 NA NA PASS SITE 113,178|26,46 NA NA 1 93 20,20 167,150 60,60 31 1.94 NA 24.98 NA FALSE 4.61 93 NA NA NA FALSE NA NA 176.75 12 227893863 HCC1395_HCC1395T 172 0.296 244 31,14 57,25 118,49 NA 0/1 NA NA NA NA 67,105,26,46 C/T PANCANCER NA FALSE DAW1_p.T129M chr2:227893863:227893864:C:T SNV 3:1 chr2:225408973:231461706:3:1:1 NA NA 0.96 +chr2 232329722 232329723 G C 13 28 0.464285714285714 MODIFIER DIS3L2 ENSG00000144535 C intron_variant Transcript ENST00000273009 protein_coding 13/13 ENST00000273009.10:c.1582-13623G>C NA 1 SNV HGNC HGNC:28648 2 CCDS58752.1 ENSP00000273009 Q8IYB7.155 UPI000006FBF7 Q8IYB7-3 1 12 NA NA PASS SITE 24,24|8,5 NA NA 1 61 20,20 141,158 60,60 35 1.30 NA 5.72 NA FALSE 6.00 60 NA NA NA FALSE NA NA 31.89 12 232329722 HCC1395_HCC1395T 15 0.474 28 3,2 5,6 9,8 NA 0/1 NA NA NA NA 7,8,8,5 G/C PANCANCER NA FALSE DIS3L2 chr2:232329722:232329723:G:C SNV 2:1 chr2:231462090:241744700:2:1:1 TRUE NA 0.96 +chr2 232556572 232556573 G C 33 71 0.464788732394366 MODIFIER EIF4E2 ENSG00000135930 C intron_variant Transcript ENST00000258416 protein_coding 2/6 ENST00000258416.8:c.135+42G>C NA 1 SNV HGNC HGNC:3293 YES NM_004846.4 1 CCDS2496.1 ENSP00000258416 O60573.187 Q53RG0.136 UPI0000073BFD O60573-1 12 NA NA PASS SITE 32,50|12,21 NA NA 1 93 20,20 169,175 60,60 34 1.47 NA 8.43 NA FALSE 6.00 93 NA NA NA FALSE NA NA 83.22 12 232556572 HCC1395_HCC1395T 38 0.449 71 8,6 6,7 26,21 NA 0/1 NA NA NA NA 13,25,12,21 G/C PANCANCER NA FALSE EIF4E2 chr2:232556572:232556573:G:C SNV 2:1 chr2:231462090:241744700:2:1:1 TRUE NA 0.96 +chr2 232767188 232767189 G A 2 7 0.285714285714286 MODIFIER KCNJ13 ENSG00000115474 A 3_prime_UTR_variant Transcript ENST00000233826 protein_coding 3/3 ENST00000233826.4:c.*1003C>T NA 2223 -1 SNV HGNC HGNC:6259 YES NM_002242.4 1 P1 CCDS2498.1 ENSP00000233826 O60928.192 UPI000012D8AF O60928-1 1 12 NA NA PASS SITE 8,13|1,1 NA NA 1 34 20,38 159,133 60,60 41 1.08 NA 3.31 NA FALSE 6.00 13 NA NA NA FALSE NA NA 7.17 12 232767188 HCC1395_HCC1395T 5 0.329 7 2,0 1,1 3,1 NA 0/1 NA NA NA NA 2,3,1,1 G/A PANCANCER NA FALSE KCNJ13 chr2:232767188:232767189:G:A SNV 2:1 chr2:231462090:241744700:2:1:1 TRUE NA 0.96 +chr2 236124225 236124226 C T 15 52 0.288461538461538 MODIFIER AGAP1 ENSG00000157985 T 3_prime_UTR_variant Transcript ENST00000304032 protein_coding 18/18 ENST00000304032.13:c.*103C>T NA 3321 1 SNV HGNC HGNC:16922 YES NM_001037131.3 5 CCDS33408.1 ENSP00000307634 Q9UPQ3.210 UPI00005E1AE1 Q9UPQ3-1 12 NA NA PASS SITE 30,60|3,12 NA NA 1 93 20,36 150,168 60,60 21 1.58 NA 10.83 NA FALSE 6.00 71 NA NA NA FALSE NA NA 41.16 12 236124225 HCC1395_HCC1395T 37 0.302 52 11,5 16,6 29,12 NA 0/1 NA NA NA NA 11,26,3,12 C/T PANCANCER NA FALSE AGAP1 chr2:236124225:236124226:C:T SNV 2:1 chr2:231462090:241744700:2:1:1 TRUE NA 0.96 +chr2 236124877 236124878 C G 27 56 0.482142857142857 MODIFIER AGAP1 ENSG00000157985 G 3_prime_UTR_variant Transcript ENST00000304032 protein_coding 18/18 ENST00000304032.13:c.*755C>G NA 3973 1 SNV HGNC HGNC:16922 YES NM_001037131.3 5 CCDS33408.1 ENSP00000307634 Q9UPQ3.210 UPI00005E1AE1 Q9UPQ3-1 12 NA NA PASS SITE 33,29|16,11 NA NA 1 91 39,36 205,210 60,60 32 1.51 NA 9.03 NA FALSE 6.00 93 NA NA NA FALSE NA NA 84.30 12 236124877 HCC1395_HCC1395T 29 0.471 56 8,8 16,14 26,23 NA 0/1 NA NA NA NA 16,13,16,11 C/G PANCANCER NA FALSE AGAP1 chr2:236124877:236124878:C:G SNV 2:1 chr2:231462090:241744700:2:1:1 TRUE NA 0.96 +chr2 240745596 240745597 G A 7 33 0.212121212121212 MODIFIER KIF1A ENSG00000130294 A intron_variant Transcript ENST00000320389 protein_coding 29/47 ENST00000320389.12:c.3072-79C>T NA rs943909312 -1 SNV HGNC HGNC:888 5 A1 CCDS92987.1 ENSP00000322791 A0A3F2YNW9.22 UPI000387C1CD 1 6.573e-06 0 0 0 0 0 0 0 1.47e-05 0 0 1.47e-05 gnomADg_NFE 12 NA NA PASS SITE 20,27|4,3 NA NA 1 63 34,36 219,191 60,60 16 1.31 NA 5.72 NA FALSE 6.00 32 NA NA NA FALSE NA NA 18.02 12 240745596 HCC1395_HCC1395T 26 0.233 33 10,2 10,4 22,6 NA 0/1 NA NA NA NA 11,15,4,3 G/A PANCANCER NA FALSE KIF1A chr2:240745596:240745597:G:A SNV 2:1 chr2:231462090:241744700:2:1:1 TRUE NA 0.96 +chr2 241062717 241062718 GGAC G 40 278 0.143884892086331 MODIFIER SNED1 ENSG00000162804 - intron_variant Transcript ENST00000310397 protein_coding 16/31 ENST00000310397.13:c.2258-73_2258-71del NA 1 deletion HGNC HGNC:24696 YES NM_001080437.3 5 P2 CCDS46562.1 ENSP00000308893 Q8TER0.155 UPI0000DD7AB0 Q8TER0-1 12 NA NA PASS SITE 278,158|25,15 NA NA 2 93 20,20 162,168 60,60 30 2.14 NA 41.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 145.38 12 241062717 HCC1395_HCC1395T 238 0.138 278 57,11 88,14 168,26 NA 0|1 0|1 241062717_GGAC_G NA 241062717 151,87,25,15 GGAC|G PANCANCER NA FALSE SNED1 chr2:241062717:241062718:GGAC:G indel 2:1 chr2:231462090:241744700:2:1:1 TRUE NA 0.96 +chr2 241062721 241062722 TAGTTTA T 40 291 0.13745704467354 MODIFIER SNED1 ENSG00000162804 - intron_variant Transcript ENST00000310397 protein_coding 16/31 ENST00000310397.13:c.2258-69_2258-64del NA 1 deletion HGNC HGNC:24696 YES NM_001080437.3 5 P2 CCDS46562.1 ENSP00000308893 Q8TER0.155 UPI0000DD7AB0 Q8TER0-1 12 NA NA PASS SITE 290,175|25,15 NA NA 2 93 20,26 161,168 60,60 30 2.16 NA 42.85 NA FALSE 6.00 93 NA NA NA FALSE NA NA 144.89 12 241062721 HCC1395_HCC1395T 251 0.133 291 56,11 90,14 176,26 NA 0|1 0|1 241062717_GGAC_G NA 241062717 159,92,25,15 TAGTTTA|T PANCANCER NA FALSE SNED1 chr2:241062721:241062722:TAGTTTA:T indel 2:1 chr2:231462090:241744700:2:1:1 TRUE NA 0.96 +chr2 241190240 241190241 C T 18 91 0.197802197802198 MODIFIER ANO7 ENSG00000146205 T intron_variant Transcript ENST00000274979 protein_coding 2/24 ENST00000274979.12:c.270+69C>T NA 1 SNV HGNC HGNC:31677 1 P4 ENSP00000274979 Q6IWH7.145 UPI0000D612DB Q6IWH7-1 12 NA NA PASS SITE 64,99|6,12 NA NA 1 93 20,37 163,156 60,60 38 1.80 NA 18.36 NA FALSE 6.00 62 NA NA NA FALSE NA NA 48.37 12 241190240 HCC1395_HCC1395T 73 0.226 91 15,5 26,8 47,13 NA 0/1 NA NA NA NA 28,45,6,12 C/T PANCANCER NA FALSE ANO7 chr2:241190240:241190241:C:T SNV 2:1 chr2:231462090:241744700:2:1:1 TRUE NA 0.96 +chr3 4467286 4467287 G C 150 150 1 MODIFIER SUMF1 ENSG00000144455 C upstream_gene_variant Transcript ENST00000272902 protein_coding NA 17 -1 SNV HGNC HGNC:20376 YES NM_182760.4 1 P1 CCDS2564.1 ENSP00000272902 Q8NBK3.177 UPI0000040734 Q8NBK3-1 1 16 NA NA PASS SITE 65,95|60,90 NA NA 1 93 20,20 153,157 60,60 37 2.03 NA 31.30 NA FALSE 6.00 93 NA NA NA FALSE NA NA 443.73 16 4467286 HCC1395_HCC1395T 0 0.990 150 0,37 0,45 0,97 NA 0/1 NA NA NA NA 0,0,60,90 G/C PANCANCER NA FALSE SUMF1 chr3:4467286:4467287:G:C SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 9930194 9930195 C G 152 152 1 MODIFIER IL17RC ENSG00000163702 G intron_variant Transcript ENST00000295981 protein_coding 14/18 ENST00000295981.7:c.1491+45C>G NA 1 SNV HGNC HGNC:18358 2 A2 CCDS2590.1 ENSP00000295981 Q8NAC3.158 UPI000013E2E3 Q8NAC3-1 1 16 NA NA PASS SITE 65,82|61,91 NA NA 1 93 20,20 149,155 60,60 28 1.98 NA 28.59 NA FALSE 6.00 93 NA NA NA FALSE NA NA 448.58 16 9930194 HCC1395_HCC1395T 0 0.990 152 0,45 0,43 0,98 NA 0/1 NA NA NA NA 0,0,61,91 C/G PANCANCER NA FALSE IL17RC chr3:9930194:9930195:C:G SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 10505537 10505538 G A 21 62 0.338709677419355 MODIFIER ATP2B2 ENSG00000157087 A 5_prime_UTR_variant Transcript ENST00000360273 protein_coding 1/23 ENST00000360273.7:c.-392C>T NA 50 rs1575433191 -1 SNV HGNC HGNC:815 YES NM_001001331.4 5 CCDS33701.1 ENSP00000353414 Q01814.225 UPI00001261EF Q01814-1 1 16 NA NA PASS SITE 45,46|9,12 NA NA 1 93 20,20 141,161 60,60 43 1.50 NA 9.03 NA FALSE 6.00 46 NA NA NA FALSE NA NA 50.81 16 10505537 HCC1395_HCC1395T 41 0.366 62 10,4 12,10 25,14 NA 0/1 NA NA NA NA 21,20,9,12 G/A PANCANCER NA FALSE ATP2B2 chr3:10505537:10505538:G:A SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 13505852 13505853 G A 19 66 0.287878787878788 MODIFIER HDAC11 ENSG00000163517 A 3_prime_UTR_variant Transcript ENST00000295757 protein_coding 10/10 ENST00000295757.8:c.*1169G>A NA 2255 rs372677963 1 SNV HGNC HGNC:19086 YES NM_024827.4 1 P1 CCDS2615.1 ENSP00000295757 Q96DB2.179 UPI000012C3A7 Q96DB2-1 0.0072 0 0 0.0089 0 0.0276 0.001058 7.238e-05 0 0 0 0.004635 0 0 0 0 0.02773 0.02773 gnomADg_SAS 16 NA NA PASS SITE 74,75|10,9 NA NA 1 93 20,36 167,190 60,60 35 1.85 NA 21.07 NA FALSE 3.65 49 NA NA NA FALSE NA NA 51.63 16 13505852 HCC1395_HCC1395T 47 0.333 66 12,11 19,4 33,16 NA 0/1 NA NA NA NA 23,24,10,9 G/A PANCANCER NA FALSE HDAC11 chr3:13505852:13505853:G:A SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 32441773 32441774 C T 20 67 0.298507462686567 MODIFIER CMTM7 ENSG00000153551 T intron_variant Transcript ENST00000334983 protein_coding 1/4 ENST00000334983.10:c.160-67C>T NA 1 SNV HGNC HGNC:19178 YES NM_138410.4 1 P1 CCDS33730.1 ENSP00000335605 Q96FZ5.144 UPI00000343F1 Q96FZ5-1 16 NA NA PASS SITE 66,23|14,6 NA NA 1 93 20,24 177,155 60,60 29 1.54 NA 9.63 NA FALSE 6.00 38 NA NA NA FALSE NA NA 48.55 16 32441773 HCC1395_HCC1395T 47 0.295 67 10,3 23,11 35,14 NA 0/1 NA NA NA NA 34,13,14,6 C/T PANCANCER NA FALSE CMTM7 chr3:32441773:32441774:C:T SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 36714947 36714948 A G 18 139 0.129496402877698 MODIFIER DCLK3 ENSG00000163673 G 3_prime_UTR_variant Transcript ENST00000416516 protein_coding 5/5 ENST00000416516.2:c.*381T>C NA 2819 -1 SNV HGNC HGNC:19005 5 CCDS43064.1 ENSP00000394484 Q9C098.149 UPI0000E2657D 16 NA NA PASS SITE 98,102|8,10 NA NA 1 93 25,39 185,214 60,60 40 1.79 NA 18.01 NA FALSE 6.00 45 NA NA NA FALSE NA NA 47.43 16 36714947 HCC1395_HCC1395T 121 0.146 139 21,3 39,5 93,15 NA 0/1 NA NA NA NA 60,61,8,10 A/G PANCANCER NA FALSE DCLK3 chr3:36714947:36714948:A:G SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 37818954 37818955 G T 89 89 1 HIGH ITGA9 ENSG00000144668 T stop_gained Transcript ENST00000264741 protein_coding 28/28 ENST00000264741.10:c.3073G>T ENSP00000264741.5:p.E1025* ENSP00000264741.5 p.E1025* 3307 3073 1025 E/* Gaa/Taa COSV53241840&COSV53254781 1 SNV HGNC HGNC:6145 YES NM_002207.3 1 P1 CCDS2669.1 ENSP00000264741 Q13797.177 UPI00001AE8BB PANTHER:PTHR23220&AlphaFold_DB_import:AF-Q13797-F1 1&1 1&1 16 NA NA PASS SITE 42,29|48,41 NA NA 1 93 20,20 157,160 60,60 28 1.70 NA 14.45 NA FALSE 6.00 93 NA NA NA FALSE NA NA 261.99 16 37818954 HCC1395_HCC1395T 0 0.984 89 0,17 0,37 0,59 NA 0/1 NA NA NA NA 0,0,48,41 G/T PANCANCER NA FALSE ITGA9_p.E1025* chr3:37818954:37818955:G:T SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 38698511 38698512 G A 50 147 0.340136054421769 MODERATE SCN10A ENSG00000185313 A missense_variant Transcript ENST00000449082 protein_coding 28/28 ENST00000449082.3:c.4709C>T ENSP00000390600.2:p.T1570M ENSP00000390600.2 p.T1570M 4922 4709 1570 T/M aCg/aTg rs772484960&CM170549&COSV101479190&COSV71860989 -1 SNV HGNC HGNC:10582 YES NM_006514.4 1 P4 CCDS33736.1 ENSP00000390600 Q9Y5Y9.173 UPI0000209BDA 1 deleterious_low_confidence(0) Gene3D:1.20.120.350&PDB-ENSP_mappings:7we4.A&PDB-ENSP_mappings:7wel.A&PDB-ENSP_mappings:7wfr.A&PDB-ENSP_mappings:7wfw.A&AlphaFold_DB_import:AF-Q9Y5Y9-F1&Pfam:PF00520&PANTHER:PTHR10037&Superfamily:SSF81324 3.587e-05 0 0 0 0 0 7.059e-05 0 3.267e-05 3.943e-05 4.824e-05 0 0 0 0 0 0 5.88e-05 0 0 7.059e-05 gnomADe_NFE uncertain_significance&likely_benign 0&0&1&1 1&1&1&1 16 NA NA PASS SITE 141,119|27,24 NA NA 1 93 20,20 160,176 60,60 31 2.05 NA 33.11 NA FALSE 4.01 84 NA NA NA FALSE NA NA 133.07 16 38698511 HCC1395_HCC1395T 97 0.351 147 24,12 42,22 71,38 NA 0/1 NA NA NA NA 58,39,27,23 G/A PANCANCER NA FALSE SCN10A_p.T1570M chr3:38698511:38698512:G:A SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 38729038 38729039 GC G 30 134 0.223880597014925 MODIFIER SCN10A ENSG00000185313 - intron_variant Transcript ENST00000449082 protein_coding 15/27 ENST00000449082.3:c.2281-138del NA -1 deletion HGNC HGNC:10582 YES NM_006514.4 1 P4 CCDS33736.1 ENSP00000390600 Q9Y5Y9.173 UPI0000209BDA 1 16 NA NA PASS SITE 83,131|11,19 NA NA 1 93 20,20 161,151 60,60 18 1.90 NA 22.87 NA FALSE 6.00 93 NA NA NA FALSE NA NA 51.74 16 38729038 HCC1395_HCC1395T 104 0.219 134 19,3 33,9 69,19 NA 0/1 NA NA NA NA 45,59,11,19 GC/G PANCANCER NA FALSE SCN10A chr3:38729038:38729039:GC:G indel 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 39093883 39093884 C G 42 42 1 LOW WDR48 ENSG00000114742 G synonymous_variant Transcript ENST00000302313 protein_coding 18/19 ENST00000302313.10:c.1755C>G ENSP00000307491.5:p.L585= ENSP00000307491.5 p.L585= 1765 1755 585 L ctC/ctG COSV56531484 1 SNV HGNC HGNC:30914 YES NM_020839.4 1 P1 CCDS33738.1 ENSP00000307491 Q8TAF3.178 A0A024R2L1.63 UPI000006FF8C Q8TAF3-1 1 PDB-ENSP_mappings:5k1a.B&PDB-ENSP_mappings:5k1a.D&PDB-ENSP_mappings:5k1a.F&PDB-ENSP_mappings:5k1a.H&PDB-ENSP_mappings:5k1b.B&PDB-ENSP_mappings:7ay1.E&PDB-ENSP_mappings:8a9j.E&PDB-ENSP_mappings:8a9k.E&AlphaFold_DB_import:AF-Q8TAF3-F1&Pfam:PF11816&CDD:cd17041 1 1 16 NA NA PASS SITE 19,11|30,12 NA NA 1 93 20,20 156,191 60,60 30 1.33 NA 6.02 NA FALSE 6.00 93 NA NA NA FALSE NA NA 139.59 16 39093883 HCC1395_HCC1395T 0 0.970 42 0,14 0,16 0,31 NA 0/1 NA NA NA NA 0,0,30,12 C/G PANCANCER NA FALSE WDR48_p.L585= chr3:39093883:39093884:C:G SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 39188115 39188116 A T 119 186 0.639784946236559 MODERATE XIRP1 ENSG00000168334 T missense_variant Transcript ENST00000340369 protein_coding 2/2 ENST00000340369.4:c.1331T>A ENSP00000343140.3:p.L444H ENSP00000343140.3 p.L444H 1561 1331 444 L/H cTt/cAt COSV61141923 -1 SNV HGNC HGNC:14301 YES NM_194293.4 1 A2 CCDS2683.1 ENSP00000343140 Q702N8.131 UPI00001BFB06 Q702N8-1 deleterious(0) probably_damaging(0.993) AlphaFold_DB_import:AF-Q702N8-F1&PROSITE_profiles:PS51389 1 1 16 NA NA PASS SITE 135,137|57,62 NA NA 1 93 20,20 162,161 60,60 34 2.13 NA 40.59 NA FALSE 6.00 93 NA NA NA FALSE NA NA 312.32 16 39188115 HCC1395_HCC1395T 67 0.627 186 16,28 24,45 46,77 NA 0/1 NA NA NA NA 34,33,57,62 A/T PANCANCER NA FALSE XIRP1_p.L444H chr3:39188115:39188116:A:T SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 39514207 39514208 C G 73 73 1 MODIFIER MOBP ENSG00000168314 G 3_prime_UTR_variant Transcript ENST00000311042 protein_coding 5/5 ENST00000311042.10:c.*824C>G NA 1594 1 SNV HGNC HGNC:7189 2 CCDS63598.1 ENSP00000312293 Q13875.145 UPI0000EE2A8E Q13875-4 16 NA NA PASS SITE 39,29|45,28 NA NA 1 93 20,20 169,165 60,60 26 1.71 NA 15.00 NA FALSE 6.00 93 NA NA NA FALSE NA NA 240.69 16 39514207 HCC1395_HCC1395T 0 0.983 73 0,25 0,27 0,55 NA 0/1 NA NA NA NA 0,0,45,28 C/G PANCANCER NA FALSE MOBP chr3:39514207:39514208:C:G SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 44242058 44242059 G A 53 138 0.384057971014493 MODERATE TOPAZ1 ENSG00000173769 A missense_variant Transcript ENST00000309765 protein_coding 1/20 ENST00000309765.4:c.5G>A ENSP00000310303.4:p.R2Q ENSP00000310303.4 p.R2Q 173 5 2 R/Q cGa/cAa COSV59070438 1 SNV HGNC HGNC:24746 YES NM_001145030.2 5 P1 CCDS46809.1 ENSP00000310303 Q8N9V7.107 UPI000047FF75 tolerated_low_confidence(0.08) benign(0.208) PANTHER:PTHR35671&MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-Q8N9V7-F1 1 1 16 NA NA PASS SITE 82,128|18,35 NA NA 1 93 34,36 178,176 60,60 24 2.00 NA 29.19 NA FALSE 6.00 93 NA NA NA FALSE NA NA 148.36 16 44242058 HCC1395_HCC1395T 85 0.371 138 26,12 20,12 73,43 NA 0/1 NA NA NA NA 29,56,18,35 G/A PANCANCER NA FALSE TOPAZ1_p.R2Q chr3:44242058:44242059:G:A SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 46893865 46893866 C G 102 102 1 MODIFIER PTH1R ENSG00000160801 G intron_variant Transcript ENST00000313049 protein_coding 1/13 ENST00000313049.9:c.76-42C>G NA 1 SNV HGNC HGNC:9608 1 P1 CCDS2747.1 ENSP00000321999 Q03431.221 A1LPH3.16 UPI000005041F 1 16 NA NA PASS SITE 49,40|55,47 NA NA 1 93 20,20 165,169 60,60 36 1.77 NA 17.11 NA FALSE 6.00 93 NA NA NA FALSE NA NA 332.57 16 46893865 HCC1395_HCC1395T 0 0.987 102 0,32 0,39 0,74 NA 0/1 NA NA NA NA 0,0,55,47 C/G PANCANCER NA FALSE PTH1R chr3:46893865:46893866:C:G SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 48584903 48584904 A T 89 91 0.978021978021978 LOW COL7A1 ENSG00000114270 T splice_region_variant&intron_variant Transcript ENST00000328333 protein_coding 33/117 ENST00000328333.12:c.4011+7T>A NA -1 SNV HGNC HGNC:2214 1 P1 CCDS2773.1 ENSP00000332371 Q02388.243 UPI0000126D20 Q02388-1 1 16 NA NA PASS SITE 55,55|42,47 NA NA 1 93 20,20 161,160 60,60 28 1.91 NA 22.83 NA FALSE 6.00 93 NA NA NA FALSE NA NA 275.04 16 48584903 HCC1395_HCC1395T 2 0.970 91 0,18 1,35 1,63 NA 0/1 NA NA NA NA 1,1,42,47 A/T PANCANCER NA FALSE COL7A1 chr3:48584903:48584904:A:T SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 48747179 48747180 C G 223 223 1 MODIFIER PRKAR2A ENSG00000114302 G 3_prime_UTR_variant Transcript ENST00000265563 protein_coding 11/11 ENST00000265563.13:c.*4406G>C NA 5899 -1 SNV HGNC HGNC:9391 YES NM_004157.4 1 P1 CCDS2778.1 ENSP00000265563 P13861.219 A0A024R2W3.65 UPI0000161B64 P13861-1 16 NA NA PASS SITE 95,63|142,81 NA NA 1 93 20,20 155,169 60,60 35 2.00 NA 29.75 NA FALSE 6.00 93 NA NA NA FALSE NA NA 694.00 16 48747179 HCC1395_HCC1395T 0 0.994 223 0,61 0,88 0,151 NA 0/1 NA NA NA NA 0,0,142,81 C/G PANCANCER NA FALSE PRKAR2A chr3:48747179:48747180:C:G SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 48750668 48750669 GCAAACAAATGGTAGGAGTTGCCCAGGAAGGTATTTGGGCTGGA G 39 144 0.270833333333333 MODIFIER PRKAR2A ENSG00000114302 - 3_prime_UTR_variant Transcript ENST00000265563 protein_coding 11/11 ENST00000265563.13:c.*874_*916del NA 2367-2409 -1 deletion HGNC HGNC:9391 YES NM_004157.4 1 P1 CCDS2778.1 ENSP00000265563 P13861.219 A0A024R2W3.65 UPI0000161B64 P13861-1 16 NA NA PASS SITE 145,72|27,12 NA NA 1 93 37,40 185,194 60,60 32 1.97 NA 27.14 NA FALSE 6.00 93 NA NA NA FALSE NA NA 143.54 16 48750668 HCC1395_HCC1395T 105 0.286 144 12,15 19,13 89,39 NA 0/1 NA NA NA NA 72,33,27,12 GCAAACAAATGGTAGGAGTTGCCCAGGAAGGTATTTGGGCTGGA/G PANCANCER NA FALSE PRKAR2A chr3:48750668:48750669:GCAAACAAATGGTAGGAGTTGCCCAGGAAGGTATTTGGGCTGGA:G indel 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 52495420 52495421 GGGCCCCGGGGCCTCCTC G 13 577 0.0225303292894281 HIGH STAB1 ENSG00000010327 - frameshift_variant Transcript ENST00000321725 protein_coding 1/69 ENST00000321725.10:c.8_24del ENSP00000312946.6:p.G3Afs*25 ENSP00000312946.6 p.G3Afs*25 84-100 8-24 3-8 GPRGLL/X gGGCCCCGGGGCCTCCTC/g 1 deletion HGNC HGNC:18628 YES NM_015136.3 1 P1 CCDS33768.1 ENSP00000312946 Q9NY15.188 UPI0000140C12 Q9NY15-1 Low_complexity_(Seg):seg&Transmembrane_helices:TMhelix&Cleavage_site_(Signalp):SignalP-noTM&AlphaFold_DB_import:AF-Q9NY15-F1 16 NA NA PASS SITE 537,586|7,6 NA NA 1 93 20,20 155,172 60,60 43 2.54 NA 103.77 NA FALSE 6.00 93 NA NA NA FALSE NA NA 38.70 16 52495420 HCC1395_HCC1395T 564 0.028 577 128,6 131,2 349,9 NA 0/1 NA NA NA NA 270,294,7,6 GGGCCCCGGGGCCTCCTC/G PANCANCER NA FALSE STAB1_p.G3Afs*25 chr3:52495420:52495421:GGGCCCCGGGGCCTCCTC:G indel 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 52513014 52513015 C T 21 127 0.165354330708661 MODIFIER STAB1 ENSG00000010327 T intron_variant Transcript ENST00000321725 protein_coding 29/68 ENST00000321725.10:c.3158+56C>T NA 1 SNV HGNC HGNC:18628 YES NM_015136.3 1 P1 CCDS33768.1 ENSP00000312946 Q9NY15.188 UPI0000140C12 Q9NY15-1 16 NA NA PASS SITE 145,88|12,9 NA NA 1 93 25,20 172,148 60,60 25 2.00 NA 29.50 NA FALSE 6.00 58 NA NA NA FALSE NA NA 38.69 16 52513014 HCC1395_HCC1395T 106 0.143 127 34,7 39,5 77,12 NA 0/1 NA NA NA NA 62,44,12,9 C/T PANCANCER NA FALSE STAB1 chr3:52513014:52513015:C:T SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 52516837 52516838 C T 5 25 0.2 MODIFIER STAB1 ENSG00000010327 T intron_variant Transcript ENST00000321725 protein_coding 41/68 ENST00000321725.10:c.4363+69C>T NA rs1228521683 1 SNV HGNC HGNC:18628 YES NM_015136.3 1 P1 CCDS33768.1 ENSP00000312946 Q9NY15.188 UPI0000140C12 Q9NY15-1 16 NA NA PASS SITE 9,29|1,4 NA NA 1 44 39,35 204,225 60,60 26 1.23 NA 4.82 NA FALSE 6.00 23 NA NA NA FALSE NA NA 14.28 16 52516837 HCC1395_HCC1395T 20 0.240 25 7,4 9,1 18,5 NA 0/1 NA NA NA NA 6,14,1,4 C/T PANCANCER NA FALSE STAB1 chr3:52516837:52516838:C:T SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 52517960 52517961 A C 216 216 1 MODERATE STAB1 ENSG00000010327 C missense_variant Transcript ENST00000321725 protein_coding 45/69 ENST00000321725.10:c.4718A>C ENSP00000312946.6:p.H1573P ENSP00000312946.6 p.H1573P 4794 4718 1573 H/P cAc/cCc COSV58734929 1 SNV HGNC HGNC:18628 YES NM_015136.3 1 P1 CCDS33768.1 ENSP00000312946 Q9NY15.188 UPI0000140C12 Q9NY15-1 deleterious(0.01) benign(0.089) PROSITE_profiles:PS50026&PANTHER:PTHR24038&Pfam:PF12947&Gene3D:2.10.25.10&SMART:SM00181&Superfamily:SSF82153&Superfamily:SSF57196&AlphaFold_DB_import:AF-Q9NY15-F1 1 1 16 NA NA PASS SITE 89,142|89,127 NA NA 1 93 20,20 158,159 60,60 28 2.19 NA 45.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 609.42 16 52517960 HCC1395_HCC1395T 0 0.993 216 0,45 0,75 0,139 NA 0/1 NA NA NA NA 0,0,89,127 A/C PANCANCER NA FALSE STAB1_p.H1573P chr3:52517960:52517961:A:C SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 53089347 53089348 G T 102 102 1 MODIFIER RFT1 ENSG00000163933 T 3_prime_UTR_variant Transcript ENST00000296292 protein_coding 13/13 ENST00000296292.8:c.*2556C>A NA 4217 -1 SNV HGNC HGNC:30220 YES NM_052859.4 1 P1 CCDS2869.1 ENSP00000296292 Q96AA3.153 UPI000000DA67 1 16 NA NA PASS SITE 57,41|59,43 NA NA 1 93 20,20 167,160 60,60 32 1.82 NA 19.57 NA FALSE 6.00 93 NA NA NA FALSE NA NA 304.34 16 53089347 HCC1395_HCC1395T 0 0.986 102 0,23 0,45 0,68 NA 0/1 NA NA NA NA 0,0,59,43 G/T PANCANCER NA FALSE RFT1 chr3:53089347:53089348:G:T SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 53724113 53724114 C T 11 32 0.34375 MODIFIER CACNA1D ENSG00000157388 T intron_variant Transcript ENST00000288139 protein_coding 15/48 ENST00000288139.11:c.2160+114C>T NA 1 SNV HGNC HGNC:1391 NM_000720.4 1 P2 CCDS2872.1 ENSP00000288139 Q01668.215 UPI000005031A Q01668-2 1 16 NA NA PASS SITE 3,34|0,11 NA NA 1 52 38,39 192,203 60,60 11 1.18 NA 4.21 NA FALSE 6.00 74 NA NA NA FALSE NA NA 36.56 16 53724113 HCC1395_HCC1395T 21 0.363 32 7,5 10,6 20,11 NA 0/1 NA NA NA NA 1,20,0,11 C/T PANCANCER NA FALSE CACNA1D chr3:53724113:53724114:C:T SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 56617279 56617280 G C 110 110 1 MODERATE CCDC66 ENSG00000180376 C missense_variant Transcript ENST00000326595 protein_coding 14/18 ENST00000326595.11:c.1909G>C ENSP00000326050.7:p.E637Q ENSP00000326050.7 p.E637Q 2047 1909 637 E/Q Gaa/Caa COSV58303190 1 SNV HGNC HGNC:27709 1 P4 CCDS33770.2 ENSP00000326050 A2RUB6.113 UPI00017BCE7E A2RUB6-3 tolerated(0.14) possibly_damaging(0.783) PANTHER:PTHR22736&AlphaFold_DB_import:AF-A2RUB6-F1 1 1 16 NA NA PASS SITE 34,45|45,65 NA NA 1 93 20,20 153,172 60,60 26 1.75 NA 16.25 NA FALSE 6.00 93 NA NA NA FALSE NA NA 366.88 16 56617279 HCC1395_HCC1395T 0 0.988 110 0,29 0,49 0,81 NA 0/1 NA NA NA NA 0,0,45,65 G/C PANCANCER NA FALSE CCDC66_p.E637Q chr3:56617279:56617280:G:C SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 57899167 57899168 G T 12 53 0.226415094339623 MODIFIER SLMAP ENSG00000163681 T intron_variant Transcript ENST00000295951 protein_coding 15/21 ENST00000295951.7:c.1399+2235G>T NA 1 SNV HGNC HGNC:16643 5 A1 CCDS33774.1 ENSP00000295951 Q14BN4.136 UPI000022C0E3 Q14BN4-3 1 16 NA NA PASS SITE 85,23|11,1 NA NA 2 93 40,37 199,189 60,60 11 1.78 NA 17.75 NA FALSE 6.00 68 NA NA NA FALSE NA NA 41.21 16 57899167 HCC1395_HCC1395T 41 0.250 53 17,5 19,7 38,12 NA 0|1 0|1 57899167_G_T NA 57899167 34,7,11,1 G|T PANCANCER NA FALSE SLMAP chr3:57899167:57899168:G:T SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 57899171 57899172 G T 12 56 0.214285714285714 MODIFIER SLMAP ENSG00000163681 T intron_variant Transcript ENST00000295951 protein_coding 15/21 ENST00000295951.7:c.1399+2239G>T NA 1 SNV HGNC HGNC:16643 5 A1 CCDS33774.1 ENSP00000295951 Q14BN4.136 UPI000022C0E3 Q14BN4-3 1 16 NA NA PASS SITE 88,25|11,1 NA NA 2 93 40,37 199,189 60,60 15 1.79 NA 17.75 NA FALSE 6.00 67 NA NA NA FALSE NA NA 40.83 16 57899171 HCC1395_HCC1395T 44 0.236 56 18,5 23,7 41,12 NA 0|1 0|1 57899167_G_T NA 57899167 37,7,11,1 G|T PANCANCER NA FALSE SLMAP chr3:57899171:57899172:G:T SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 58204923 58204924 T G 205 205 1 MODIFIER DNASE1L3 ENSG00000163687 G intron_variant Transcript ENST00000394549 protein_coding 3/7 ENST00000394549.7:c.321-42A>C NA -1 SNV HGNC HGNC:2959 YES NM_004944.4 1 P1 CCDS2886.1 ENSP00000378053 Q13609.196 A0A024R365.49 UPI0000129890 Q13609-1 1 16 NA NA PASS SITE 71,85|91,114 NA NA 1 93 20,20 154,165 60,60 36 2.02 NA 30.70 NA FALSE 6.00 93 NA NA NA FALSE NA NA 586.35 16 58204923 HCC1395_HCC1395T 0 0.993 205 0,61 0,65 0,134 NA 0/1 NA NA NA NA 0,0,91,114 T/G PANCANCER NA FALSE DNASE1L3 chr3:58204923:58204924:T:G SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 58210852 58210853 G C 50 50 1 MODERATE DNASE1L3 ENSG00000163687 C missense_variant Transcript ENST00000394549 protein_coding 1/8 ENST00000394549.7:c.55C>G ENSP00000378053.2:p.L19V ENSP00000378053.2 p.L19V 121 55 19 L/V Ctg/Gtg rs763778721&COSV59157725 -1 SNV HGNC HGNC:2959 YES NM_004944.4 1 P1 CCDS2886.1 ENSP00000378053 Q13609.196 A0A024R365.49 UPI0000129890 Q13609-1 1 tolerated(0.13) benign(0.374) AlphaFold_DB_import:AF-Q13609-F1&PIRSF:PIRSF000988&SMART:SM00476&Cleavage_site_(Signalp):SignalP-noTM&Low_complexity_(Seg):seg 3.583e-05 0 0 0 0 0.0002772 0 0.0004891 0 0.0004891 gnomADe_OTH 0&1 0&1 16 NA NA PASS SITE 33,42|15,35 NA NA 1 93 20,32 150,181 60,60 31 1.72 NA 15.65 NA FALSE 6.00 93 NA NA NA FALSE NA NA 165.00 16 58210852 HCC1395_HCC1395T 0 0.977 50 0,10 0,26 0,41 NA 0/1 NA NA NA NA 0,0,15,35 G/C PANCANCER NA FALSE DNASE1L3_p.L19V chr3:58210852:58210853:G:C SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 64650461 64650462 C A 24 24 1 MODIFIER ADAMTS9 ENSG00000163638 A intron_variant Transcript ENST00000295903 protein_coding 8/38 ENST00000295903.8:c.1379+556G>T NA -1 SNV HGNC HGNC:13202 1 CCDS82801.1 ENSP00000295903 Q9P2N4.197 UPI000004971A Q9P2N4-4 1 16 NA NA PASS SITE 12,12|10,14 NA NA 1 75 23,36 181,201 60,60 37 1.31 NA 5.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 86.81 16 64650461 HCC1395_HCC1395T 0 0.957 24 0,6 0,15 0,21 NA 0/1 NA NA NA NA 0,0,10,14 C/A PANCANCER NA FALSE ADAMTS9 chr3:64650461:64650462:C:A SNV 3:0 chr3:319825:68976478:3:0:1 NA NA 0.96 +chr3 77647668 77647669 CTTGTGACATTTTCCCATGGGTTTCCTACACAATCTTAAATTTTA C 121 121 1 MODIFIER ROBO2 ENSG00000185008 - downstream_gene_variant Transcript ENST00000332191 protein_coding NA 553 1 deletion HGNC HGNC:10250 5 A1 CCDS93318.1 ENSP00000327536 F8W703.79 UPI00020E31F9 1 16 NA NA PASS SITE 206,191|75,46 NA NA 1 93 20,39 173,226 60,60 36 2.42 NA 77.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 541.84 16 77647668 HCC1395_HCC1395T 0 0.991 121 0,38 0,47 0,114 NA 0/1 NA NA NA NA 0,0,75,46 CTTGTGACATTTTCCCATGGGTTTCCTACACAATCTTAAATTTTA/C PANCANCER TRUE FALSE ROBO2 chr3:77647668:77647669:CTTGTGACATTTTCCCATGGGTTTCCTACACAATCTTAAATTTTA:C indel 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 100401698 100401699 C T 76 76 1 MODIFIER TOMM70 ENSG00000154174 T upstream_gene_variant Transcript ENST00000284320 protein_coding NA 609 -1 SNV HGNC HGNC:11985 YES NM_014820.5 1 P1 CCDS33807.1 ENSP00000284320 O94826.195 UPI0000000C55 16 NA NA PASS SITE 48,41|42,34 NA NA 1 93 20,20 180,170 60,60 38 1.81 NA 18.87 NA FALSE 6.00 93 NA NA NA FALSE NA NA 233.49 16 100401698 HCC1395_HCC1395T 0 0.982 76 0,22 0,29 0,53 NA 0/1 NA NA NA NA 0,0,42,34 C/T PANCANCER NA FALSE TOMM70 chr3:100401698:100401699:C:T SNV 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 108050741 108050742 C A 3 11 0.272727272727273 MODIFIER CD47 ENSG00000196776 A intron_variant Transcript ENST00000355354 protein_coding 8/8 ENST00000355354.13:c.909+1198G>T NA -1 SNV HGNC HGNC:1682 1 A1 CCDS43125.1 ENSP00000347512 Q08722.197 UPI000002A5FE Q08722-3 16 NA NA PASS SITE 21,4|2,2 NA NA 1 41 38,20 191,116 60,60 39 1.10 NA 3.82 NA FALSE 6.00 5 NA NA NA FALSE NA NA 7.10 16 108050741 HCC1395_HCC1395T 8 0.197 11 3,0 3,1 7,1 NA 0/1 NA NA NA NA 7,1,1,2 C/A PANCANCER NA FALSE CD47 chr3:108050741:108050742:C:A SNV 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 109337335 109337337 A AT 14 24 0.583333333333333 MODIFIER DPPA4 ENSG00000121570 T intron_variant Transcript ENST00000335658 protein_coding 1/6 ENST00000335658.7:c.54+128_54+129insA NA -1 insertion HGNC HGNC:19200 YES NM_018189.4 1 P1 CCDS33814.1 ENSP00000335306 Q7L190.132 UPI000022C153 16 NA NA PASS SITE 25,5|12,2 NA NA 1 30 35,39 186,186 60,60 24 1.23 NA 4.78 NA FALSE 6.00 93 NA NA NA FALSE NA NA 24.83 16 109337335 HCC1395_HCC1395T 10 0.567 24 2,6 6,6 9,12 NA 0/1 NA NA NA NA 9,1,12,2 A/AT PANCANCER NA FALSE DPPA4 chr3:109337335:109337337:A:AT indel 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 113890853 113890854 C T 12 19 0.631578947368421 MODIFIER GRAMD1C ENSG00000178075 T intron_variant Transcript ENST00000358160 protein_coding 6/17 ENST00000358160.9:c.540+8021C>T NA 1 SNV HGNC HGNC:25252 YES NM_017577.5 1 P1 CCDS33826.1 ENSP00000350881 Q8IYS0.136 UPI00001AF15F Q8IYS0-1 16 NA NA PASS SITE 2,17|1,11 NA NA 1 29 41,34 200,197 60,60 11 1.04 NA 3.01 NA FALSE 6.00 58 NA NA NA FALSE NA NA 34.75 16 113890853 HCC1395_HCC1395T 7 0.600 19 2,3 4,4 7,11 NA 0/1 NA NA NA NA 0,7,1,11 C/T PANCANCER NA FALSE GRAMD1C chr3:113890853:113890854:C:T SNV 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 116086277 116086278 A G 14 62 0.225806451612903 MODIFIER LSAMP ENSG00000185565 G intron_variant Transcript ENST00000333617 protein_coding 2/8 ENST00000333617.8:c.340+47T>C NA -1 cds_start_NF SNV HGNC HGNC:6705 2 ENSP00000328455 H3BLU2.66 UPI0001B797FE 16 NA NA PASS SITE 87,38|8,6 NA NA 1 93 30,20 180,128 60,60 27 1.77 NA 17.15 NA FALSE 6.00 51 NA NA NA FALSE NA NA 29.70 16 116086277 HCC1395_HCC1395T 48 0.204 62 11,4 27,5 38,9 NA 0/1 NA NA NA NA 35,13,8,6 A/G PANCANCER NA FALSE LSAMP chr3:116086277:116086278:A:G SNV 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 121473195 121473196 G C 9 20 0.45 MODIFIER POLQ ENSG00000051341 C intron_variant Transcript ENST00000264233 protein_coding 21/29 ENST00000264233.6:c.6543+155C>G NA -1 SNV HGNC HGNC:9186 YES NM_199420.4 1 P1 CCDS33833.1 ENSP00000264233 O75417.162 UPI0000D61B5F O75417-1 1 16 NA NA PASS SITE 34,1|9,0 NA NA 1 71 41,40 196,197 60,60 13 1.40 NA 7.22 NA FALSE 6.00 68 NA NA NA FALSE NA NA 32.14 16 121473195 HCC1395_HCC1395T 11 0.476 20 4,3 6,6 10,9 NA 0/1 NA NA NA NA 10,1,9,0 G/C PANCANCER TRUE FALSE POLQ chr3:121473195:121473196:G:C SNV 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 121697677 121697678 G C 87 87 1 MODERATE GOLGB1 ENSG00000173230 C missense_variant Transcript ENST00000340645 protein_coding 13/22 ENST00000340645.10:c.2831C>G ENSP00000341848.5:p.A944G ENSP00000341848.5 p.A944G 2969 2831 944 A/G gCa/gGa COSV61472359 -1 SNV HGNC HGNC:4429 1 A2 CCDS3004.1 ENSP00000341848 Q14789.187 UPI000013F0A1 Q14789-1 tolerated(0.33) benign(0.003) Coiled-coils_(Ncoils):Coil&PANTHER:PTHR18887 1 1 16 NA NA PASS SITE 73,77|36,51 NA NA 1 93 20,20 164,173 60,60 31 2.02 NA 31.30 NA FALSE 6.00 93 NA NA NA FALSE NA NA 291.56 16 121697677 HCC1395_HCC1395T 0 0.985 87 0,21 0,37 0,65 NA 0/1 NA NA NA NA 0,0,36,51 G/C PANCANCER NA FALSE GOLGB1_p.A944G chr3:121697677:121697678:G:C SNV 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 122615322 122615323 T G 142 144 0.986111111111111 MODIFIER PARP15 ENSG00000173200 G upstream_gene_variant Transcript ENST00000310366 protein_coding NA 293 1 SNV HGNC HGNC:26876 1 CCDS3016.1 ENSP00000308436 Q460N3.143 UPI0000073F40 Q460N3-2 16 NA NA PASS SITE 113,70|86,56 NA NA 1 93 20,20 156,156 60,60 27 2.08 NA 36.12 NA FALSE 6.00 93 NA NA NA FALSE NA NA 436.74 16 122615322 HCC1395_HCC1395T 2 0.980 144 1,28 0,63 1,97 NA 0/1 NA NA NA NA 1,1,86,56 T/G PANCANCER NA FALSE PARP15 chr3:122615322:122615323:T:G SNV 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 122927971 122927972 G C 51 52 0.980769230769231 MODERATE SEMA5B ENSG00000082684 C missense_variant Transcript ENST00000195173 protein_coding 7/22 ENST00000195173.8:c.495C>G ENSP00000195173.5:p.I165M ENSP00000195173.5 p.I165M 894 495 165 I/M atC/atG COSV52110638 -1 SNV HGNC HGNC:10737 5 CCDS74995.1 ENSP00000195173 C9JKR3.95 UPI0002065013 deleterious_low_confidence(0.03) probably_damaging(0.924) PROSITE_profiles:PS51004&CDD:cd11264&PANTHER:PTHR11036&Gene3D:2.130.10.10&SMART:SM00630&Superfamily:SSF101912&AlphaFold_DB_import:AF-C9JKR3-F1 1 1 16 NA NA PASS SITE 40,46|23,28 NA NA 1 93 20,20 160,158 60,60 35 1.76 NA 16.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 153.17 16 122927971 HCC1395_HCC1395T 1 0.947 52 0,11 1,19 1,35 NA 0/1 NA NA NA NA 0,1,23,28 G/C PANCANCER NA FALSE SEMA5B_p.I165M chr3:122927971:122927972:G:C SNV 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 126498142 126498143 G A 13 28 0.464285714285714 LOW UROC1 ENSG00000159650 A synonymous_variant Transcript ENST00000290868 protein_coding 14/20 ENST00000290868.7:c.1347C>T ENSP00000290868.2:p.F449= ENSP00000290868.2 p.F449= 1401 1347 449 F ttC/ttT -1 SNV HGNC HGNC:26444 YES NM_144639.3 1 P1 CCDS3038.1 ENSP00000290868 Q96N76.154 UPI000012CEC2 Q96N76-1 1 Gene3D:3.40.1770.10&AlphaFold_DB_import:AF-Q96N76-F1&HAMAP:MF_00577&Pfam:PF17392&PIRSF:PIRSF001423&PANTHER:PTHR12216&Superfamily:SSF111326 16 NA NA PASS SITE 30,42|4,9 NA NA 1 93 20,20 141,181 60,60 37 1.57 NA 10.74 NA FALSE 6.00 58 NA NA NA FALSE NA NA 34.87 16 126498142 HCC1395_HCC1395T 15 0.476 28 4,5 2,3 10,9 NA 0/1 NA NA NA NA 6,9,4,9 G/A PANCANCER NA FALSE UROC1_p.F449= chr3:126498142:126498143:G:A SNV 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 126656127 126656128 G A 23 50 0.46 MODIFIER NUP210P1 ENSG00000198284 A upstream_gene_variant Transcript ENST00000504322 transcribed_processed_pseudogene NA 4482 1 SNV HGNC HGNC:27399 YES 16 NA NA PASS SITE 50,62|11,12 NA NA 1 93 20,20 165,129 60,60 31 1.74 NA 15.95 NA FALSE 6.00 70 NA NA NA FALSE NA NA 45.54 16 126656127 HCC1395_HCC1395T 27 0.406 50 8,5 9,6 18,12 NA 0/1 NA NA NA NA 11,16,11,12 G/A PANCANCER NA FALSE NUP210P1 chr3:126656127:126656128:G:A SNV 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 127621319 127621320 A G 12 12 1 MODIFIER MCM2 ENSG00000073111 G intron_variant Transcript ENST00000265056 protein_coding 15/15 ENST00000265056.12:c.2604+91A>G NA 1 SNV HGNC HGNC:6944 YES NM_004526.4 1 P1 CCDS3043.1 ENSP00000265056 P49736.232 UPI00001A3E4E 1 16 NA NA PASS SITE 1,13|0,12 NA NA 1 69 38,40 202,237 60,60 21 1.17 NA 3.91 NA FALSE 6.00 93 NA NA NA FALSE NA NA 51.89 16 127621319 HCC1395_HCC1395T 0 0.930 12 0,4 0,8 0,12 NA 0/1 NA NA NA NA 0,0,0,12 A/G PANCANCER NA FALSE MCM2 chr3:127621319:127621320:A:G SNV 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 127986757 127986758 G A 18 18 1 MODIFIER KBTBD12 ENSG00000187715 A 3_prime_UTR_variant Transcript ENST00000343941 protein_coding 5/5 ENST00000343941.4:c.*2479G>A NA 3216 1 SNV HGNC HGNC:25731 2 ENSP00000345478 Q3ZCT8.130 UPI00001C0F70 Q3ZCT8-2 16 NA NA PASS SITE 12,5|15,3 NA NA 1 83 20,35 174,215 60,60 17 1.15 NA 3.91 NA FALSE 6.00 88 NA NA NA FALSE NA NA 60.68 16 127986757 HCC1395_HCC1395T 0 0.941 18 0,3 0,12 0,15 NA 0/1 NA NA NA NA 0,0,15,3 G/A PANCANCER NA FALSE KBTBD12 chr3:127986757:127986758:G:A SNV 2:0 chr3:68987527:128909090:2:0:1 TRUE NA 0.96 +chr3 128967818 128967819 G A 14 58 0.241379310344828 MODIFIER CFAP92 ENSG00000114656 A 3_prime_UTR_variant Transcript ENST00000265068 protein_coding 8/8 ENST00000265068.9:c.*3407C>T NA 4805 -1 SNV HGNC HGNC:29231 1 A2 CCDS46905.1 ENSP00000265068 Q9ULG3.119 UPI00001C1DE3 Q9ULG3-1 16 NA NA PASS SITE 57,29|8,6 NA NA 1 93 20,20 165,155 60,60 29 1.46 NA 8.43 NA FALSE 6.00 44 NA NA NA FALSE NA NA 27.76 16 128967818 HCC1395_HCC1395T 44 0.214 58 12,3 19,5 32,8 NA 0/1 NA NA NA NA 29,15,8,6 G/A PANCANCER NA FALSE CFAP92 chr3:128967818:128967819:G:A SNV 4:0 chr3:128932693:142689764:4:0:1 NA NA 0.96 +chr3 129561740 129561741 G A 75 220 0.340909090909091 MODIFIER PLXND1 ENSG00000004399 A intron_variant Transcript ENST00000324093 protein_coding 28/35 ENST00000324093.9:c.4930-31C>T NA rs1360093005 -1 SNV HGNC HGNC:9107 YES NM_015103.3 1 P1 CCDS33854.1 ENSP00000317128 Q9Y4D7.179 UPI00003671AD Q9Y4D7-1 1 0 0 0 0 0 0 0 0 0 0 gnomADe_AFR&gnomADe_AMR&gnomADe_ASJ&gnomADe_EAS&gnomADe_FIN&gnomADe_NFE&gnomADe_OTH&gnomADe_SAS 16 NA NA PASS SITE 119,186|29,46 NA NA 1 93 20,20 146,152 60,60 21 2.07 NA 33.97 NA FALSE 6.00 93 NA NA NA FALSE NA NA 175.44 16 129561740 HCC1395_HCC1395T 145 0.344 220 27,18 47,19 105,55 NA 0/1 NA NA NA NA 58,87,29,46 G/A PANCANCER NA FALSE PLXND1 chr3:129561740:129561741:G:A SNV 4:0 chr3:128932693:142689764:4:0:1 NA NA 0.96 +chr3 129654769 129654770 C A 4 22 0.181818181818182 MODIFIER TMCC1 ENSG00000172765 A intron_variant Transcript ENST00000393238 protein_coding 6/6 ENST00000393238.8:c.1647+199G>T NA -1 SNV HGNC HGNC:29116 YES NM_001017395.5 1 P3 CCDS33855.1 ENSP00000376930 O94876.151 UPI0000197B80 O94876-1 16 NA NA PASS SITE 27,0|4,0 NA NA 1 36 40,38 235,280 60,60 49 1.000 NA 2.71 NA FALSE 6.00 13 NA NA NA FALSE NA NA 11.87 16 129654769 HCC1395_HCC1395T 18 0.208 22 4,1 14,3 18,4 NA 0/1 NA NA NA NA 18,0,4,0 C/A PANCANCER NA FALSE TMCC1 chr3:129654769:129654770:C:A SNV 4:0 chr3:128932693:142689764:4:0:1 NA NA 0.96 +chr3 130409353 130409354 G T 138 309 0.446601941747573 MODERATE COL6A5 ENSG00000172752 T missense_variant&NMD_transcript_variant Transcript ENST00000312481 nonsense_mediated_decay 18/42 ENST00000312481.11:c.4507G>T ENSP00000309762.7:p.G1503W ENSP00000309762.7 p.G1503W 5001 4507 1503 G/W Ggg/Tgg 1 SNV HGNC HGNC:26674 1 ENSP00000309762 A8TX70.122 UPI00015E564F A8TX70-1 deleterious(0) probably_damaging(1) AlphaFold_DB_import:AF-A8TX70-F1 16 NA NA PASS SITE 178,166|71,67 NA NA 1 93 20,20 167,165 60,60 23 2.09 NA 36.64 NA FALSE 6.00 93 NA NA NA FALSE NA NA 356.63 16 130409353 HCC1395_HCC1395T 171 0.438 309 40,36 72,60 126,98 NA 0/1 NA NA NA NA 87,84,71,67 G/T PANCANCER NA FALSE COL6A5_p.G1503W chr3:130409353:130409354:G:T SNV 4:0 chr3:128932693:142689764:4:0:1 NA NA 0.96 +chr3 132505476 132505477 A G 5 14 0.357142857142857 MODIFIER DNAJC13 ENSG00000138246 G intron_variant Transcript ENST00000260818 protein_coding 42/55 ENST00000260818.11:c.4998+61A>G NA 1 SNV HGNC HGNC:30343 YES NM_015268.4 1 P1 CCDS33857.1 ENSP00000260818 O75165.178 UPI000022C1FD 1 16 NA NA PASS SITE 12,18|1,4 NA NA 1 46 20,41 206,217 60,60 49 1.20 NA 4.52 NA FALSE 6.00 39 NA NA NA FALSE NA NA 17.64 16 132505476 HCC1395_HCC1395T 9 0.429 14 1,3 6,2 7,5 NA 0/1 NA NA NA NA 4,5,1,4 A/G PANCANCER NA FALSE DNAJC13 chr3:132505476:132505477:A:G SNV 4:0 chr3:128932693:142689764:4:0:1 NA NA 0.96 +chr3 135259630 135259631 GCTCCTGAGT G 118 402 0.293532338308458 MODIFIER EPHB1 ENSG00000154928 - 3_prime_UTR_variant Transcript ENST00000398015 protein_coding 16/16 ENST00000398015.8:c.*515_*523del NA 3838-3846 1 deletion HGNC HGNC:3392 YES NM_004441.5 1 P1 CCDS46921.1 ENSP00000381097 P54762.222 UPI000012A07E P54762-1 4 16 NA NA PASS SITE 315,189|69,49 NA NA 1 93 20,20 163,172 60,60 30 2.19 NA 44.32 NA FALSE 6.00 93 NA NA NA FALSE NA NA 454.80 16 135259630 HCC1395_HCC1395T 284 0.297 402 60,27 101,42 194,81 NA 0/1 NA NA NA NA 179,105,69,49 GCTCCTGAGT/G PANCANCER NA FALSE EPHB1 chr3:135259630:135259631:GCTCCTGAGT:G indel 4:0 chr3:128932693:142689764:4:0:1 NA NA 0.96 +chr3 136261756 136261757 ATCAGCCTATTAAATATCTGGTCCTT A 12 49 0.244897959183673 MODIFIER PCCB ENSG00000114054 - intron_variant Transcript ENST00000251654 protein_coding 4/14 ENST00000251654.9:c.430-194_430-170del NA 1 deletion HGNC HGNC:8654 YES NM_000532.5 1 P2 CCDS3089.1 ENSP00000251654 P05166.210 UPI000006FE6C P05166-1 1 1 16 NA NA PASS SITE 52,31|7,5 NA NA 1 82 20,28 160,191 60,60 37 1.48 NA 8.73 NA FALSE 6.00 93 NA NA NA FALSE NA NA 45.41 16 136261756 HCC1395_HCC1395T 37 0.251 49 7,2 8,5 26,8 NA 0/1 NA NA NA NA 24,13,7,5 ATCAGCCTATTAAATATCTGGTCCTT/A PANCANCER NA FALSE PCCB chr3:136261756:136261757:ATCAGCCTATTAAATATCTGGTCCTT:A indel 4:0 chr3:128932693:142689764:4:0:1 NA NA 0.96 +chr3 138318345 138318346 G C 3 14 0.214285714285714 MODIFIER NME9 ENSG00000181322 C intron_variant Transcript ENST00000317876 protein_coding 2/8 ENST00000317876.8:c.130-126C>G NA -1 SNV HGNC HGNC:21343 5 CCDS3099.1 ENSP00000321929 Q86XW9.150 UPI0000073EC5 Q86XW9-2 16 NA NA PASS SITE 0,22|0,3 NA NA 1 38 40,37 242,223 60,60 47 1.09 NA 3.31 NA FALSE 6.00 44 NA NA NA FALSE NA NA 7.70 16 138318345 HCC1395_HCC1395T 11 0.248 14 1,2 10,1 11,3 NA 0/1 NA NA NA NA 0,11,0,3 G/C PANCANCER NA FALSE NME9 chr3:138318345:138318346:G:C SNV 4:0 chr3:128932693:142689764:4:0:1 NA NA 0.96 +chr3 142807736 142807737 G A 66 176 0.375 MODIFIER TRPC1 ENSG00000144935 A 3_prime_UTR_variant Transcript ENST00000273482 protein_coding 12/12 ENST00000273482.10:c.*1501G>A NA 4172 rs1259979320 1 SNV HGNC HGNC:12333 1 CCDS3126.1 ENSP00000273482 P48995.194 UPI000002B61B P48995-2 6.576e-06 0 0 0 0 0 0 0 1.47e-05 0 0 1.47e-05 gnomADg_NFE 16 NA NA PASS SITE 149,88|43,23 NA NA 1 93 20,20 174,162 60,60 26 1.95 NA 26.74 NA FALSE 6.00 38 NA NA NA FALSE NA NA 160.19 16 142807736 HCC1395_HCC1395T 110 0.386 176 21,8 50,37 72,45 NA 0/1 NA NA NA NA 67,43,43,23 G/A PANCANCER NA FALSE TRPC1 chr3:142807736:142807737:G:A SNV 3:0 chr3:142694565:146102897:3:0:1 NA NA 0.96 +chr3 155935224 155935225 C A 25 25 1 MODIFIER GMPS ENSG00000163655 A intron_variant Transcript ENST00000295920 protein_coding 12/13 ENST00000295920.7:c.1510+178C>A NA 1 SNV HGNC HGNC:4378 2 ENSP00000295920 P49915.213 UPI0001B79651 P49915-2 1 16 NA NA PASS SITE 1,12|0,25 NA NA 1 93 40,35 232,240 60,60 28 1.11 NA 3.61 NA FALSE 6.00 93 NA NA NA FALSE NA NA 95.13 16 155935224 HCC1395_HCC1395T 0 0.964 25 0,7 0,18 0,25 NA 0/1 NA NA NA NA 0,0,0,25 C/A PANCANCER NA FALSE GMPS chr3:155935224:155935225:C:A SNV 4:0 chr3:146106691:164171596:4:0:1 NA NA 0.96 +chr3 167441859 167441860 C A 2 6 0.333333333333333 MODIFIER SERPINI2 ENSG00000114204 A downstream_gene_variant Transcript ENST00000264677 protein_coding NA 74 -1 SNV HGNC HGNC:8945 YES NM_006217.6 1 P1 CCDS3200.1 ENSP00000264677 O75830.183 UPI0000135E26 16 NA NA PASS SITE 13,8|1,1 NA NA 1 49 39,33 231,160 60,60 18 1.23 NA 4.82 NA FALSE 6.00 6 NA NA NA FALSE NA NA 5.98 16 167441859 HCC1395_HCC1395T 4 0.286 6 1,0 3,1 4,1 NA 0/1 NA NA NA NA 2,2,1,1 C/A PANCANCER NA FALSE SERPINI2 chr3:167441859:167441860:C:A SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 171085022 171085023 C G 25 56 0.446428571428571 MODIFIER TNIK ENSG00000154310 G intron_variant Transcript ENST00000284483 protein_coding 24/31 ENST00000284483.12:c.2974+96G>C NA -1 SNV HGNC HGNC:30765 1 P4 CCDS54679.1 ENSP00000284483 Q9UKE5.208 UPI000002B587 Q9UKE5-4 1 16 NA NA PASS SITE 47,23|19,6 NA NA 1 82 20,38 181,158 60,60 23 1.47 NA 8.43 NA FALSE 6.00 81 NA NA NA FALSE NA NA 74.27 16 171085022 HCC1395_HCC1395T 31 0.455 56 7,6 16,13 23,19 NA 0/1 NA NA NA NA 21,10,19,6 C/G PANCANCER NA FALSE TNIK chr3:171085022:171085023:C:G SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 171138370 171138371 G T 21 174 0.120689655172414 MODERATE TNIK ENSG00000154310 T missense_variant Transcript ENST00000284483 protein_coding 15/32 ENST00000284483.12:c.1429C>A ENSP00000284483.8:p.R477S ENSP00000284483.8 p.R477S 1429 1429 477 R/S Cgc/Agc COSV52698702 -1 SNV HGNC HGNC:30765 1 P4 CCDS54679.1 ENSP00000284483 Q9UKE5.208 UPI000002B587 Q9UKE5-4 1 deleterious_low_confidence(0) unknown(0) Low_complexity_(Seg):seg&PANTHER:PTHR47096&Coiled-coils_(Ncoils):Coil&AlphaFold_DB_import:AF-Q9UKE5-F1 1 1 16 NA NA PASS SITE 133,151|8,13 NA NA 1 93 20,20 165,171 60,60 38 1.95 NA 26.09 NA FALSE 6.00 58 NA NA NA FALSE NA NA 46.59 16 171138370 HCC1395_HCC1395T 153 0.138 174 37,4 53,10 99,15 NA 0/1 NA NA NA NA 71,82,8,13 G/T PANCANCER NA FALSE TNIK_p.R477S chr3:171138370:171138371:G:T SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 172353067 172353068 C T 47 179 0.262569832402235 MODERATE FNDC3B ENSG00000075420 T missense_variant Transcript ENST00000336824 protein_coding 22/26 ENST00000336824.8:c.2779C>T ENSP00000338523.4:p.P927S ENSP00000338523.4 p.P927S 2878 2779 927 P/S Cca/Tca COSV61051399 1 SNV HGNC HGNC:24670 1 P1 CCDS3217.1 ENSP00000338523 Q53EP0.142 UPI00001AE8B2 Q53EP0-1 deleterious(0) Gene3D:2.60.40.10&AlphaFold_DB_import:AF-Q53EP0-F1&Pfam:PF00041&PROSITE_profiles:PS50853&PANTHER:PTHR24099&SMART:SM00060&Superfamily:SSF49265&CDD:cd00063 1 1 16 NA NA PASS SITE 114,143|20,27 NA NA 1 93 20,20 158,158 60,60 33 1.91 NA 24.38 NA FALSE 6.00 93 NA NA NA FALSE NA NA 108.22 16 172353067 HCC1395_HCC1395T 132 0.267 179 28,16 49,14 84,30 NA 0/1 NA NA NA NA 62,70,20,27 C/T PANCANCER NA FALSE FNDC3B_p.P927S chr3:172353067:172353068:C:T SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 179563151 179563152 T A 50 308 0.162337662337662 MODIFIER ACTL6A ENSG00000136518 A 5_prime_UTR_variant Transcript ENST00000392662 protein_coding 1/14 ENST00000392662.5:c.-116T>A NA 232 1 SNV HGNC HGNC:24124 2 CCDS43174.1 ENSP00000376430 O96019.216 UPI000002A4A6 O96019-2 1 16 NA NA PASS SITE 153,325|16,34 NA NA 1 93 20,20 155,153 60,60 30 2.18 NA 44.45 NA FALSE 6.00 93 NA NA NA FALSE NA NA 104.54 16 179563151 HCC1395_HCC1395T 258 0.160 308 64,13 71,11 183,34 NA 0/1 NA NA NA NA 78,180,16,34 T/A PANCANCER NA FALSE ACTL6A chr3:179563151:179563152:T:A SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 182919139 182919140 C G 54 180 0.3 MODIFIER ATP11B ENSG00000058063 G 3_prime_UTR_variant Transcript ENST00000323116 protein_coding 30/30 ENST00000323116.10:c.*1035C>G NA 4825 1 SNV HGNC HGNC:13553 YES NM_014616.3 2 P1 CCDS33896.1 ENSP00000321195 Q9Y2G3.186 UPI000004124E 16 NA NA PASS SITE 153,80|37,17 NA NA 1 93 20,38 164,187 60,60 34 1.90 NA 23.48 NA FALSE 6.00 93 NA NA NA FALSE NA NA 151.61 16 182919139 HCC1395_HCC1395T 126 0.317 180 27,17 64,23 91,42 NA 0/1 NA NA NA NA 83,43,37,17 C/G PANCANCER NA FALSE ATP11B chr3:182919139:182919140:C:G SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 182944703 182944704 T C 7 333 0.021021021021021 MODIFIER DCUN1D1 ENSG00000043093 C 3_prime_UTR_variant Transcript ENST00000292782 protein_coding 7/7 ENST00000292782.9:c.*391A>G NA 1220 -1 SNV HGNC HGNC:18184 YES NM_020640.4 1 P1 CCDS3240.1 ENSP00000292782 Q96GG9.164 UPI0000073D68 16 NA NA PASS SITE 180,294|2,5 NA NA 1 93 20,20 175,179 60,60 56 2.02 NA 31.00 NA FALSE 6.00 27 NA NA NA FALSE NA NA 9.44 16 182944703 HCC1395_HCC1395T 326 0.026 333 84,3 126,2 225,5 NA 0/1 NA NA NA NA 122,204,2,5 T/C PANCANCER NA FALSE DCUN1D1 chr3:182944703:182944704:T:C SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 183071212 183071213 T G 37 330 0.112121212121212 MODERATE MCCC1 ENSG00000078070 G missense_variant&splice_region_variant Transcript ENST00000265594 protein_coding 6/19 ENST00000265594.9:c.637A>C ENSP00000265594.4:p.K213Q ENSP00000265594.4 p.K213Q 693 637 213 K/Q Aaa/Caa -1 SNV HGNC HGNC:6936 YES NM_020166.5 1 P1 CCDS3241.1 ENSP00000265594 Q96RQ3.217 A0A0S2Z693.39 UPI000013D646 1 deleterious(0.01) possibly_damaging(0.894) Gene3D:3.30.470.20&AlphaFold_DB_import:AF-Q96RQ3-F1&Pfam:PF02786&PROSITE_profiles:PS50975&PROSITE_profiles:PS50979&PANTHER:PTHR18866&Superfamily:SSF56059 16 NA NA PASS SITE 270,220|23,14 NA NA 1 93 20,20 164,165 60,60 32 2.14 NA 40.29 NA FALSE 6.00 66 NA NA NA FALSE NA NA 77.28 16 183071212 HCC1395_HCC1395T 293 0.113 330 67,7 124,17 199,25 NA 0/1 NA NA NA NA 162,131,23,14 T/G PANCANCER NA FALSE MCCC1_p.K213Q chr3:183071212:183071213:T:G SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 183179683 183179684 G A 71 148 0.47972972972973 MODERATE MCF2L2 ENSG00000053524 A missense_variant Transcript ENST00000328913 protein_coding 29/30 ENST00000328913.8:c.3115C>T ENSP00000328118.3:p.L1039F ENSP00000328118.3 p.L1039F 3757 3115 1039 L/F Ctt/Ttt rs1560327395&COSV61063157 -1 SNV HGNC HGNC:30319 YES NM_015078.4 5 P4 CCDS3243.1 ENSP00000328118 Q86YR7.145 UPI00001A962F Q86YR7-1 deleterious_low_confidence(0) probably_damaging(0.934) AlphaFold_DB_import:AF-Q86YR7-F1&PANTHER:PTHR22826&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite 3.981e-06 6.169e-05 0 0 0 0 0 0 0 6.169e-05 gnomADe_AFR 0&1 0&1 16 NA NA PASS SITE 95,128|28,43 NA NA 1 93 20,20 157,161 60,60 38 1.99 NA 29.19 NA FALSE 6.00 93 NA NA NA FALSE NA NA 178.90 16 183179683 HCC1395_HCC1395T 77 0.475 148 16,15 32,29 51,46 NA 0/1 NA NA NA NA 32,45,28,43 G/A PANCANCER NA FALSE MCF2L2_p.L1039F chr3:183179683:183179684:G:A SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 183179827 183179828 G A 3 4 0.75 MODIFIER MCF2L2 ENSG00000053524 A intron_variant Transcript ENST00000328913 protein_coding 28/29 ENST00000328913.8:c.3106-135C>T NA rs1432342171 -1 SNV HGNC HGNC:30319 YES NM_015078.4 5 P4 CCDS3243.1 ENSP00000328118 Q86YR7.145 UPI00001A962F Q86YR7-1 16 NA NA PASS SITE 5,11|0,3 NA NA 1 45 38,37 201,244 60,60 12 1.19 NA 4.21 NA FALSE 6.00 38 NA NA NA FALSE NA NA 11.23 16 183179827 HCC1395_HCC1395T 1 0.667 4 0,2 1,1 1,3 NA 0/1 NA NA NA NA 1,0,0,3 G/A PANCANCER NA FALSE MCF2L2 chr3:183179827:183179828:G:A SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 183228132 183228133 G C 60 210 0.285714285714286 MODIFIER MCF2L2 ENSG00000053524 C intron_variant Transcript ENST00000328913 protein_coding 18/29 ENST00000328913.8:c.2115+165C>G NA COSV105823631 -1 SNV HGNC HGNC:30319 YES NM_015078.4 5 P4 CCDS3243.1 ENSP00000328118 Q86YR7.145 UPI00001A962F Q86YR7-1 1 1 16 NA NA PASS SITE 196,92|43,17 NA NA 1 93 20,20 174,175 60,60 26 1.99 NA 28.25 NA FALSE 6.00 93 NA NA NA FALSE NA NA 149.52 16 183228132 HCC1395_HCC1395T 150 0.286 210 34,13 73,27 109,44 NA 0/1 NA NA NA NA 109,41,43,17 G/C PANCANCER NA FALSE MCF2L2 chr3:183228132:183228133:G:C SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 184136964 184136965 C A 101 435 0.232183908045977 MODIFIER EIF2B5 ENSG00000145191 A 3_prime_UTR_variant Transcript ENST00000432569 protein_coding 2/2 ENST00000432569.2:c.*224C>A NA 569 1 SNV HGNC HGNC:3261 1 ENSP00000414775 C9JRD9.86 UPI0000160BBE 1 16 NA NA PASS SITE 305,354|44,57 NA NA 1 93 20,33 177,186 60,60 27 2.38 NA 70.09 NA FALSE 6.00 93 NA NA NA FALSE NA NA 258.61 16 184136964 HCC1395_HCC1395T 334 0.250 435 73,27 152,47 239,79 NA 0/1 NA NA NA NA 152,182,44,57 C/A PANCANCER NA FALSE EIF2B5 chr3:184136964:184136965:C:A SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 184141962 184141963 G C 52 209 0.248803827751196 MODIFIER EIF2B5 ENSG00000145191 C downstream_gene_variant Transcript ENST00000432569 protein_coding NA rs1172545279 4982 1 SNV HGNC HGNC:3261 1 ENSP00000414775 C9JRD9.86 UPI0000160BBE 1 3.977e-06 0 0 0 0 0 8.791e-06 0 0 8.791e-06 gnomADe_NFE 16 NA NA PASS SITE 186,116|31,21 NA NA 1 93 20,20 161,150 60,60 31 1.98 NA 28.60 NA FALSE 6.00 93 NA NA NA FALSE NA NA 122.59 16 184141962 HCC1395_HCC1395T 157 0.252 209 40,15 60,19 106,35 NA 0/1 NA NA NA NA 98,59,31,21 G/C PANCANCER NA FALSE EIF2B5 chr3:184141962:184141963:G:C SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 184357968 184357969 G A 51 148 0.344594594594595 LOW CLCN2 ENSG00000114859 A synonymous_variant Transcript ENST00000265593 protein_coding 5/24 ENST00000265593.9:c.609C>T ENSP00000265593.4:p.G203= ENSP00000265593.4 p.G203= 735 609 203 G ggC/ggT -1 SNV HGNC HGNC:2020 YES NM_004366.6 1 P1 CCDS3263.1 ENSP00000265593 P51788.199 UPI000013D645 P51788-1 1 Gene3D:1.10.3080.10&AlphaFold_DB_import:AF-P51788-F1&Pfam:PF00654&Prints:PR00762&PANTHER:PTHR45720&Superfamily:SSF81340&CDD:cd03683 16 NA NA PASS SITE 104,125|30,22 NA NA 1 93 34,32 174,180 60,60 29 0.607 NA 26.12 NA FALSE 6.00 93 NA NA NA FALSE NA NA 132.58 16 184357968 HCC1395_HCC1395T 97 0.342 148 32,19 44,17 78,40 NA 0/1 NA NA NA NA 45,52,30,21 G/A PANCANCER NA FALSE CLCN2_p.G203= chr3:184357968:184357969:G:A SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 185473801 185473802 C G 3 6 0.5 MODIFIER MAP3K13 ENSG00000073803 G intron_variant Transcript ENST00000265026 protein_coding 11/13 ENST00000265026.8:c.2430+40C>G NA 1 SNV HGNC HGNC:6852 YES NM_004721.5 1 P1 CCDS3270.1 ENSP00000265026 O43283.180 UPI000006CF91 O43283-1 1 16 NA NA PASS SITE 0,20|0,3 NA NA 1 52 41,40 255,200 60,60 19 1.26 NA 5.12 NA FALSE 6.00 28 NA NA NA FALSE NA NA 11.19 16 185473801 HCC1395_HCC1395T 3 0.500 6 1,0 2,3 3,3 NA 0/1 NA NA NA NA 0,3,0,3 C/G PANCANCER NA FALSE MAP3K13 chr3:185473801:185473802:C:G SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 186164998 186164999 C T 101 150 0.673333333333333 MODERATE DGKG ENSG00000058866 T missense_variant Transcript ENST00000265022 protein_coding 23/25 ENST00000265022.8:c.2116G>A ENSP00000265022.3:p.E706K ENSP00000265022.3 p.E706K 2653 2116 706 E/K Gaa/Aaa COSV53974492 -1 SNV HGNC HGNC:2853 YES NM_001346.3 1 P1 CCDS3274.1 ENSP00000265022 P49619.202 UPI000013D5AB P49619-1 deleterious_low_confidence(0) probably_damaging(1) PANTHER:PTHR11255&Pfam:PF00609&Gene3D:2.60.200.40&SMART:SM00045&Superfamily:SSF111331&AlphaFold_DB_import:AF-P49619-F1 1 1 16 NA NA PASS SITE 89,75|56,46 NA NA 1 93 20,20 166,168 60,60 36 1.92 NA 24.03 NA FALSE 6.00 93 NA NA NA FALSE NA NA 286.07 16 186164998 HCC1395_HCC1395T 49 0.676 150 13,21 20,47 34,72 NA 0/1 NA NA NA NA 26,23,56,45 C/T PANCANCER NA FALSE DGKG_p.E706K chr3:186164998:186164999:C:T SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 186571977 186571978 C T 2 5 0.4 MODIFIER DNAJB11 ENSG00000090520 T intron_variant Transcript ENST00000265028 protein_coding 1/9 ENST00000265028.8:c.69-118C>T NA 1 SNV HGNC HGNC:14889 YES NM_016306.6 1 P1 CCDS3277.1 ENSP00000265028 Q9UBS4.198 UPI0000001BF7 1 16 NA NA PASS SITE 11,0|2,0 NA NA 1 25 39,37 239,289 60,60 9 0.954 NA 2.41 NA FALSE 6.00 33 NA NA NA FALSE NA NA 6.48 16 186571977 HCC1395_HCC1395T 3 0.429 5 1,1 2,1 3,2 NA 0/1 NA NA NA NA 3,0,2,0 C/T PANCANCER NA FALSE DNAJB11 chr3:186571977:186571978:C:T SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 187223151 187223152 T C 55 165 0.333333333333333 LOW MASP1 ENSG00000127241 C synonymous_variant Transcript ENST00000337774 protein_coding 14/16 ENST00000337774.10:c.1785A>G ENSP00000336792.5:p.Q595= ENSP00000336792.5 p.Q595= 1890 1785 595 Q caA/caG COSV61825703 -1 SNV HGNC HGNC:6901 NM_001879.6 1 P1 CCDS33907.1 ENSP00000336792 P48740.208 UPI0000161FB8 P48740-1 1 Gene3D:2.40.10.10&PDB-ENSP_mappings:3gov.B&PDB-ENSP_mappings:4djz.B&PDB-ENSP_mappings:4djz.D&PDB-ENSP_mappings:4igd.A&PDB-ENSP_mappings:4iw4.E&PDB-ENSP_mappings:4iw4.F&PDB-ENSP_mappings:4kkd.A&PDB-ENSP_mappings:4kkd.B&PDB-ENSP_mappings:7arx.B&PDB-ENSP_mappings:7pqo.A&PDB-ENSP_mappings:7pqo.B&PDB-ENSP_mappings:7pqo.C&AlphaFold_DB_import:AF-P48740-F1&Pfam:PF00089&PIRSF:PIRSF001155&PROSITE_profiles:PS50240&PANTHER:PTHR24255&SMART:SM00020&Superfamily:SSF50494&CDD:cd00190 1 1 16 NA NA PASS SITE 137,101|33,22 NA NA 1 93 20,20 158,162 60,60 29 1.92 NA 24.68 NA FALSE 6.00 84 NA NA NA FALSE NA NA 133.03 16 187223151 HCC1395_HCC1395T 110 0.335 165 21,12 51,24 74,37 NA 0/1 NA NA NA NA 65,45,33,22 T/C PANCANCER NA FALSE MASP1_p.Q595= chr3:187223151:187223152:T:C SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 187229706 187229707 C T 42 98 0.428571428571429 MODIFIER MASP1 ENSG00000127241 T downstream_gene_variant Transcript ENST00000296280 protein_coding NA 4376 -1 SNV HGNC HGNC:6901 YES NM_139125.4 1 CCDS33908.1 ENSP00000296280 P48740.208 UPI000007256E P48740-2 1 16 NA NA PASS SITE 87,81|20,22 NA NA 1 93 20,20 156,154 60,60 30 1.89 NA 22.87 NA FALSE 6.00 84 NA NA NA FALSE NA NA 104.35 16 187229706 HCC1395_HCC1395T 56 0.424 98 17,9 17,18 37,27 NA 0/1 NA NA NA NA 31,25,20,22 C/T PANCANCER NA FALSE MASP1 chr3:187229706:187229707:C:T SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 189738589 189738590 A G 48 156 0.307692307692308 MODIFIER TP63 ENSG00000073282 G intron_variant Transcript ENST00000264731 protein_coding 2/13 ENST00000264731.8:c.192-53A>G NA 1 SNV HGNC HGNC:15979 YES NM_003722.5 1 A1 CCDS3293.1 ENSP00000264731 Q9H3D4.213 A0A0S2Z4N5.52 UPI0000073CF2 Q9H3D4-1 1 16 NA NA PASS SITE 169,65|32,16 NA NA 1 93 20,20 168,173 60,60 28 1.97 NA 27.64 NA FALSE 6.00 93 NA NA NA FALSE NA NA 121.02 16 189738589 HCC1395_HCC1395T 108 0.293 156 25,14 54,19 81,33 NA 0/1 NA NA NA NA 79,29,32,16 A/G PANCANCER TRUE FALSE TP63 chr3:189738589:189738590:A:G SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 190322527 190322528 C T 12 28 0.428571428571429 MODIFIER CLDN1 ENSG00000163347 T upstream_gene_variant Transcript ENST00000295522 protein_coding NA 81 -1 SNV HGNC HGNC:2032 YES NM_021101.5 1 P1 CCDS3295.1 ENSP00000295522 O95832.187 A5JSJ9.132 UPI0000046D1E 1 16 NA NA PASS SITE 1,34|2,10 NA NA 1 60 41,32 195,181 60,60 19 1.31 NA 5.72 NA FALSE 6.00 74 NA NA NA FALSE NA NA 32.32 16 190322527 HCC1395_HCC1395T 16 0.407 28 7,5 5,5 15,10 NA 0/1 NA NA NA NA 1,15,2,10 C/T PANCANCER NA FALSE CLDN1 chr3:190322527:190322528:C:T SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 190657232 190657233 C T 24 76 0.315789473684211 MODIFIER IL1RAP ENSG00000196083 T 3_prime_UTR_variant Transcript ENST00000317757 protein_coding 12/12 ENST00000317757.8:c.*625C>T NA 2912 COSV58513432 1 SNV HGNC HGNC:5995 1 CCDS54696.1 ENSP00000314807 Q9NPH3.184 UPI000020A9C1 Q9NPH3-5 1 1 16 NA NA PASS SITE 56,69|6,18 NA NA 1 93 39,34 215,217 60,60 24 1.86 NA 21.07 NA FALSE 6.00 93 NA NA NA FALSE NA NA 72.75 16 190657232 HCC1395_HCC1395T 52 0.320 76 18,10 33,10 52,24 NA 0/1 NA NA NA NA 16,36,6,18 C/T PANCANCER NA FALSE IL1RAP chr3:190657232:190657233:C:T SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 194137671 194137672 TCTGGCCCGCAGCTGCGCTGAGCACAGACCCAA T 116 116 1 HIGH HES1 ENSG00000114315 - splice_acceptor_variant&coding_sequence_variant&intron_variant Transcript ENST00000232424 protein_coding 4/4 3/3 ENST00000232424.4:c.293-11_313del NA ?-546 ?-313 ?-105 1 deletion HGNC HGNC:5192 YES NM_005524.4 1 P1 CCDS3305.1 ENSP00000232424 Q14469.200 UPI0000037B01 16 NA NA PASS SITE 193,108|76,40 NA NA 1 93 20,37 162,202 60,60 35 2.30 NA 59.38 NA FALSE 6.00 93 NA NA NA FALSE NA NA 520.74 16 194137671 HCC1395_HCC1395T 0 0.989 116 0,37 0,41 0,86 NA 0/1 NA NA NA NA 0,0,76,40 TCTGGCCCGCAGCTGCGCTGAGCACAGACCCAA/T PANCANCER NA FALSE HES1 chr3:194137671:194137672:TCTGGCCCGCAGCTGCGCTGAGCACAGACCCAA:T indel 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 195269953 195269954 G C 5 5 1 MODIFIER XXYLT1 ENSG00000173950 C intron_variant Transcript ENST00000310380 protein_coding 1/3 ENST00000310380.11:c.504+602C>G NA -1 SNV HGNC HGNC:26639 YES NM_152531.5 1 P1 CCDS43188.1 ENSP00000309640 Q8NBI6.138 UPI000003B10F Q8NBI6-1 16 NA NA PASS SITE 8,2|5,0 NA NA 1 35 28,40 165,252 60,60 26 0.954 NA 2.41 NA FALSE 6.00 68 NA NA NA FALSE NA NA 20.93 16 195269953 HCC1395_HCC1395T 0 0.857 5 0,4 0,1 0,5 NA 0/1 NA NA NA NA 0,0,5,0 G/C PANCANCER NA FALSE XXYLT1 chr3:195269953:195269954:G:C SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr3 195781344 195781345 A G 23 1342 0.0171385991058122 MODIFIER MUC4 ENSG00000145113 G upstream_gene_variant Transcript ENST00000308466 nonsense_mediated_decay NA rs201939860&COSV57766939 2534 -1 cds_start_NF SNV HGNC HGNC:7514 1 ENSP00000310528 H7BXN7.59 UPI000198CBE1 1 0.0244 0.0303 0.0144 0.0258 0.0189 0.0276 0.001291 0.002921 0.00248 0.001255 0.004244 0.0004789 0.0008115 0.003061 0.0007903 0.009457 0.0152 0.009677 0.00897 0.00936 0.01574 0.004975 0.01724 0.006967 0.007732 0.006 0.0303 AFR 0&1 0&1 16 NA NA PASS SITE 1039,1084|15,13 NA NA 1 93 20,20 158,130 60,53 5 0.683 NA 150.05 NA FALSE 2.18 28 NA NA NA FALSE NA NA 26.88 16 195781344 HCC1395_HCC1395T 1319 0.014 1342 302,3 483,4 896,16 NA 0/1 NA NA NA NA 646,673,12,11 A/G PANCANCER NA FALSE MUC4 chr3:195781344:195781345:A:G SNV 2:0 chr3:164982210:198038561:2:0:1 TRUE NA 0.96 +chr4 373602 373603 C T 108 265 0.407547169811321 MODERATE ZNF141 ENSG00000131127 T missense_variant Transcript ENST00000240499 protein_coding 4/4 ENST00000240499.8:c.1165C>T ENSP00000240499.7:p.H389Y ENSP00000240499.7 p.H389Y 1335 1165 389 H/Y Cat/Tat rs544940326&COSV53657295&COSV53657658 1 SNV HGNC HGNC:12926 YES NM_003441.4 1 P1 CCDS33931.1 ENSP00000240499 Q15928.184 UPI000013C2FB 1 deleterious_low_confidence(0) probably_damaging(0.999) Gene3D:3.30.160.60&AlphaFold_DB_import:AF-Q15928-F1&Pfam:PF13912&PROSITE_patterns:PS00028&PROSITE_profiles:PS50157&PANTHER:PTHR24390&SMART:SM00355&Superfamily:SSF57667 0.0002 0 0 0 0.001 0 6.573e-06 0 0 0 0 0 9.422e-05 0 0 0 0 0.001 EUR 0&1&1 0&1&1 17 NA NA PASS SITE 264,240|49,59 NA NA 1 93 20,20 160,179 60,60 35 2.36 NA 68.28 NA FALSE 6.00 93 NA NA NA FALSE NA NA 290.37 17 373602 HCC1395_HCC1395T 157 0.445 265 44,24 49,49 100,80 NA 0/1 NA NA NA NA 78,79,49,59 C/T PANCANCER NA FALSE ZNF141_p.H389Y chr4:373602:373603:C:T SNV 2:0 chr4:271152:15007608:2:0:1 TRUE NA 0.96 +chr4 383242 383243 G A 18 18 1 MODIFIER ZNF141 ENSG00000131127 A 3_prime_UTR_variant Transcript ENST00000240499 protein_coding 4/4 ENST00000240499.8:c.*9380G>A NA 10975 1 SNV HGNC HGNC:12926 YES NM_003441.4 1 P1 CCDS33931.1 ENSP00000240499 Q15928.184 UPI000013C2FB 1 17 NA NA PASS SITE 0,15|0,18 NA NA 1 93 40,38 220,233 60,60 28 1.22 NA 4.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 73.90 17 383242 HCC1395_HCC1395T 0 0.950 18 0,7 0,8 0,18 NA 0/1 NA NA NA NA 0,0,0,18 G/A PANCANCER NA FALSE ZNF141 chr4:383242:383243:G:A SNV 2:0 chr4:271152:15007608:2:0:1 TRUE NA 0.96 +chr4 442068 442069 T C 38 133 0.285714285714286 MODERATE ZNF721 ENSG00000182903 C missense_variant Transcript ENST00000338977 protein_coding 2/2 ENST00000338977.5:c.2363A>G ENSP00000340524.5:p.K788R ENSP00000340524.5 p.K788R 2412 2363 788 K/R aAg/aGg -1 SNV HGNC HGNC:29425 2 ENSP00000340524 Q8TF20.147 UPI000020B95C Q8TF20-1 tolerated(0.17) possibly_damaging(0.897) Gene3D:3.30.160.60&AlphaFold_DB_import:AF-Q8TF20-F1&Pfam:PF00096&PROSITE_patterns:PS00028&PROSITE_profiles:PS50157&SMART:SM00355&Superfamily:SSF57667 17 NA NA PASS SITE 99,142|14,24 NA NA 1 93 20,34 166,189 60,60 25 2.05 NA 33.02 NA FALSE 6.00 93 NA NA NA FALSE NA NA 102.61 17 442068 HCC1395_HCC1395T 95 0.306 133 30,14 33,14 67,29 NA 0/1 NA NA NA NA 40,55,14,24 T/C PANCANCER NA FALSE ZNF721_p.K788R chr4:442068:442069:T:C SNV 2:0 chr4:271152:15007608:2:0:1 TRUE NA 0.96 +chr4 730855 730856 C T 8 17 0.470588235294118 MODIFIER PCGF3 ENSG00000185619 T intron_variant Transcript ENST00000362003 protein_coding 2/10 ENST00000362003.10:c.-150-115C>T NA 1 SNV HGNC HGNC:10066 YES NM_006315.7 5 P1 CCDS3339.2 ENSP00000354724 Q3KNV8.143 UPI00001A9628 Q3KNV8-1 17 NA NA PASS SITE 20,9|6,2 NA NA 1 52 39,39 197,194 60,60 36 1.28 NA 5.42 NA FALSE 6.00 22 NA NA NA FALSE NA NA 25.92 17 730855 HCC1395_HCC1395T 9 0.471 17 1,1 7,6 8,7 NA 0/1 NA NA NA NA 6,3,6,2 C/T PANCANCER NA FALSE PCGF3 chr4:730855:730856:C:T SNV 2:0 chr4:271152:15007608:2:0:1 TRUE NA 0.96 +chr4 1740801 1740802 G A 38 39 0.974358974358974 MODIFIER TACC3 ENSG00000013810 A intron_variant Transcript ENST00000313288 protein_coding 12/15 ENST00000313288.9:c.2063-25G>A NA rs1324989952 1 SNV HGNC HGNC:11524 YES NM_006342.3 1 P2 CCDS3352.1 ENSP00000326550 Q9Y6A5.184 UPI0000136869 1 6.571e-06 2.414e-05 0 0 0 0 0 0 0 0 0 2.414e-05 gnomADg_AFR 17 NA NA PASS SITE 41,15|28,10 NA NA 1 93 20,31 156,170 60,60 20 1.63 NA 12.34 NA FALSE 4.61 93 NA NA NA FALSE NA NA 119.46 17 1740801 HCC1395_HCC1395T 1 0.938 39 1,9 0,20 1,29 NA 0/1 NA NA NA NA 1,0,28,10 G/A PANCANCER NA FALSE TACC3 chr4:1740801:1740802:G:A SNV 2:0 chr4:271152:15007608:2:0:1 TRUE NA 0.96 +chr4 1823175 1823176 G C 104 104 1 MODIFIER LETM1 ENSG00000168924 C intron_variant Transcript ENST00000302787 protein_coding 8/13 ENST00000302787.3:c.1333-44C>G NA -1 SNV HGNC HGNC:6556 YES NM_012318.3 1 P1 CCDS3355.1 ENSP00000305653 O95202.185 UPI0000073989 O95202-1 1 17 NA NA PASS SITE 72,100|47,57 NA NA 1 93 20,20 158,161 60,60 38 2.06 NA 34.27 NA FALSE 6.00 93 NA NA NA FALSE NA NA 294.88 17 1823175 HCC1395_HCC1395T 0 0.985 104 0,23 0,38 0,63 NA 0/1 NA NA NA NA 0,0,47,57 G/C PANCANCER NA FALSE LETM1 chr4:1823175:1823176:G:C SNV 2:0 chr4:271152:15007608:2:0:1 TRUE NA 0.96 +chr4 2009336 2009337 C T 98 98 1 MODIFIER NELFA ENSG00000185049 T upstream_gene_variant Transcript ENST00000333877 nonsense_mediated_decay NA rs1039420997 153 -1 SNV HGNC HGNC:12768 2 ENSP00000330311 F8W954.55 UPI000198C7E6 1 17 NA NA PASS SITE 71,90|41,57 NA NA 1 93 20,20 157,163 60,60 37 2.04 NA 32.80 NA FALSE 6.00 93 NA NA NA FALSE NA NA 309.06 17 2009336 HCC1395_HCC1395T 0 0.986 98 0,31 0,33 0,70 NA 0/1 NA NA NA NA 0,0,41,57 C/T PANCANCER NA FALSE NELFA chr4:2009336:2009337:C:T SNV 2:0 chr4:271152:15007608:2:0:1 TRUE NA 0.96 +chr4 3417681 3417682 G A 32 32 1 MODIFIER RGS12 ENSG00000159788 A intron_variant Transcript ENST00000336727 protein_coding 9/17 ENST00000336727.8:c.2761+140G>A NA 1 SNV HGNC HGNC:9994 YES NM_001394154.1 1 P3 CCDS3366.1 ENSP00000338509 O14924.196 UPI0000133830 O14924-1 17 NA NA PASS SITE 14,42|7,25 NA NA 1 93 37,36 176,171 60,60 16 1.68 NA 13.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 110.32 17 3417681 HCC1395_HCC1395T 0 0.964 32 0,11 0,13 0,25 NA 0/1 NA NA NA NA 0,0,7,25 G/A PANCANCER NA FALSE RGS12 chr4:3417681:3417682:G:A SNV 2:0 chr4:271152:15007608:2:0:1 TRUE NA 0.96 +chr4 5745424 5745425 G C 25 25 1 MODIFIER EVC ENSG00000072840 C intron_variant Transcript ENST00000264956 protein_coding 7/20 ENST00000264956.11:c.939+83G>C NA 1 SNV HGNC HGNC:3497 YES NM_153717.3 1 P1 CCDS3383.1 ENSP00000264956 P57679.158 UPI000012A2A5 1 17 NA NA PASS SITE 4,18|4,21 NA NA 1 93 37,41 210,185 60,60 21 1.29 NA 5.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 92.50 17 5745424 HCC1395_HCC1395T 0 0.958 25 0,6 0,11 0,21 NA 0/1 NA NA NA NA 0,0,4,21 G/C PANCANCER NA FALSE EVC chr4:5745424:5745425:G:C SNV 2:0 chr4:271152:15007608:2:0:1 TRUE NA 0.96 +chr4 5757954 5757956 GG AT 106 106 1 MODIFIER EVC ENSG00000072840 AT intron_variant Transcript ENST00000264956 protein_coding 11/20 ENST00000264956.11:c.1563+1592_1563+1593delinsAT NA 1 substitution HGNC HGNC:3497 YES NM_153717.3 1 P1 CCDS3383.1 ENSP00000264956 P57679.158 UPI000012A2A5 1 17 NA NA PASS SITE 68,54|66,40 NA NA 1 93 20,26 148,182 60,60 35 1.90 NA 23.47 NA FALSE 6.00 93 NA NA NA FALSE NA NA 464.43 17 5757954 HCC1395_HCC1395T 0 0.988 106 0,33 0,41 0,80 NA 0/1 NA NA NA NA 0,0,66,40 GG/AT PANCANCER NA FALSE EVC chr4:5757954:5757956:GG:AT indel 2:0 chr4:271152:15007608:2:0:1 TRUE NA 0.96 +chr4 5988667 5988668 T A 10 56 0.178571428571429 MODERATE C4orf50 ENSG00000181215 A missense_variant Transcript ENST00000531445 protein_coding 28/34 ENST00000531445.3:c.3379A>T ENSP00000437121.2:p.M1127L ENSP00000437121.2 p.M1127L 8775 3379 1127 M/L Atg/Ttg -1 SNV HGNC HGNC:33766 YES 5 P1 CCDS93473.1 ENSP00000437121 E9PNW5.57 UPI0007E52BBE tolerated(0.55) benign(0.003) PANTHER:PTHR36866 17 NA NA PASS SITE 75,46|8,2 NA NA 1 93 20,34 164,159 60,60 37 1.75 NA 15.91 NA FALSE 6.00 61 NA NA NA FALSE NA NA 25.08 17 5988667 HCC1395_HCC1395T 46 0.205 56 15,4 19,4 34,8 NA 0/1 NA NA NA NA 32,14,8,2 T/A PANCANCER NA FALSE C4orf50_p.M1127L chr4:5988667:5988668:T:A SNV 2:0 chr4:271152:15007608:2:0:1 TRUE NA 0.96 +chr4 7938998 7938999 C G 71 71 1 MODIFIER AFAP1 ENSG00000196526 G intron_variant Transcript ENST00000358461 protein_coding 1/16 ENST00000358461.6:c.-3+658G>C NA -1 SNV HGNC HGNC:24017 2 P1 CCDS3397.1 ENSP00000351245 Q8N556.149 UPI0000233618 Q8N556-1 17 NA NA PASS SITE 75,42|41,30 NA NA 2 93 20,20 172,161 60,60 37 1.94 NA 25.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 206.72 17 7938998 HCC1395_HCC1395T 0 0.980 71 0,14 0,28 0,48 NA 0/1 NA NA NA NA 0,0,41,30 C/G PANCANCER NA FALSE AFAP1 chr4:7938998:7938999:C:G SNV 2:0 chr4:271152:15007608:2:0:1 TRUE NA 0.96 +chr4 10440270 10440271 G C 23 162 0.141975308641975 MODIFIER ZNF518B ENSG00000178163 C 3_prime_UTR_variant Transcript ENST00000326756 protein_coding 3/3 ENST00000326756.4:c.*2834C>G NA 6564 -1 SNV HGNC HGNC:29365 YES NM_053042.3 3 P1 CCDS33960.1 ENSP00000317614 Q9C0D4.140 UPI0000160B97 17 NA NA PASS SITE 110,201|10,13 NA NA 2 93 20,20 174,154 60,60 24 2.10 NA 36.23 NA FALSE 6.00 89 NA NA NA FALSE NA NA 41.81 17 10440270 HCC1395_HCC1395T 139 0.131 162 23,6 35,7 108,16 NA 0/1 NA NA NA NA 44,95,10,13 G/C PANCANCER NA FALSE ZNF518B chr4:10440270:10440271:G:C SNV 2:0 chr4:271152:15007608:2:0:1 TRUE NA 0.96 +chr4 15519875 15519876 G C 12 12 1 MODIFIER CC2D2A ENSG00000048342 C intron_variant Transcript ENST00000389652 protein_coding 10/37 ENST00000389652.11:c.1149+3119G>C NA 1 SNV HGNC HGNC:29253 5 ENSP00000374303 A0A140T8Y7.30 UPI0016333B39 1 17 NA NA PASS SITE 11,16|5,7 NA NA 1 88 20,20 148,156 60,60 32 1.28 NA 5.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 32.63 17 15519875 HCC1395_HCC1395T 0 0.900 12 0,3 0,3 0,8 NA 0/1 NA NA NA NA 0,0,5,7 G/C PANCANCER NA FALSE CC2D2A chr4:15519875:15519876:G:C SNV 1:0 chr4:15040348:24091254:1:0:1 NA NA 0.96 +chr4 17781512 17781513 C G 38 38 1 MODIFIER FAM184B ENSG00000047662 G 5_prime_UTR_variant Transcript ENST00000265018 protein_coding 1/18 ENST00000265018.4:c.-213G>C NA 110 -1 SNV HGNC HGNC:29235 YES NM_015688.2 1 P1 CCDS47033.1 ENSP00000265018 Q9ULE4.125 UPI000020BD7C 17 NA NA PASS SITE 23,55|11,27 NA NA 1 93 31,28 168,175 60,60 37 1.79 NA 17.76 NA FALSE 6.00 93 NA NA NA FALSE NA NA 121.62 17 17781512 HCC1395_HCC1395T 0 0.966 38 0,11 0,13 0,27 NA 0/1 NA NA NA NA 0,0,11,27 C/G PANCANCER NA FALSE FAM184B chr4:17781512:17781513:C:G SNV 1:0 chr4:15040348:24091254:1:0:1 NA NA 0.96 +chr4 25405826 25405828 CT AA 2 4 0.5 MODIFIER ANAPC4 ENSG00000053900 AA intron_variant Transcript ENST00000315368 protein_coding 18/28 ENST00000315368.8:c.1317+207_1317+208delinsAA NA 1 substitution HGNC HGNC:19990 YES NM_013367.3 1 P4 CCDS3434.1 ENSP00000318775 Q9UJX5.183 UPI000013D583 Q9UJX5-1 17 NA NA PASS SITE 1,13|1,1 NA NA 1 36 40,20 229,130 60,60 11 1.11 NA 3.61 NA FALSE 6.00 18 NA NA NA FALSE NA NA 7.84 17 25405826 HCC1395_HCC1395T 2 0.394 4 1,1 1,0 2,1 NA 0/1 NA NA NA NA 0,2,1,1 CT/AA PANCANCER NA FALSE ANAPC4 chr4:25405826:25405828:CT:AA indel 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 25676653 25676654 C G 98 180 0.544444444444444 LOW SLC34A2 ENSG00000157765 G synonymous_variant Transcript ENST00000382051 protein_coding 13/13 ENST00000382051.8:c.1977C>G ENSP00000371483.3:p.V659= ENSP00000371483.3 p.V659= 2020 1977 659 V gtC/gtG 1 SNV HGNC HGNC:11020 YES NM_006424.3 1 P4 CCDS3435.1 ENSP00000371483 O95436.162 UPI000013DF24 O95436-1 1 AlphaFold_DB_import:AF-O95436-F1&PANTHER:PTHR10010 17 NA NA PASS SITE 143,140|51,47 NA NA 1 93 20,20 156,161 60,60 39 2.11 NA 37.87 NA FALSE 6.00 93 NA NA NA FALSE NA NA 271.08 17 25676653 HCC1395_HCC1395T 82 0.563 180 23,28 26,35 51,66 NA 0/1 NA NA NA NA 43,39,51,47 C/G PANCANCER TRUE FALSE SLC34A2_p.V659= chr4:25676653:25676654:C:G SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 25678192 25678193 A G 31 80 0.3875 MODIFIER SLC34A2 ENSG00000157765 G 3_prime_UTR_variant Transcript ENST00000382051 protein_coding 13/13 ENST00000382051.8:c.*1443A>G NA 3559 rs1263638181 1 SNV HGNC HGNC:11020 YES NM_006424.3 1 P4 CCDS3435.1 ENSP00000371483 O95436.162 UPI000013DF24 O95436-1 1 1.316e-05 0 0 0 0 0 0 0 2.942e-05 0 0 2.942e-05 gnomADg_NFE 17 NA NA PASS SITE 58,39|22,9 NA NA 1 93 20,20 176,167 60,60 46 1.56 NA 10.53 NA FALSE 6.00 58 NA NA NA FALSE NA NA 73.33 17 25678192 HCC1395_HCC1395T 49 0.387 80 13,6 22,15 35,22 NA 0/1 NA NA NA NA 28,21,22,9 A/G PANCANCER TRUE FALSE SLC34A2 chr4:25678192:25678193:A:G SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 25682035 25682036 C T 29 47 0.617021276595745 MODIFIER SLC34A2 ENSG00000157765 T downstream_gene_variant Transcript ENST00000382051 protein_coding NA 3287 1 SNV HGNC HGNC:11020 YES NM_006424.3 1 P4 CCDS3435.1 ENSP00000371483 O95436.162 UPI000013DF24 O95436-1 1 17 NA NA PASS SITE 8,45|4,25 NA NA 1 88 39,33 203,184 60,60 29 1.51 NA 9.03 NA FALSE 6.00 93 NA NA NA FALSE NA NA 85.44 17 25682035 HCC1395_HCC1395T 18 0.594 47 4,9 12,12 17,25 NA 0/1 NA NA NA NA 2,16,4,25 C/T PANCANCER TRUE FALSE SLC34A2 chr4:25682035:25682036:C:T SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 39454364 39454365 G A 3 6 0.5 MODIFIER KLB ENSG00000134962 A downstream_gene_variant Transcript ENST00000257408 protein_coding NA rs188042991 2831 1 SNV HGNC HGNC:15527 YES NM_175737.4 1 P1 CCDS3451.1 ENSP00000257408 Q86Z14.156 UPI000000D726 0.0002 0.0008 0 0 0 0 6.573e-06 0 0 0 0 0 0 0 1.47e-05 0 0 0.0008 AFR 17 NA NA PASS SITE 12,1|2,1 NA NA 1 30 33,38 257,258 60,60 24 1.04 NA 3.01 NA FALSE 6.00 29 NA NA NA FALSE NA NA 9.99 17 39454364 HCC1395_HCC1395T 3 0.500 6 1,1 2,2 3,3 NA 0/1 NA NA NA NA 3,0,2,1 G/A PANCANCER NA FALSE KLB chr4:39454364:39454365:G:A SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 40808809 40808810 A G 174 284 0.612676056338028 MODIFIER APBB2 ENSG00000163697 G downstream_gene_variant Transcript ENST00000295974 protein_coding NA rs1560568410 1218 -1 SNV HGNC HGNC:582 2 A1 CCDS54761.1 ENSP00000295974 Q92870.183 UPI000059675C Q92870-1 1.274e-05 0 8.099e-05 0 0 0 0 0 0 8.099e-05 gnomADe_AMR 17 NA NA PASS SITE 177,185|78,97 NA NA 1 93 20,20 157,165 60,60 28 2.25 NA 52.67 NA FALSE 6.00 93 NA NA NA FALSE NA NA 490.00 17 40808809 HCC1395_HCC1395T 110 0.609 284 37,58 34,52 74,116 NA 0/1 NA NA NA NA 51,59,78,96 A/G PANCANCER NA FALSE APBB2 chr4:40808809:40808810:A:G SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 41984552 41984553 TTAGAACTGG T 18 77 0.233766233766234 MODIFIER DCAF4L1 ENSG00000182308 - 3_prime_UTR_variant Transcript ENST00000333141 protein_coding 1/1 ENST00000333141.7:c.*1574_*1582del NA 2798-2806 1 deletion HGNC HGNC:27723 YES NM_001029955.4 P1 CCDS33978.1 ENSP00000327796 Q3SXM0.130 UPI0000160C25 4 17 NA NA PASS SITE 106,45|18,0 NA NA 1 93 29,38 182,207 60,60 35 1.83 NA 19.82 NA FALSE 6.00 93 NA NA NA FALSE NA NA 63.51 17 41984552 HCC1395_HCC1395T 59 0.276 77 20,3 26,15 49,18 NA 0/1 NA NA NA NA 42,17,18,0 TTAGAACTGG/T PANCANCER NA FALSE DCAF4L1 chr4:41984552:41984553:TTAGAACTGG:T indel 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 44707451 44707452 C G 25 69 0.36231884057971 MODIFIER GNPDA2 ENSG00000163281 G intron_variant Transcript ENST00000295448 protein_coding 6/6 ENST00000295448.8:c.769+301G>C NA -1 SNV HGNC HGNC:21526 YES NM_138335.3 1 P1 CCDS3469.1 ENSP00000295448 Q8TDQ7.153 A0A024R9X5.46 UPI000004D013 Q8TDQ7-1 17 NA NA PASS SITE 33,56|10,15 NA NA 1 92 20,20 157,154 60,60 25 1.49 NA 9.03 NA FALSE 6.00 93 NA NA NA FALSE NA NA 58.31 17 44707451 HCC1395_HCC1395T 44 0.348 69 9,7 19,7 29,15 NA 0/1 NA NA NA NA 16,28,10,15 C/G PANCANCER NA FALSE GNPDA2 chr4:44707451:44707452:C:G SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 46368552 46368553 A T 262 458 0.572052401746725 MODIFIER GABRA2 ENSG00000151834 T intron_variant Transcript ENST00000356504 protein_coding 2/8 ENST00000356504.5:c.187+17522T>A NA -1 SNV HGNC HGNC:4076 2 P2 CCDS3471.1 ENSP00000348897 P47869.199 A0A024R9X6.62 UPI000013DC88 P47869-1 1 17 NA NA PASS SITE 257,270|132,130 NA NA 1 93 20,32 170,171 60,60 26 2.38 NA 72.15 NA FALSE 6.00 93 NA NA NA FALSE NA NA 770.71 17 46368552 HCC1395_HCC1395T 196 0.587 458 59,71 72,113 140,199 NA 0/1 NA NA NA NA 99,97,132,130 A/T PANCANCER NA FALSE GABRA2 chr4:46368552:46368553:A:T SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 47624021 47624022 G A 22 79 0.278481012658228 MODIFIER CORIN ENSG00000145244 A intron_variant Transcript ENST00000273857 protein_coding 17/21 ENST00000273857.9:c.2316-73C>T NA -1 SNV HGNC HGNC:19012 YES NM_006587.4 1 P2 CCDS3477.1 ENSP00000273857 Q9Y5Q5.196 UPI0000168657 Q9Y5Q5-1 1 17 NA NA PASS SITE 47,63|11,11 NA NA 1 93 20,20 165,148 60,60 36 1.54 NA 10.23 NA FALSE 6.00 39 NA NA NA FALSE NA NA 47.16 17 47624021 HCC1395_HCC1395T 57 0.269 79 9,9 24,3 37,13 NA 0/1 NA NA NA NA 26,31,11,11 G/A PANCANCER NA FALSE CORIN chr4:47624021:47624022:G:A SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 47786565 47786566 CA C 10 21 0.476190476190476 MODIFIER CORIN ENSG00000145244 - intron_variant Transcript ENST00000273857 protein_coding 3/21 ENST00000273857.9:c.409+159del NA -1 deletion HGNC HGNC:19012 YES NM_006587.4 1 P2 CCDS3477.1 ENSP00000273857 Q9Y5Q5.196 UPI0000168657 Q9Y5Q5-1 1 17 NA NA PASS SITE 20,2|9,1 NA NA 1 18 38,39 205,225 60,60 17 1.08 NA 3.31 NA FALSE 6.00 93 3,2 A NA TRUE NA 93 27.84 17 47786565 HCC1395_HCC1395T 11 0.500 21 3,2 6,8 10,10 NA 0/1 NA NA NA NA 9,2,9,1 CA/C PANCANCER NA FALSE CORIN chr4:47786565:47786566:CA:C indel 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 51891744 51891746 T TA 20 48 0.416666666666667 LOW DCUN1D4 ENSG00000109184 A splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000334635 protein_coding 6/10 ENST00000334635.10:c.415-15dup NA 1 insertion HGNC HGNC:28998 YES NM_001040402.3 1 P1 CCDS33982.1 ENSP00000334625 Q92564.157 UPI00001C1E10 Q92564-1 1 17 NA NA PASS SITE 37,17|17,3 NA NA 1 50 32,34 190,171 60,60 21 1.38 NA 6.61 NA FALSE 6.00 93 1,2 A NA TRUE NA 93 51.98 17 51891744 HCC1395_HCC1395T 28 0.419 48 6,7 15,10 24,17 NA 0/1 NA NA NA NA 21,7,17,3 T/TA PANCANCER NA FALSE DCUN1D4 chr4:51891744:51891746:T:TA indel 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 52862472 52862473 C G 138 244 0.565573770491803 MODIFIER RASL11B ENSG00000128045 G 5_prime_UTR_variant Transcript ENST00000248706 protein_coding 1/4 ENST00000248706.5:c.-36C>G NA 156 rs775522886 1 SNV HGNC HGNC:23804 YES NM_023940.3 1 P1 CCDS3490.1 ENSP00000248706 Q9BPW5.165 UPI0000070B4C 1.811e-05 0.0003529 0 0 0 0 0 0 0 0.0001249 0.0004102 0 0.000131 0 0 0 0 0 0 0 0.0004102 gnomADg_AFR 17 NA NA PASS SITE 186,187|74,64 NA NA 1 93 20,20 162,161 60,60 28 2.24 NA 51.47 NA FALSE 4.31 93 NA NA NA FALSE NA NA 361.68 17 52862472 HCC1395_HCC1395T 106 0.565 244 29,50 33,34 69,90 NA 0/1 NA NA NA NA 52,54,74,64 C/G PANCANCER NA FALSE RASL11B chr4:52862472:52862473:C:G SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 54064732 54064733 G C 26 35 0.742857142857143 MODIFIER CHIC2 ENSG00000109220 C upstream_gene_variant Transcript ENST00000263921 protein_coding NA rs1220943041 127 -1 SNV HGNC HGNC:1935 YES NM_012110.4 1 P1 CCDS3493.1 ENSP00000263921 Q9UKJ5.148 UPI0000072E65 1 5.306e-05 2.427e-05 0 0.0003959 0 0 0 0 1.482e-05 0 0 0.0003959 gnomADg_AMR 17 NA NA PASS SITE 6,42|2,24 NA NA 1 93 40,34 186,194 60,60 25 1.55 NA 10.23 NA FALSE 4.61 93 NA NA NA FALSE NA NA 84.54 17 54064732 HCC1395_HCC1395T 9 0.714 35 4,7 3,15 9,24 NA 0/1 NA NA NA NA 0,9,2,24 G/C PANCANCER NA FALSE CHIC2 chr4:54064732:54064733:G:C SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 56312993 56312994 G C 21 34 0.617647058823529 MODIFIER CRACD ENSG00000109265 C intron_variant Transcript ENST00000264229 protein_coding 6/10 ENST00000264229.11:c.355-204G>C NA 1 SNV HGNC HGNC:29219 2 P4 CCDS43230.1 ENSP00000264229 Q6ZU35.132 UPI0000237309 17 NA NA PASS SITE 31,23|13,8 NA NA 1 73 20,20 166,157 60,60 39 1.42 NA 7.53 NA FALSE 6.00 78 NA NA NA FALSE NA NA 52.39 17 56312993 HCC1395_HCC1395T 13 0.622 34 3,4 4,8 8,14 NA 0/1 NA NA NA NA 7,6,13,8 G/C PANCANCER NA FALSE CRACD chr4:56312993:56312994:G:C SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 56436233 56436234 G A 64 168 0.380952380952381 MODIFIER PPAT ENSG00000128059 A upstream_gene_variant Transcript ENST00000264220 protein_coding NA 618 -1 SNV HGNC HGNC:9238 YES NM_002703.5 1 P1 CCDS3505.1 ENSP00000264220 Q06203.198 A8K4H7.124 UPI0000000C5A 17 NA NA PASS SITE 160,122|40,24 NA NA 1 93 20,20 161,170 60,60 29 2.10 NA 35.45 NA FALSE 6.00 93 NA NA NA FALSE NA NA 163.36 17 56436233 HCC1395_HCC1395T 104 0.385 168 27,16 40,27 72,45 NA 0/1 NA NA NA NA 60,44,40,24 G/A PANCANCER NA FALSE PPAT chr4:56436233:56436234:G:A SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 69200378 69200379 TG T 23 46 0.5 MODIFIER UGT2B11 ENSG00000213759 - 3_prime_UTR_variant Transcript ENST00000446444 protein_coding 6/6 ENST00000446444.2:c.*61del NA 1677 -1 deletion HGNC HGNC:12545 YES NM_001073.3 1 P1 CCDS3527.1 ENSP00000387683 O75310.168 UPI0000137A97 17 NA NA PASS SITE 59,15|22,1 NA NA 1 93 34,37 180,197 60,60 12 1.68 NA 13.22 NA FALSE 6.00 93 NA NA NA FALSE NA NA 74.90 17 69200378 HCC1395_HCC1395T 23 0.523 46 9,8 11,14 20,22 NA 0/1 NA NA NA NA 19,4,22,1 TG/T PANCANCER NA FALSE UGT2B11 chr4:69200378:69200379:TG:T indel 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 70482112 70482113 C T 115 356 0.323033707865169 MODIFIER MUC7 ENSG00000171195 T 3_prime_UTR_variant Transcript ENST00000304887 protein_coding 3/3 ENST00000304887.6:c.*234C>T NA 1478 1 SNV HGNC HGNC:7518 YES NM_152291.3 1 P1 CCDS3541.1 ENSP00000302021 Q8TAX7.148 UPI000013E9DD 1 17 NA NA PASS SITE 212,260|47,68 NA NA 1 93 20,20 164,174 60,60 31 2.22 NA 48.12 NA FALSE 6.00 93 NA NA NA FALSE NA NA 297.49 17 70482112 HCC1395_HCC1395T 241 0.331 356 44,36 107,39 167,82 NA 0/1 NA NA NA NA 104,137,47,68 C/T PANCANCER NA FALSE MUC7 chr4:70482112:70482113:C:T SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 70482617 70482618 G C 110 173 0.635838150289017 MODIFIER MUC7 ENSG00000171195 C 3_prime_UTR_variant Transcript ENST00000304887 protein_coding 3/3 ENST00000304887.6:c.*739G>C NA 1983 1 SNV HGNC HGNC:7518 YES NM_152291.3 1 P1 CCDS3541.1 ENSP00000302021 Q8TAX7.148 UPI000013E9DD 1 17 NA NA PASS SITE 69,136|38,72 NA NA 1 93 20,20 180,177 60,60 26 2.04 NA 31.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 311.58 17 70482617 HCC1395_HCC1395T 63 0.612 173 16,19 25,44 48,76 NA 0/1 NA NA NA NA 17,46,38,72 G/C PANCANCER NA FALSE MUC7 chr4:70482617:70482618:G:C SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 75793916 75793917 A C 40 100 0.4 MODIFIER USO1 ENSG00000138768 C intron_variant Transcript ENST00000264904 protein_coding 14/25 ENST00000264904.8:c.1464+15A>C NA 1 SNV HGNC HGNC:30904 2 A2 CCDS77929.1 ENSP00000264904 O60763.188 UPI0001D1479E O60763-2 17 NA NA PASS SITE 38,89|12,28 NA NA 1 93 20,20 176,155 60,60 29 1.69 NA 14.15 NA FALSE 6.00 93 NA NA NA FALSE NA NA 104.19 17 75793916 HCC1395_HCC1395T 60 0.382 100 21,13 19,15 46,28 NA 0/1 NA NA NA NA 16,44,12,28 A/C PANCANCER NA FALSE USO1 chr4:75793916:75793917:A:C SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 77772922 77772923 C G 13 34 0.382352941176471 MODIFIER CNOT6L ENSG00000138767 G intron_variant Transcript ENST00000504123 protein_coding 4/11 ENST00000504123.7:c.400+159G>C NA -1 SNV HGNC HGNC:18042 YES NM_144571.3 2 ENSP00000424896 Q96LI5.166 UPI0000E445DF Q96LI5-1 17 NA NA PASS SITE 31,18|8,5 NA NA 1 55 20,20 185,145 60,60 30 1.28 NA 5.42 NA FALSE 6.00 56 NA NA NA FALSE NA NA 30.56 17 77772922 HCC1395_HCC1395T 21 0.321 34 7,6 9,2 18,8 NA 0/1 NA NA NA NA 14,7,8,5 C/G PANCANCER NA FALSE CNOT6L chr4:77772922:77772923:C:G SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 80204238 80204239 T A 4 16 0.25 MODIFIER PRDM8 ENSG00000152784 A 3_prime_UTR_variant Transcript ENST00000339711 protein_coding 10/10 ENST00000339711.8:c.*706T>A NA 4007 1 SNV HGNC HGNC:13993 1 P1 CCDS43243.1 ENSP00000339764 Q9NQV8.173 A0A024RDC4.59 UPI0000422A1D Q9NQV8-1 1 17 NA NA PASS SITE 1,25|3,1 NA NA 1 45 35,34 229,123 60,60 12 1.20 NA 4.21 NA FALSE 6.00 13 NA NA NA FALSE NA NA 9.06 17 80204238 HCC1395_HCC1395T 12 0.217 16 4,0 8,2 12,3 NA 0/1 NA NA NA NA 1,11,3,1 T/A PANCANCER NA FALSE PRDM8 chr4:80204238:80204239:T:A SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 81457713 81457714 G A 22 25 0.88 MODIFIER RASGEF1B ENSG00000138670 A intron_variant Transcript ENST00000264400 protein_coding 2/13 ENST00000264400.7:c.178-92C>T NA -1 SNV HGNC HGNC:24881 YES NM_152545.3 2 P4 CCDS34022.1 ENSP00000264400 Q0VAM2.119 UPI0000044685 Q0VAM2-1 17 NA NA PASS SITE 0,22|0,22 NA NA 1 80 39,38 206,226 60,60 20 1.31 NA 5.72 NA FALSE 6.00 93 NA NA NA FALSE NA NA 86.21 17 81457713 HCC1395_HCC1395T 3 0.853 25 2,8 1,14 3,22 NA 0/1 NA NA NA NA 0,3,0,22 G/A PANCANCER NA FALSE RASGEF1B chr4:81457713:81457714:G:A SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 86769842 86769843 T C 22 76 0.289473684210526 LOW PTPN13 ENSG00000163629 C synonymous_variant Transcript ENST00000316707 protein_coding 26/45 ENST00000316707.10:c.3990T>C ENSP00000322675.6:p.L1330= ENSP00000322675.6 p.L1330= 4053 3990 1330 L ctT/ctC COSV57420597 1 SNV HGNC HGNC:9646 1 A2 CCDS47096.1 ENSP00000322675 Q12923.229 UPI000002B1D5 Q12923-2 1 PROSITE_profiles:PS50106&CDD:cd00992&Pfam:PF00595&Gene3D:2.30.42.10&PIRSF:PIRSF000933&SMART:SM00228&Superfamily:SSF50156&AlphaFold_DB_import:AF-Q12923-F1 1 1 17 NA NA PASS SITE 80,30|16,6 NA NA 1 93 20,35 173,183 60,60 39 1.64 NA 12.59 NA FALSE 6.00 91 NA NA NA FALSE NA NA 60.01 17 86769842 HCC1395_HCC1395T 54 0.300 76 16,8 25,9 41,17 NA 0/1 NA NA NA NA 40,14,16,6 T/C PANCANCER NA FALSE PTPN13_p.L1330= chr4:86769842:86769843:T:C SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 87007234 87007235 G T 53 205 0.258536585365854 MODIFIER AFF1 ENSG00000172493 T 5_prime_UTR_variant Transcript ENST00000307808 protein_coding 1/20 ENST00000307808.10:c.-174G>T NA 247 1 SNV HGNC HGNC:7135 1 A2 CCDS3616.1 ENSP00000305689 P51825.181 UPI0000125658 P51825-1 1 17 NA NA PASS SITE 205,212|24,29 NA NA 1 93 20,20 163,158 60,60 25 2.28 NA 55.55 NA FALSE 6.00 84 NA NA NA FALSE NA NA 134.39 17 87007234 HCC1395_HCC1395T 152 0.296 205 41,22 42,13 94,39 NA 0/1 NA NA NA NA 75,77,24,29 G/T PANCANCER NA FALSE AFF1 chr4:87007234:87007235:G:T SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 87529167 87529168 C G 25 46 0.543478260869565 MODIFIER SPARCL1 ENSG00000152583 G 5_prime_UTR_variant Transcript ENST00000282470 protein_coding 1/11 ENST00000282470.11:c.-134G>C NA 210 -1 SNV HGNC HGNC:11220 YES NM_004684.6 1 P2 CCDS3622.1 ENSP00000282470 Q14515.186 UPI000013DCE3 Q14515-1 17 NA NA PASS SITE 50,31|16,9 NA NA 1 93 20,20 162,156 60,60 33 1.59 NA 11.14 NA FALSE 6.00 93 NA NA NA FALSE NA NA 63.66 17 87529167 HCC1395_HCC1395T 21 0.512 46 6,8 10,7 16,17 NA 0/1 NA NA NA NA 14,7,16,9 C/G PANCANCER NA FALSE SPARCL1 chr4:87529167:87529168:C:G SNV 2:1 chr4:24806696:87981540:2:1:1 TRUE NA 0.96 +chr4 94291222 94291223 G A 6 18 0.333333333333333 MODIFIER SMARCAD1 ENSG00000163104 A 3_prime_UTR_variant Transcript ENST00000354268 protein_coding 24/24 ENST00000354268.9:c.*1688G>A NA 5024 1 SNV HGNC HGNC:18398 YES NM_020159.5 1 P4 CCDS3639.1 ENSP00000346217 Q9H4L7.191 UPI000013E22F Q9H4L7-1 1 17 NA NA PASS SITE 34,25|4,2 NA NA 1 93 20,20 183,159 60,60 35 1.54 NA 9.88 NA FALSE 6.00 9 NA NA NA FALSE NA NA 13.04 17 94291222 HCC1395_HCC1395T 12 0.315 18 2,0 7,4 10,4 NA 0/1 NA NA NA NA 8,4,4,2 G/A PANCANCER NA FALSE SMARCAD1 chr4:94291222:94291223:G:A SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 97187392 97187393 C A 13 91 0.142857142857143 MODIFIER STPG2 ENSG00000163116 A 3_prime_UTR_variant Transcript ENST00000522676 protein_coding 5/5 ENST00000522676.5:c.*343G>T NA 904 -1 cds_start_NF SNV HGNC HGNC:28712 1 ENSP00000428346 H0YAZ7.42 UPI00005A935C 17 NA NA PASS SITE 87,14|12,1 NA NA 1 93 38,37 197,203 60,60 7 1.33 NA 6.02 NA FALSE 6.00 24 NA NA NA FALSE NA NA 35.03 17 97187392 HCC1395_HCC1395T 78 0.158 91 20,3 48,9 68,12 NA 0/1 NA NA NA NA 68,10,12,1 C/A PANCANCER NA FALSE STPG2 chr4:97187392:97187393:C:A SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 99654591 99654592 C T 19 108 0.175925925925926 MODERATE C4orf54 ENSG00000248713 T missense_variant Transcript ENST00000511828 protein_coding 2/3 ENST00000511828.2:c.58G>A ENSP00000427555.1:p.V20M ENSP00000427555.1 p.V20M 423 58 20 V/M Gtg/Atg rs1331693962 -1 SNV HGNC HGNC:27741 YES NM_001354435.2 1 P1 CCDS87246.1 ENSP00000427555 D6RIA3.73 UPI0001D3B6FE tolerated_low_confidence(0.08) benign(0.106) AlphaFold_DB_import:AF-D6RIA3-F1 2.228e-05 0 4.087e-05 0 9.517e-05 0 0 0.0002414 0 6.572e-06 0 0 0 0 0 0 0 0 0 0.000207 0.0002414 gnomADe_OTH 17 NA NA PASS SITE 79,130|4,15 NA NA 1 93 20,34 153,186 60,60 21 1.91 NA 23.38 NA FALSE 6.00 64 NA NA NA FALSE NA NA 47.07 17 99654591 HCC1395_HCC1395T 89 0.211 108 28,7 28,6 59,15 NA 0/1 NA NA NA NA 32,57,4,15 C/T PANCANCER NA FALSE C4orf54_p.V20M chr4:99654591:99654592:C:T SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 100410302 100410303 G C 57 286 0.199300699300699 MODIFIER EMCN ENSG00000164035 C 3_prime_UTR_variant Transcript ENST00000296420 protein_coding 11/12 ENST00000296420.9:c.*19C>G NA 913 -1 SNV HGNC HGNC:16041 YES NM_016242.4 1 P1 CCDS3655.1 ENSP00000296420 Q9ULC0.151 Q4W5J1.126 UPI000003777D Q9ULC0-1 17 NA NA PASS SITE 197,199|28,29 NA NA 1 93 20,20 154,176 60,60 27 2.04 NA 31.77 NA FALSE 6.00 93 NA NA NA FALSE NA NA 132.64 17 100410302 HCC1395_HCC1395T 229 0.208 286 43,14 93,20 144,37 NA 0/1 NA NA NA NA 117,112,28,29 G/C PANCANCER NA FALSE EMCN chr4:100410302:100410303:G:C SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 103145956 103145957 C G 62 265 0.233962264150943 MODERATE CENPE ENSG00000138778 G missense_variant Transcript ENST00000265148 protein_coding 30/49 ENST00000265148.9:c.4286G>C ENSP00000265148.3:p.R1429T ENSP00000265148.3 p.R1429T 4310 4286 1429 R/T aGa/aCa COSV54379738 -1 SNV HGNC HGNC:1856 YES NM_001813.3 2 A2 CCDS34042.1 ENSP00000265148 Q02224.215 UPI000020B28A Q02224-1 1 deleterious(0) benign(0.121) 1 1 17 NA NA PASS SITE 204,170|38,24 NA NA 1 93 20,20 157,185 60,60 32 2.06 NA 34.31 NA FALSE 6.00 93 NA NA NA FALSE NA NA 156.45 17 103145956 HCC1395_HCC1395T 203 0.246 265 46,14 79,28 134,43 NA 0/1 NA NA NA NA 109,94,38,24 C/G PANCANCER NA FALSE CENPE_p.R1429T chr4:103145956:103145957:C:G SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 103198496 103198497 G A 6 33 0.181818181818182 MODIFIER CENPE ENSG00000138778 A upstream_gene_variant Transcript ENST00000265148 protein_coding NA 153 -1 SNV HGNC HGNC:1856 YES NM_001813.3 2 A2 CCDS34042.1 ENSP00000265148 Q02224.215 UPI000020B28A Q02224-1 1 17 NA NA PASS SITE 15,40|0,6 NA NA 1 81 38,39 184,226 60,60 38 1.38 NA 6.92 NA FALSE 6.00 21 NA NA NA FALSE NA NA 18.99 17 103198496 HCC1395_HCC1395T 27 0.218 33 7,1 14,4 24,6 NA 0/1 NA NA NA NA 6,21,0,6 G/A PANCANCER NA FALSE CENPE chr4:103198496:103198497:G:A SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 107950646 107950647 G C 44 167 0.263473053892216 MODIFIER CYP2U1 ENSG00000155016 C 3_prime_UTR_variant Transcript ENST00000332884 protein_coding 5/5 ENST00000332884.11:c.*223G>C NA 1953 1 SNV HGNC HGNC:20582 YES NM_183075.3 1 P1 CCDS34047.1 ENSP00000333212 Q7Z449.169 UPI0000044231 Q7Z449-1 1 17 NA NA PASS SITE 152,78|30,14 NA NA 1 93 39,33 195,166 60,60 22 1.97 NA 27.39 NA FALSE 6.00 89 NA NA NA FALSE NA NA 115.92 17 107950646 HCC1395_HCC1395T 123 0.252 167 30,10 66,24 103,34 NA 0/1 NA NA NA NA 80,43,30,14 G/C PANCANCER NA FALSE CYP2U1 chr4:107950646:107950647:G:C SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 108009752 108009753 G A 13 56 0.232142857142857 LOW HADH ENSG00000138796 A splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000309522 protein_coding 1/7 ENST00000309522.8:c.133-7G>A NA rs1198653302 1 SNV HGNC HGNC:4799 YES NM_005327.7 1 P2 CCDS3678.1 ENSP00000312288 Q16836.221 A0A140VK76.25 UPI000013EECF Q16836-1 1 3.978e-06 0 0 0 0 0 0 0 3.266e-05 3.266e-05 gnomADe_SAS 17 NA NA PASS SITE 56,20|10,3 NA NA 1 87 20,30 175,211 60,60 38 1.44 NA 7.48 NA FALSE 6.00 6 NA NA NA FALSE NA NA 29.83 17 108009752 HCC1395_HCC1395T 43 0.250 56 8,1 22,8 32,10 NA 0/1 NA NA NA NA 31,12,10,3 G/A PANCANCER NA FALSE HADH chr4:108009752:108009753:G:A SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 108650682 108650683 C G 123 235 0.523404255319149 MODERATE OSTC ENSG00000198856 G missense_variant Transcript ENST00000361564 protein_coding 1/4 ENST00000361564.9:c.27C>G ENSP00000354676.4:p.F9L ENSP00000354676.4 p.F9L 84 27 9 F/L ttC/ttG COSV64232066&COSV64232567 1 SNV HGNC HGNC:24448 YES NM_021227.4 1 P1 CCDS3681.1 ENSP00000354676 Q9NRP0.152 A0A024RDJ1.44 UPI00000724D2 Q9NRP0-1 deleterious(0.02) benign(0.115) PDB-ENSP_mappings:6s7o.H&PDB-ENSP_mappings:8b6l.J&AlphaFold_DB_import:AF-Q9NRP0-F1&PANTHER:PTHR13160 1&1 1&1 17 NA NA PASS SITE 134,121|56,67 NA NA 1 93 38,38 190,187 60,60 26 2.09 NA 36.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 412.93 17 108650682 HCC1395_HCC1395T 112 0.527 235 43,43 50,62 99,110 NA 0/1 NA NA NA NA 64,48,56,67 C/G PANCANCER NA FALSE OSTC_p.F9L chr4:108650682:108650683:C:G SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 109827971 109827972 C T 12 83 0.144578313253012 MODIFIER GAR1 ENSG00000109534 T downstream_gene_variant Transcript ENST00000226796 protein_coding NA 3234 1 SNV HGNC HGNC:14264 YES NM_018983.4 1 P1 CCDS34050.1 ENSP00000226796 Q9NY12.178 UPI0000070C13 Q9NY12-1 17 NA NA PASS SITE 98,42|9,3 NA NA 1 93 20,27 173,136 60,60 24 1.70 NA 14.45 NA FALSE 6.00 45 NA NA NA FALSE NA NA 26.23 17 109827971 HCC1395_HCC1395T 71 0.154 83 16,4 35,5 54,9 NA 0/1 NA NA NA NA 53,18,9,3 C/T PANCANCER NA FALSE GAR1 chr4:109827971:109827972:C:T SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 110050425 110050426 C G 132 299 0.441471571906354 MODIFIER ELOVL6 ENSG00000170522 G 3_prime_UTR_variant Transcript ENST00000302274 protein_coding 4/4 ENST00000302274.8:c.*913G>C NA 1991 -1 SNV HGNC HGNC:15829 YES NM_024090.3 2 P1 CCDS3690.1 ENSP00000304736 Q9H5J4.152 A1LV06.15 UPI00000343F5 17 NA NA PASS SITE 203,167|78,54 NA NA 1 93 20,20 163,163 60,60 36 2.15 NA 41.49 NA FALSE 6.00 93 NA NA NA FALSE NA NA 354.59 17 110050425 HCC1395_HCC1395T 167 0.464 299 33,30 69,57 104,90 NA 0/1 NA NA NA NA 87,80,78,54 C/G PANCANCER NA FALSE ELOVL6 chr4:110050425:110050426:C:G SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 110559664 110559665 G C 46 241 0.190871369294606 MODERATE ENPEP ENSG00000138792 C missense_variant Transcript ENST00000265162 protein_coding 19/20 ENST00000265162.10:c.2660G>C ENSP00000265162.5:p.R887T ENSP00000265162.5 p.R887T 2920 2660 887 R/T aGa/aCa COSV54448015&COSV54458861 1 SNV HGNC HGNC:3355 YES NM_001977.4 1 P1 CCDS3691.1 ENSP00000265162 Q07075.200 UPI000013D5C6 deleterious(0) probably_damaging(1) Gene3D:1.25.50.20&PDB-ENSP_mappings:4kx7.A&PDB-ENSP_mappings:4kx8.A&PDB-ENSP_mappings:4kx9.A&PDB-ENSP_mappings:4kxa.A&PDB-ENSP_mappings:4kxb.A&PDB-ENSP_mappings:4kxc.A&PDB-ENSP_mappings:4kxd.A&AlphaFold_DB_import:AF-Q07075-F1&Pfam:PF11838&PANTHER:PTHR11533 1&1 1&1 17 NA NA PASS SITE 199,152|23,23 NA NA 1 93 20,20 161,162 60,60 29 1.99 NA 28.90 NA FALSE 6.00 72 NA NA NA FALSE NA NA 96.17 17 110559664 HCC1395_HCC1395T 195 0.184 241 46,7 70,19 119,26 NA 0/1 NA NA NA NA 110,85,23,23 G/C PANCANCER NA FALSE ENPEP_p.R887T chr4:110559664:110559665:G:C SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 112277977 112277978 GATCTTGGAGATAAAATAAATTGAGTCTCAAAAAATTCCAATGACTCGCC G 36 251 0.143426294820717 MODIFIER AP1AR ENSG00000138660 - downstream_gene_variant Transcript ENST00000274000 protein_coding NA 4868 1 deletion HGNC HGNC:28808 YES NM_018569.6 1 P1 CCDS3696.1 ENSP00000274000 Q63HQ0.146 UPI000013D9E5 Q63HQ0-1 17 NA NA PASS SITE 176,221|16,20 NA NA 1 93 20,41 169,224 60,60 44 2.10 NA 35.61 NA FALSE 6.00 93 NA NA NA FALSE NA NA 130.06 17 112277977 HCC1395_HCC1395T 215 0.182 251 32,8 54,15 141,39 NA 0/1 NA NA NA NA 96,119,16,20 GATCTTGGAGATAAAATAAATTGAGTCTCAAAAAATTCCAATGACTCGCC/G PANCANCER NA FALSE AP1AR chr4:112277977:112277978:GATCTTGGAGATAAAATAAATTGAGTCTCAAAAAATTCCAATGACTCGCC:G indel 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 112278288 112278289 G A 77 246 0.313008130081301 LOW TIFA ENSG00000145365 A synonymous_variant Transcript ENST00000361717 protein_coding 2/2 ENST00000361717.4:c.129C>T ENSP00000354911.2:p.S43= ENSP00000354911.2 p.S43= 412 129 43 S tcC/tcT COSV64631780 -1 SNV HGNC HGNC:19075 YES NM_052864.3 1 P1 CCDS34051.1 ENSP00000354911 Q96CG3.159 UPI0000070568 PDB-ENSP_mappings:4ym4.A&PDB-ENSP_mappings:4zgi.A&CDD:cd22714&PANTHER:PTHR31266&Superfamily:SSF49879&AlphaFold_DB_import:AF-Q96CG3-F1 1 1 17 NA NA PASS SITE 191,157|38,39 NA NA 1 93 20,20 155,162 60,60 34 2.06 NA 34.01 NA FALSE 6.00 91 NA NA NA FALSE NA NA 179.87 17 112278288 HCC1395_HCC1395T 169 0.309 246 39,16 67,31 111,49 NA 0/1 NA NA NA NA 89,80,38,39 G/A PANCANCER NA FALSE TIFA_p.S43= chr4:112278288:112278289:G:A SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 113460311 113460312 A T 8 38 0.210526315789474 MODIFIER CAMK2D ENSG00000145349 T intron_variant Transcript ENST00000296402 protein_coding 15/17 ENST00000296402.9:c.1110-70T>A NA -1 SNV HGNC HGNC:1462 5 CCDS3704.1 ENSP00000296402 Q13557.225 UPI000006FF25 Q13557-8 17 NA NA PASS SITE 6,40|0,8 NA NA 1 49 36,34 195,189 60,60 15 1.16 NA 3.91 NA FALSE 6.00 42 NA NA NA FALSE NA NA 22.43 17 113460311 HCC1395_HCC1395T 30 0.243 38 7,2 12,1 27,8 NA 0/1 NA NA NA NA 3,27,0,8 A/T PANCANCER NA FALSE CAMK2D chr4:113460311:113460312:A:T SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 118740663 118740664 C T 84 337 0.249258160237389 LOW SEC24D ENSG00000150961 T splice_region_variant&synonymous_variant Transcript ENST00000280551 protein_coding 17/23 ENST00000280551.11:c.2238G>A ENSP00000280551.6:p.Q746= ENSP00000280551.6 p.Q746= 2465 2238 746 Q caG/caA rs1468639787&COSV99756684 -1 SNV HGNC HGNC:10706 YES NM_014822.4 1 P1 CCDS3710.1 ENSP00000280551 O94855.185 UPI00001AEA4F O94855-1 1 PDB-ENSP_mappings:3efo.B&PDB-ENSP_mappings:3eg9.B&PDB-ENSP_mappings:5kyu.B&PDB-ENSP_mappings:5kyw.B&PDB-ENSP_mappings:5kyx.B&PDB-ENSP_mappings:5kyy.B&PANTHER:PTHR13803&Gene3D:2.60.40.1670&Pfam:PF08033&Superfamily:SSF81995&AlphaFold_DB_import:AF-O94855-F1 3.99e-06 0 0 0 0 0 0 0 3.277e-05 3.277e-05 gnomADe_SAS 0&1 0&1 17 NA NA PASS SITE 225,205|48,36 NA NA 1 93 20,20 159,172 60,60 35 2.05 NA 33.41 NA FALSE 6.00 82 NA NA NA FALSE NA NA 208.59 17 118740663 HCC1395_HCC1395T 253 0.261 337 53,16 98,40 163,57 NA 0/1 NA NA NA NA 130,123,48,36 C/T PANCANCER NA FALSE SEC24D_p.Q746= chr4:118740663:118740664:C:T SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 119494562 119494563 C G 52 256 0.203125 MODIFIER PDE5A ENSG00000138735 G downstream_gene_variant Transcript ENST00000264805 protein_coding NA 3979 -1 SNV HGNC HGNC:8784 1 P1 CCDS34055.1 ENSP00000264805 O76074.205 UPI0000191D36 O76074-2 17 NA NA PASS SITE 131,212|18,34 NA NA 1 93 20,20 168,175 60,60 34 1.98 NA 28.55 NA FALSE 6.00 93 NA NA NA FALSE NA NA 122.53 17 119494562 HCC1395_HCC1395T 204 0.205 256 40,13 80,20 139,35 NA 0/1 NA NA NA NA 70,134,18,34 C/G PANCANCER NA FALSE PDE5A chr4:119494562:119494563:C:G SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 121932626 121932627 C A 111 541 0.205175600739372 MODERATE TRPC3 ENSG00000138741 A missense_variant Transcript ENST00000264811 protein_coding 1/11 ENST00000264811.9:c.413G>T ENSP00000264811.5:p.C138F ENSP00000264811.5 p.C138F 832 413 138 C/F tGt/tTt -1 SNV HGNC HGNC:12335 1 A2 CCDS3725.1 ENSP00000264811 Q13507.200 UPI00001374AD Q13507-3 1 tolerated_low_confidence(0.15) benign(0.029) Gene3D:1.25.40.20&PDB-ENSP_mappings:6djs.A&PDB-ENSP_mappings:6djs.B&PDB-ENSP_mappings:6djs.C&PDB-ENSP_mappings:6djs.D&AlphaFold_DB_import:AF-Q13507-F1&PANTHER:PTHR10117&Superfamily:SSF48403&TIGRFAM:TIGR00870 17 NA NA PASS SITE 390,399|53,58 NA NA 1 93 20,20 157,166 60,60 31 2.37 NA 70.34 NA FALSE 6.00 93 NA NA NA FALSE NA NA 249.18 17 121932626 HCC1395_HCC1395T 430 0.207 541 110,26 147,41 282,73 NA 0/1 NA NA NA NA 211,219,53,58 C/A PANCANCER NA FALSE TRPC3_p.C138F chr4:121932626:121932627:C:A SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 122411481 122411482 C A 12 49 0.244897959183673 MODIFIER ADAD1 ENSG00000164113 A intron_variant Transcript ENST00000296513 protein_coding 9/12 ENST00000296513.7:c.1019+89C>A NA 1 SNV HGNC HGNC:30713 YES NM_139243.4 2 P1 CCDS34058.1 ENSP00000296513 Q96M93.141 UPI000006DF76 Q96M93-1 17 NA NA PASS SITE 12,60|1,11 NA NA 1 93 40,36 199,193 60,60 36 1.51 NA 9.33 NA FALSE 6.00 33 NA NA NA FALSE NA NA 33.35 17 122411481 HCC1395_HCC1395T 37 0.266 49 9,3 20,7 32,11 NA 0/1 NA NA NA NA 7,30,1,11 C/A PANCANCER NA FALSE ADAD1 chr4:122411481:122411482:C:A SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 129096299 129096300 G A 7 21 0.333333333333333 MODIFIER SCLT1 ENSG00000151466 A upstream_gene_variant Transcript ENST00000281142 protein_coding NA rs554111346&COSV55404845 2760 -1 SNV HGNC HGNC:26406 YES NM_144643.4 2 P1 CCDS3740.1 ENSP00000281142 Q96NL6.142 UPI000013DC5F Q96NL6-1 1 3.288e-05 0 0 0.0001964 0 0.0003852 0 0 0 0 0 0.0003852 gnomADg_EAS 0&1 0&1 17 NA NA PASS SITE 9,20|2,5 NA NA 1 32 20,20 180,205 60,60 28 1.06 NA 3.01 NA FALSE 6.00 9 NA NA NA FALSE NA NA 17.97 17 129096299 HCC1395_HCC1395T 14 0.353 21 3,0 5,4 10,5 NA 0/1 NA NA NA NA 4,10,2,5 G/A PANCANCER NA FALSE SCLT1 chr4:129096299:129096300:G:A SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 133155028 133155029 G T 76 180 0.422222222222222 LOW PCDH10 ENSG00000138650 T splice_donor_5th_base_variant&intron_variant Transcript ENST00000264360 protein_coding 3/4 ENST00000264360.7:c.2797+5G>T NA 1 SNV HGNC HGNC:13404 YES NM_032961.3 1 P1 CCDS34063.1 ENSP00000264360 Q9P2E7.165 X5D999.57 UPI0000161C61 Q9P2E7-1 17 NA NA PASS SITE 77,123|32,44 NA NA 1 93 20,20 167,157 60,60 29 1.83 NA 19.56 NA FALSE 6.00 93 NA NA NA FALSE NA NA 197.58 17 133155028 HCC1395_HCC1395T 104 0.429 180 31,15 32,28 67,50 NA 0/1 NA NA NA NA 42,62,32,44 G/T PANCANCER NA FALSE PCDH10 chr4:133155028:133155029:G:T SNV 2:2 chr4:88038229:138171565:2:2:1 FALSE NA 0.96 +chr4 139418302 139418303 CTTTTTTTT C 38 43 0.883720930232558 MODIFIER NAA15 ENSG00000164134 - 3_prime_UTR_variant Transcript ENST00000515576 protein_coding 4/4 ENST00000515576.1:c.*365_*372del NA 726-733 rs3044457 1 cds_start_NF deletion HGNC HGNC:30782 2 ENSP00000421839 D6RAP7.47 UPI0000372178 1 11 2.359e-05 3.07e-05 0 0 0 0 0 0 3.242e-05 0 0 3.242e-05 gnomADg_NFE 17 NA NA PASS SITE 5,14|13,25 NA NA 1 50 38,20 194,189 60,60 38 0.885 NA 3.55 NA FALSE 6.00 93 19,11 T NA TRUE NA 93 163.78 17 139418302 HCC1395_HCC1395T 5 0.870 43 1,8 1,14 4,31 NA 0/1 NA NA NA NA 2,3,13,25 CTTTTTTTT/C PANCANCER NA FALSE NAA15 chr4:139418302:139418303:CTTTTTTTT:C indel 2:0 chr4:138219340:189407803:2:0:1 TRUE NA 0.96 +chr4 139533433 139533434 C G 22 117 0.188034188034188 MODIFIER SETD7 ENSG00000145391 G intron_variant Transcript ENST00000274031 protein_coding 2/7 ENST00000274031.8:c.171-67G>C NA -1 SNV HGNC HGNC:30412 YES NM_030648.4 1 P1 CCDS3748.1 ENSP00000274031 Q8WTS6.188 UPI0000135893 17 NA NA PASS SITE 77,108|7,15 NA NA 1 93 20,35 160,191 60,60 36 1.78 NA 17.76 NA FALSE 6.00 93 NA NA NA FALSE NA NA 57.73 17 139533433 HCC1395_HCC1395T 95 0.212 117 28,8 32,7 66,17 NA 0/1 NA NA NA NA 39,56,7,15 C/G PANCANCER NA FALSE SETD7 chr4:139533433:139533434:C:G SNV 2:0 chr4:138219340:189407803:2:0:1 TRUE NA 0.96 +chr4 150579230 150579231 A G 27 90 0.3 MODIFIER MAB21L2 ENSG00000181541 G upstream_gene_variant Transcript ENST00000317605 protein_coding NA rs1222814948 2921 1 SNV HGNC HGNC:6758 YES NM_006439.5 P1 CCDS3774.1 ENSP00000324701 Q9Y586.144 UPI000007290D 1 0 0 0 0 0 0 0 0 0 0 gnomADe_AFR&gnomADe_AMR&gnomADe_ASJ&gnomADe_EAS&gnomADe_FIN&gnomADe_NFE&gnomADe_OTH&gnomADe_SAS 17 NA NA PASS SITE 105,102|16,11 NA NA 1 93 20,20 151,157 60,60 36 1.95 NA 26.74 NA FALSE 6.00 59 NA NA NA FALSE NA NA 62.93 17 150579230 HCC1395_HCC1395T 63 0.317 90 16,6 21,11 40,18 NA 0/1 NA NA NA NA 33,30,16,11 A/G PANCANCER NA FALSE MAB21L2 chr4:150579230:150579231:A:G SNV 2:0 chr4:138219340:189407803:2:0:1 TRUE NA 0.96 +chr4 153622026 153622027 G C 14 14 1 MODIFIER TMEM131L ENSG00000121210 C intron_variant Transcript ENST00000240487 protein_coding 22/28 ENST00000240487.5:c.3190+177G>C NA 1 cds_start_NF SNV HGNC HGNC:29146 1 ENSP00000240487 H0Y2M0.62 UPI00018814E3 17 NA NA PASS SITE 15,29|4,10 NA NA 1 93 20,20 145,165 60,60 22 1.48 NA 8.73 NA FALSE 6.00 93 NA NA NA FALSE NA NA 44.06 17 153622026 HCC1395_HCC1395T 0 0.919 14 0,5 0,5 0,10 NA 0/1 NA NA NA NA 0,0,4,10 G/C PANCANCER NA FALSE TMEM131L chr4:153622026:153622027:G:C SNV 2:0 chr4:138219340:189407803:2:0:1 TRUE NA 0.96 +chr4 154322810 154322811 G C 106 106 1 MODIFIER DCHS2 ENSG00000197410 C 3_prime_UTR_variant Transcript ENST00000339452 protein_coding 8/8 ENST00000339452.2:c.*428C>G NA 4899 -1 SNV HGNC HGNC:23111 1 CCDS47150.1 ENSP00000345062 Q6V1P9.150 A0A0A0MRC0.51 UPI00002372F1 Q6V1P9-5 17 NA NA PASS SITE 45,90|26,80 NA NA 1 93 20,23 155,178 60,60 30 1.97 NA 27.69 NA FALSE 6.00 93 NA NA NA FALSE NA NA 361.83 17 154322810 HCC1395_HCC1395T 0 0.988 106 0,25 0,41 0,80 NA 0/1 NA NA NA NA 0,0,26,80 G/C PANCANCER NA FALSE DCHS2 chr4:154322810:154322811:G:C SNV 2:0 chr4:138219340:189407803:2:0:1 TRUE NA 0.96 +chr4 154391099 154391100 T G 4 15 0.266666666666667 MODIFIER DCHS2 ENSG00000197410 G intron_variant Transcript ENST00000339452 protein_coding 1/7 ENST00000339452.2:c.2053-13655A>C NA -1 SNV HGNC HGNC:23111 1 CCDS47150.1 ENSP00000345062 Q6V1P9.150 A0A0A0MRC0.51 UPI00002372F1 Q6V1P9-5 17 NA NA PASS SITE 26,0|2,2 NA NA 2 50 35,38 232,81 60,60 50 1.20 NA 4.52 NA FALSE 6.00 35 NA NA NA FALSE NA NA 14.96 17 154391099 HCC1395_HCC1395T 11 0.200 15 0,2 11,0 11,2 NA 0|1 0|1 154391099_T_G NA 154391099 11,0,2,2 T|G PANCANCER NA FALSE DCHS2 chr4:154391099:154391100:T:G SNV 2:0 chr4:138219340:189407803:2:0:1 TRUE NA 0.96 +chr4 154391101 154391102 T G 4 15 0.266666666666667 MODIFIER DCHS2 ENSG00000197410 G intron_variant Transcript ENST00000339452 protein_coding 1/7 ENST00000339452.2:c.2053-13657A>C NA -1 SNV HGNC HGNC:23111 1 CCDS47150.1 ENSP00000345062 Q6V1P9.150 A0A0A0MRC0.51 UPI00002372F1 Q6V1P9-5 17 NA NA PASS SITE 26,0|2,2 NA NA 2 50 36,38 232,81 60,60 48 1.20 NA 4.52 NA FALSE 6.00 28 NA NA NA FALSE NA NA 14.96 17 154391101 HCC1395_HCC1395T 11 0.200 15 0,2 11,0 11,2 NA 0|1 0|1 154391099_T_G NA 154391099 11,0,2,2 T|G PANCANCER NA FALSE DCHS2 chr4:154391101:154391102:T:G SNV 2:0 chr4:138219340:189407803:2:0:1 TRUE NA 0.96 +chr4 154491219 154491220 G C 172 172 1 MODERATE DCHS2 ENSG00000197410 C missense_variant Transcript ENST00000339452 protein_coding 1/8 ENST00000339452.2:c.137C>G ENSP00000345062.1:p.S46C ENSP00000345062.1 p.S46C 498 137 46 S/C tCc/tGc -1 SNV HGNC HGNC:23111 1 CCDS47150.1 ENSP00000345062 Q6V1P9.150 A0A0A0MRC0.51 UPI00002372F1 Q6V1P9-5 tolerated(0.18) benign(0.441) 17 NA NA PASS SITE 158,206|81,91 NA NA 1 93 20,20 160,162 60,60 33 2.40 NA 73.61 NA FALSE 6.00 93 NA NA NA FALSE NA NA 516.61 17 154491219 HCC1395_HCC1395T 0 0.992 172 0,39 0,66 0,114 NA 0/1 NA NA NA NA 0,0,81,91 G/C PANCANCER NA FALSE DCHS2_p.S46C chr4:154491219:154491220:G:C SNV 2:0 chr4:138219340:189407803:2:0:1 TRUE NA 0.96 +chr4 168896455 168896456 A G 4 19 0.210526315789474 MODIFIER PALLD ENSG00000129116 G intron_variant Transcript ENST00000261509 protein_coding 12/20 ENST00000261509.10:c.2199+1778A>G NA 1 SNV HGNC HGNC:17068 1 P3 CCDS34098.1 ENSP00000261509 Q8WX93.182 B2RTX2.112 UPI000049DFF8 Q8WX93-2 1 17 NA NA PASS SITE 29,1|4,0 NA NA 1 54 33,42 196,195 60,60 34 1.24 NA 4.47 NA FALSE 6.00 22 NA NA NA FALSE NA NA 13.01 17 168896455 HCC1395_HCC1395T 15 0.250 19 3,1 11,3 14,4 NA 0/1 NA NA NA NA 14,1,4,0 A/G PANCANCER NA FALSE PALLD chr4:168896455:168896456:A:G SNV 2:0 chr4:138219340:189407803:2:0:1 TRUE NA 0.96 +chr4 169095206 169095207 C G 36 36 1 MODIFIER SH3RF1 ENSG00000154447 G 3_prime_UTR_variant Transcript ENST00000284637 protein_coding 12/12 ENST00000284637.14:c.*1313G>C NA 4173 -1 SNV HGNC HGNC:17650 YES NM_020870.4 1 P1 CCDS34099.1 ENSP00000284637 Q7Z6J0.152 UPI0000160033 Q7Z6J0-1 17 NA NA PASS SITE 41,27|24,12 NA NA 1 93 20,33 166,202 60,60 20 1.70 NA 14.75 NA FALSE 6.00 93 NA NA NA FALSE NA NA 118.12 17 169095206 HCC1395_HCC1395T 0 0.968 36 0,13 0,15 0,29 NA 0/1 NA NA NA NA 0,0,24,12 C/G PANCANCER NA FALSE SH3RF1 chr4:169095206:169095207:C:G SNV 2:0 chr4:138219340:189407803:2:0:1 TRUE NA 0.96 +chr4 174320290 174320291 T C 4 4 1 MODIFIER CEP44 ENSG00000164118 C 3_prime_UTR_variant Transcript ENST00000296519 protein_coding 10/10 ENST00000296519.6:c.*2907T>C NA 4132 1 SNV HGNC HGNC:29356 1 P1 CCDS34106.1 ENSP00000296519 Q9C0F1.138 UPI0000074306 Q9C0F1-1 17 NA NA PASS SITE 1,7|0,4 NA NA 1 36 37,31 261,256 60,60 11 0.954 NA 2.41 NA FALSE 6.00 50 NA NA NA FALSE NA NA 13.34 17 174320290 HCC1395_HCC1395T 0 0.841 4 0,2 0,1 0,4 NA 0/1 NA NA NA NA 0,0,0,4 T/C PANCANCER NA FALSE CEP44 chr4:174320290:174320291:T:C SNV 2:0 chr4:138219340:189407803:2:0:1 TRUE NA 0.96 +chr4 175633113 175633114 G A 24 75 0.32 MODIFIER GPM6A ENSG00000150625 A 3_prime_UTR_variant Transcript ENST00000280187 protein_coding 8/8 ENST00000280187.11:c.*1792C>T NA 2675 rs570175689&COSV54550293 -1 SNV HGNC HGNC:4460 1 P1 CCDS3824.1 ENSP00000280187 P51674.181 UPI000012EAE1 P51674-1 0&1 0&1 17 NA NA PASS SITE 41,102|5,19 NA NA 1 93 20,33 180,173 60,60 25 1.83 NA 19.80 NA FALSE 6.00 30 NA NA NA FALSE NA NA 62.07 17 175633113 HCC1395_HCC1395T 51 0.333 75 9,3 27,12 39,19 NA 0/1 NA NA NA NA 12,39,5,19 G/A PANCANCER NA FALSE GPM6A chr4:175633113:175633114:G:A SNV 2:0 chr4:138219340:189407803:2:0:1 TRUE NA 0.96 +chr4 176120051 176120053 AG GA 30 76 0.394736842105263 MODERATE WDR17 ENSG00000150627 GA missense_variant Transcript ENST00000280190 protein_coding 5/31 ENST00000280190.8:c.564_565delinsGA ENSP00000280190.4:p.V189I ENSP00000280190.4 p.V189I 720-721 564-565 188-189 KV/KI aaAGtt/aaGAtt 1 substitution HGNC HGNC:16661 1 CCDS3825.1 ENSP00000280190 Q8IZU2.149 UPI000019C575 Q8IZU2-1 Gene3D:2.130.10.10&SMART:SM00320&Superfamily:SSF50978&PANTHER:PTHR44464&AlphaFold_DB_import:AF-Q8IZU2-F1 17 NA NA PASS SITE 44,93|8,22 NA NA 1 93 20,20 158,179 60,60 41 1.81 NA 18.96 NA FALSE 6.00 93 NA NA NA FALSE NA NA 100.78 17 176120051 HCC1395_HCC1395T 46 0.396 76 15,10 16,10 34,22 NA 0/1 NA NA NA NA 13,33,8,22 AG/GA PANCANCER NA FALSE WDR17_p.V189I chr4:176120051:176120053:AG:GA indel 2:0 chr4:138219340:189407803:2:0:1 TRUE NA 0.96 +chr5 432462 432463 G A 86 259 0.332046332046332 HIGH AHRR ENSG00000063438 A splice_acceptor_variant Transcript ENST00000316418 protein_coding 8/10 ENST00000316418.10:c.909-1G>A NA COSV100327726&COSV57084883 1 SNV HGNC HGNC:346 1 P1 CCDS93682.1 ENSP00000323816 A0A7I2PK40.8 UPI0012FAC88A 1&1 1&1 18 NA NA PASS SITE 170,121|51,35 NA NA 1 93 20,20 165,158 60,60 31 1.88 NA 22.58 NA FALSE 6.00 93 NA NA NA FALSE NA NA 207.31 18 432462 HCC1395_HCC1395T 173 0.338 259 56,21 48,31 110,56 NA 0/1 NA NA NA NA 102,71,51,35 G/A PANCANCER NA FALSE AHRR chr5:432462:432463:G:A SNV 4:2 chr5:140417:7900720:4:2:1 NA NA 0.96 +chr5 1331836 1331837 C A 136 421 0.323040380047506 MODERATE CLPTM1L ENSG00000049656 A missense_variant Transcript ENST00000320895 protein_coding 8/17 ENST00000320895.10:c.939G>T ENSP00000313854.5:p.K313N ENSP00000313854.5 p.K313N 1197 939 313 K/N aaG/aaT COSV57993417 -1 SNV HGNC HGNC:24308 YES NM_030782.5 1 P1 CCDS3862.1 ENSP00000313854 Q96KA5.154 UPI00000707DF Q96KA5-1 deleterious(0.02) possibly_damaging(0.812) AlphaFold_DB_import:AF-Q96KA5-F1&Pfam:PF05602&PANTHER:PTHR21347 1 1 18 NA NA PASS SITE 269,195|78,58 NA NA 1 93 20,20 164,161 60,60 34 2.08 NA 35.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 317.18 18 1331836 HCC1395_HCC1395T 285 0.323 421 82,39 98,47 190,90 NA 0/1 NA NA NA NA 167,118,78,58 C/A PANCANCER NA FALSE CLPTM1L_p.K313N chr5:1331836:1331837:C:A SNV 4:2 chr5:140417:7900720:4:2:1 NA NA 0.96 +chr5 1394461 1394462 C G 8 519 0.0154142581888247 MODIFIER SLC6A3 ENSG00000142319 G 3_prime_UTR_variant Transcript ENST00000270349 protein_coding 15/15 ENST00000270349.12:c.*274G>C NA 2275 -1 SNV HGNC HGNC:11049 YES NM_001044.5 1 P1 CCDS3863.1 ENSP00000270349 Q01959.216 UPI000013548F 1 18 NA NA PASS SITE 342,403|3,5 NA NA 1 93 20,20 163,119 60,60 25 2.18 NA 44.55 NA FALSE 6.00 11 NA NA NA FALSE NA NA 10.62 18 1394461 HCC1395_HCC1395T 511 0.017 519 101,0 177,4 335,5 NA 0/1 NA NA NA NA 238,273,3,5 C/G PANCANCER NA FALSE SLC6A3 chr5:1394461:1394462:C:G SNV 4:2 chr5:140417:7900720:4:2:1 NA NA 0.96 +chr5 1814505 1814506 G A 168 532 0.315789473684211 MODIFIER NDUFS6 ENSG00000145494 A intron_variant Transcript ENST00000274137 protein_coding 3/3 ENST00000274137.10:c.309+44G>A NA rs375252736 1 SNV HGNC HGNC:7713 YES NM_004553.6 1 P1 CCDS3866.1 ENSP00000274137 O75380.172 Q6IBC4.131 UPI000000DB49 1 2.395e-05 0 0.0001448 0 0 0 8.839e-06 0 0 1.972e-05 2.414e-05 0 6.546e-05 0 0 0 0 1.47e-05 0 0 0.0001448 gnomADe_AMR 18 NA NA PASS SITE 286,300|72,96 NA NA 1 93 20,20 160,169 60,60 37 2.18 NA 44.45 NA FALSE 4.61 93 NA NA NA FALSE NA NA 421.41 18 1814505 HCC1395_HCC1395T 364 0.335 532 93,44 123,71 235,118 NA 0/1 NA NA NA NA 176,188,72,96 G/A PANCANCER NA FALSE NDUFS6 chr5:1814505:1814506:G:A SNV 4:2 chr5:140417:7900720:4:2:1 NA NA 0.96 +chr5 6668718 6668719 C G 105 297 0.353535353535354 MODIFIER SRD5A1 ENSG00000145545 G 3_prime_UTR_variant Transcript ENST00000274192 protein_coding 5/5 ENST00000274192.7:c.*450C>G NA 1367 1 SNV HGNC HGNC:11284 YES NM_001047.4 1 P1 CCDS3870.1 ENSP00000274192 P18405.193 UPI00000534C8 18 NA NA PASS SITE 140,174|48,58 NA NA 1 93 20,20 161,160 60,60 32 1.93 NA 24.98 NA FALSE 6.00 93 NA NA NA FALSE NA NA 259.92 18 6668718 HCC1395_HCC1395T 192 0.347 297 46,19 71,43 131,69 NA 0/1 NA NA NA NA 84,108,47,58 C/G PANCANCER NA FALSE SRD5A1 chr5:6668718:6668719:C:G SNV 4:2 chr5:140417:7900720:4:2:1 NA NA 0.96 +chr5 7886680 7886681 G C 123 351 0.35042735042735 MODERATE MTRR ENSG00000124275 C missense_variant Transcript ENST00000264668 protein_coding 8/15 ENST00000264668.6:c.1204G>C ENSP00000264668.2:p.E402Q ENSP00000264668.2 p.E402Q 1234 1204 402 E/Q Gaa/Caa rs772547714&COSV52943712 1 SNV HGNC HGNC:7473 1 ENSP00000264668 Q9UBK8.204 UPI000013D550 Q9UBK8-1 1 deleterious(0) probably_damaging(0.983) Gene3D:1.20.990.10&Gene3D:2.40.30.10&AlphaFold_DB_import:AF-Q9UBK8-F1&Pfam:PF00667&PROSITE_profiles:PS51384&PANTHER:PTHR19384&Superfamily:SSF63380&CDD:cd06203 2.784e-05 0 0 0 0 0 6.155e-05 0 0 1.972e-05 0 0 0 0 0 0 0 4.411e-05 0 0 6.155e-05 gnomADe_NFE 0&1 1&1 18 NA NA PASS SITE 125,235|37,86 NA NA 1 93 20,20 169,166 60,60 30 1.97 NA 27.39 NA FALSE 6.00 93 NA NA NA FALSE NA NA 334.10 18 7886680 HCC1395_HCC1395T 228 0.360 351 54,26 84,54 158,89 NA 0/1 NA NA NA NA 76,152,37,86 G/C PANCANCER NA FALSE MTRR_p.E402Q chr5:7886680:7886681:G:C SNV 4:2 chr5:140417:7900720:4:2:1 NA NA 0.96 +chr5 10353764 10353765 C G 81 272 0.297794117647059 MODIFIER MARCHF6 ENSG00000145495 G 5_prime_UTR_variant Transcript ENST00000274140 protein_coding 1/26 ENST00000274140.10:c.-135C>G NA 70 1 SNV HGNC HGNC:30550 YES NM_005885.4 1 P1 CCDS34135.1 ENSP00000274140 O60337.166 UPI00001B94D6 O60337-4 1 18 NA NA PASS SITE 198,147|45,36 NA NA 1 93 20,20 157,153 60,60 32 2.06 NA 33.06 NA FALSE 6.00 93 NA NA NA FALSE NA NA 182.05 18 10353764 HCC1395_HCC1395T 191 0.295 272 53,14 75,38 137,57 NA 0/1 NA NA NA NA 106,85,45,36 C/G PANCANCER NA FALSE MARCHF6 chr5:10353764:10353765:C:G SNV 2:2 chr5:9036678:38370435:2:2:1 FALSE NA 0.96 +chr5 14507135 14507136 C T 47 172 0.273255813953488 MODIFIER TRIO ENSG00000038382 T non_coding_transcript_exon_variant Transcript ENST00000344135 retained_intron 9/10 ENST00000344135.5:n.1616C>T NA 1616 rs755026998&COSV59991364 1 SNV HGNC HGNC:12303 2 1 4.212e-06 0 0 0 0 0 9.138e-06 0 0 3.941e-05 4.823e-05 0 0 0 0 0 0 5.878e-05 0 0 5.878e-05 gnomADg_NFE uncertain_significance 0&1 1&1 18 NA NA PASS SITE 79,142|19,28 NA NA 1 93 20,20 161,166 60,60 34 1.85 NA 19.81 NA FALSE 4.13 85 NA NA NA FALSE NA NA 109.94 18 14507135 HCC1395_HCC1395T 125 0.273 172 37,17 41,11 84,31 NA 0/1 NA NA NA NA 44,81,19,28 C/T PANCANCER NA FALSE TRIO chr5:14507135:14507136:C:T SNV 2:2 chr5:9036678:38370435:2:2:1 FALSE NA 0.96 +chr5 16473681 16473682 G T 17 37 0.459459459459459 MODIFIER RETREG1 ENSG00000154153 T 3_prime_UTR_variant Transcript ENST00000306320 protein_coding 9/9 ENST00000306320.10:c.*1060C>A NA 2580 -1 SNV HGNC HGNC:25964 YES NM_001034850.3 1 CCDS43304.1 ENSP00000304642 Q9H6L5.149 UPI000006D7DB Q9H6L5-1 1 18 NA NA PASS SITE 4,38|0,17 NA NA 1 63 38,39 198,204 60,60 13 1.37 NA 6.27 NA FALSE 6.00 59 NA NA NA FALSE NA NA 61.47 18 16473681 HCC1395_HCC1395T 20 0.461 37 6,4 12,11 20,17 NA 0/1 NA NA NA NA 0,20,0,17 G/T PANCANCER NA FALSE RETREG1 chr5:16473681:16473682:G:T SNV 2:2 chr5:9036678:38370435:2:2:1 FALSE NA 0.96 +chr5 16673921 16673922 G A 6 330 0.0181818181818182 MODIFIER MYO10 ENSG00000145555 A intron_variant Transcript ENST00000274203 protein_coding 35/40 ENST00000274203.13:c.4998-32C>T NA -1 SNV HGNC HGNC:7593 5 ENSP00000274203 A0A0A0MQX1.63 UPI0000D61603 18 NA NA PASS SITE 168,325|3,3 NA NA 1 93 20,20 165,131 60,60 17 2.07 NA 34.92 NA FALSE 6.00 11 NA NA NA FALSE NA NA 7.70 18 16673921 HCC1395_HCC1395T 324 0.021 330 71,1 125,2 229,4 NA 0/1 NA NA NA NA 109,215,3,3 G/A PANCANCER NA FALSE MYO10 chr5:16673921:16673922:G:A SNV 2:2 chr5:9036678:38370435:2:2:1 FALSE NA 0.96 +chr5 23521054 23521055 C G 185 412 0.449029126213592 MODERATE PRDM9 ENSG00000164256 G missense_variant Transcript ENST00000296682 protein_coding 6/11 ENST00000296682.4:c.383C>G ENSP00000296682.4:p.S128C ENSP00000296682.4 p.S128C 571 383 128 S/C tCt/tGt rs1376432727&COSV104616737&COSV57009120&COSV99691235 1 SNV HGNC HGNC:13994 YES NM_020227.4 1 P1 CCDS43307.1 ENSP00000296682 Q9NQV7.179 UPI00006C9E90 tolerated(0.07) possibly_damaging(0.679) AlphaFold_DB_import:AF-Q9NQV7-F1&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite 0&1&1&1 0&1&1&1 18 NA NA PASS SITE 225,224|94,91 NA NA 1 93 20,20 160,161 60,60 30 2.16 NA 43.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 494.06 18 23521054 HCC1395_HCC1395T 227 0.456 412 58,47 81,72 151,126 NA 0/1 NA NA NA NA 114,113,94,91 C/G PANCANCER NA FALSE PRDM9_p.S128C chr5:23521054:23521055:C:G SNV 2:2 chr5:9036678:38370435:2:2:1 FALSE NA 0.96 +chr5 32711618 32711619 T C 43 163 0.263803680981595 MODIFIER NPR3 ENSG00000113389 C 5_prime_UTR_variant Transcript ENST00000265074 protein_coding 1/8 ENST00000265074.13:c.-159T>C NA 298 rs1247363887 1 SNV HGNC HGNC:7945 YES NM_001204375.2 1 P4 CCDS56357.1 ENSP00000265074 P17342.203 UPI0000125B46 P17342-1 1 6.592e-06 0 0 0 0 0 0 0 1.471e-05 0 0 1.471e-05 gnomADg_NFE 18 NA NA PASS SITE 99,109|17,26 NA NA 1 93 33,20 176,161 60,60 36 1.86 NA 21.06 NA FALSE 4.61 78 NA NA NA FALSE NA NA 101.98 18 32711618 HCC1395_HCC1395T 120 0.244 163 24,7 31,8 92,29 NA 0/1 NA NA NA NA 53,67,17,26 T/C PANCANCER NA FALSE NPR3 chr5:32711618:32711619:T:C SNV 2:2 chr5:9036678:38370435:2:2:1 FALSE NA 0.96 +chr5 35878606 35878607 G T 48 182 0.263736263736264 MODIFIER IL7R ENSG00000168685 T 3_prime_UTR_variant Transcript ENST00000303115 protein_coding 8/8 ENST00000303115.8:c.*2120G>T NA 3587 1 SNV HGNC HGNC:6024 YES NM_002185.5 1 P1 CCDS3911.1 ENSP00000306157 P16871.216 UPI000013E861 P16871-1 1 18 NA NA PASS SITE 138,64|38,10 NA NA 1 93 37,35 180,193 60,60 21 1.72 NA 15.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 127.40 18 35878606 HCC1395_HCC1395T 134 0.270 182 31,17 75,21 107,39 NA 0/1 NA NA NA NA 92,42,38,10 G/T PANCANCER TRUE FALSE IL7R chr5:35878606:35878607:G:T SNV 2:2 chr5:9036678:38370435:2:2:1 FALSE NA 0.96 +chr5 37299405 37299406 C G 38 84 0.452380952380952 MODIFIER NUP155 ENSG00000113569 G intron_variant Transcript ENST00000231498 protein_coding 31/34 ENST00000231498.8:c.3682+43G>C NA -1 SNV HGNC HGNC:8063 YES NM_153485.3 1 P1 CCDS3921.1 ENSP00000231498 O75694.193 A0A024R071.61 UPI0000001C7F O75694-1 1 18 NA NA PASS SITE 78,43|27,12 NA NA 1 93 20,20 161,166 60,60 29 0.421 NA 12.07 NA FALSE 6.00 93 NA NA NA FALSE NA NA 106.00 18 37299405 HCC1395_HCC1395T 46 0.431 84 15,12 20,15 36,27 NA 0/1 NA NA NA NA 34,12,26,12 C/G PANCANCER NA FALSE NUP155 chr5:37299405:37299406:C:G SNV 2:2 chr5:9036678:38370435:2:2:1 FALSE NA 0.96 +chr5 37812526 37812527 C T 12 33 0.363636363636364 MODIFIER GDNF ENSG00000168621 T downstream_gene_variant Transcript ENST00000326524 protein_coding NA 151 -1 SNV HGNC HGNC:4232 YES NM_000514.4 1 P1 CCDS3922.1 ENSP00000317145 P39905.215 A0A0S2Z3V2.35 UPI00000326A1 P39905-1 1 18 NA NA PASS SITE 36,1|12,0 NA NA 2 46 40,39 206,199 60,60 25 1.20 NA 4.51 NA FALSE 6.00 29 NA NA NA FALSE NA NA 41.34 18 37812526 HCC1395_HCC1395T 21 0.371 33 10,2 9,10 21,12 NA 0|1 0|1 37812526_C_T NA 37812526 21,0,12,0 C|T PANCANCER NA FALSE GDNF chr5:37812526:37812527:C:T SNV 2:2 chr5:9036678:38370435:2:2:1 FALSE NA 0.96 +chr5 37812532 37812533 G A 14 36 0.388888888888889 MODIFIER GDNF ENSG00000168621 A downstream_gene_variant Transcript ENST00000326524 protein_coding NA 145 -1 SNV HGNC HGNC:4232 YES NM_000514.4 1 P1 CCDS3922.1 ENSP00000317145 P39905.215 A0A0S2Z3V2.35 UPI00000326A1 P39905-1 1 18 NA NA PASS SITE 39,1|14,0 NA NA 2 51 40,35 212,205 60,60 31 1.25 NA 5.07 NA FALSE 6.00 39 NA NA NA FALSE NA NA 50.48 18 37812532 HCC1395_HCC1395T 22 0.395 36 11,3 11,10 22,14 NA 0|1 0|1 37812526_C_T NA 37812526 22,0,14,0 G|A PANCANCER NA FALSE GDNF chr5:37812532:37812533:G:A SNV 2:2 chr5:9036678:38370435:2:2:1 FALSE NA 0.96 +chr5 38478677 38478678 C G 94 336 0.279761904761905 MODIFIER LIFR ENSG00000113594 G 3_prime_UTR_variant Transcript ENST00000263409 protein_coding 20/20 ENST00000263409.8:c.*2918G>C NA 6375 -1 SNV HGNC HGNC:6597 1 P1 CCDS3927.1 ENSP00000263409 P42702.201 UPI000004CAC2 P42702-1 1 18 NA NA PASS SITE 282,151|63,31 NA NA 1 93 20,20 149,145 60,60 35 2.11 NA 38.18 NA FALSE 6.00 93 NA NA NA FALSE NA NA 229.67 18 38478677 HCC1395_HCC1395T 242 0.285 336 72,27 90,37 162,64 NA 0/1 NA NA NA NA 162,80,63,31 C/G PANCANCER NA FALSE LIFR chr5:38478677:38478678:C:G SNV 2:1 chr5:38424906:44310390:2:1:1 TRUE NA 0.96 +chr5 38960004 38960005 G T 7 16 0.4375 MODIFIER RICTOR ENSG00000164327 T intron_variant Transcript ENST00000296782 protein_coding 20/38 ENST00000296782.9:c.1852-26C>A NA -1 SNV HGNC HGNC:28611 1 A1 CCDS68861.1 ENSP00000296782 Q6R327.163 UPI0000EE67F5 Q6R327-3 18 NA NA PASS SITE 2,24|0,7 NA NA 1 45 38,39 237,277 60,60 42 1.24 NA 4.51 NA FALSE 6.00 36 NA NA NA FALSE NA NA 21.07 18 38960004 HCC1395_HCC1395T 9 0.437 16 7,3 1,2 9,7 NA 0/1 NA NA NA NA 0,9,0,7 G/T PANCANCER NA FALSE RICTOR chr5:38960004:38960005:G:T SNV 2:1 chr5:38424906:44310390:2:1:1 TRUE NA 0.96 +chr5 39074491 39074492 C A 15 40 0.375 MODIFIER RICTOR ENSG00000164327 A upstream_gene_variant Transcript ENST00000296782 protein_coding NA 92 -1 SNV HGNC HGNC:28611 1 A1 CCDS68861.1 ENSP00000296782 Q6R327.163 UPI0000EE67F5 Q6R327-3 18 NA NA PASS SITE 12,52|2,13 NA NA 1 93 32,39 201,187 60,60 24 1.54 NA 10.23 NA FALSE 6.00 44 NA NA NA FALSE NA NA 45.98 18 39074491 HCC1395_HCC1395T 25 0.389 40 12,4 6,9 21,13 NA 0/1 NA NA NA NA 5,20,2,13 C/A PANCANCER NA FALSE RICTOR chr5:39074491:39074492:C:A SNV 2:1 chr5:38424906:44310390:2:1:1 TRUE NA 0.96 +chr5 39270316 39270317 T C 45 63 0.714285714285714 MODIFIER FYB1 ENSG00000082074 C intron_variant&non_coding_transcript_variant Transcript ENST00000503065 protein_coding_CDS_not_defined 2/2 ENST00000503065.1:n.330+253A>G NA -1 SNV HGNC HGNC:4036 2 1 18 NA NA PASS SITE 43,20|30,15 NA NA 1 93 20,20 174,164 60,60 31 1.53 NA 9.93 NA FALSE 6.00 83 NA NA NA FALSE NA NA 122.46 18 39270316 HCC1395_HCC1395T 18 0.695 63 6,9 7,20 13,31 NA 0/1 NA NA NA NA 13,5,30,15 T/C PANCANCER NA FALSE FYB1 chr5:39270316:39270317:T:C SNV 2:1 chr5:38424906:44310390:2:1:1 TRUE NA 0.96 +chr5 42688843 42688844 T A 113 182 0.620879120879121 MODIFIER GHR ENSG00000112964 A intron_variant Transcript ENST00000230882 protein_coding 3/9 ENST00000230882.9:c.137-47T>A NA 1 SNV HGNC HGNC:4263 YES NM_000163.5 1 P1 CCDS3940.1 ENSP00000230882 P10912.238 UPI000012B416 P10912-1 1 18 NA NA PASS SITE 94,82|60,53 NA NA 1 93 20,20 166,166 60,60 33 1.87 NA 21.97 NA FALSE 6.00 93 NA NA NA FALSE NA NA 312.61 18 42688843 HCC1395_HCC1395T 69 0.621 182 20,17 25,55 47,78 NA 0/1 NA NA NA NA 39,30,60,53 T/A PANCANCER NA FALSE GHR chr5:42688843:42688844:T:A SNV 2:1 chr5:38424906:44310390:2:1:1 TRUE NA 0.96 +chr5 53042008 53042009 G C 13 13 1 MODIFIER ITGA2 ENSG00000164171 C intron_variant Transcript ENST00000296585 protein_coding 2/29 ENST00000296585.10:c.186-104G>C NA 1 SNV HGNC HGNC:6137 YES NM_002203.4 1 P1 CCDS3957.1 ENSP00000296585 P17301.234 UPI0000169C36 1 18 NA NA PASS SITE 23,0|13,0 NA NA 1 93 41,38 235,263 60,60 31 1.39 NA 6.92 NA FALSE 6.00 93 NA NA NA FALSE NA NA 53.39 18 53042008 HCC1395_HCC1395T 0 0.933 13 0,3 0,10 0,13 NA 0/1 NA NA NA NA 0,0,13,0 G/C PANCANCER NA FALSE ITGA2 chr5:53042008:53042009:G:C SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 54310435 54310436 A T 17 130 0.130769230769231 MODIFIER ARL15 ENSG00000185305 T 5_prime_UTR_variant Transcript ENST00000502271 protein_coding 1/5 ENST00000502271.5:c.-407T>A NA 148 -1 SNV HGNC HGNC:25945 1 ENSP00000473508 R4GN67.46 UPI00024D113D 18 NA NA PASS SITE 178,134|10,7 NA NA 1 93 20,20 156,184 60,60 41 2.10 NA 37.62 NA FALSE 6.00 55 NA NA NA FALSE NA NA 31.99 18 54310435 HCC1395_HCC1395T 113 0.125 130 31,4 42,6 76,10 NA 0/1 NA NA NA NA 69,44,10,7 A/T PANCANCER NA FALSE ARL15 chr5:54310435:54310436:A:T SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 62308236 62308237 G C 19 40 0.475 MODIFIER KIF2A ENSG00000068796 C intron_variant Transcript ENST00000381103 protein_coding 1/20 ENST00000381103.7:c.-220-73G>C NA 1 SNV HGNC HGNC:6318 1 CCDS58949.2 ENSP00000370493 O00139.196 UPI00000712D2 O00139-1 1 18 NA NA PASS SITE 66,1|19,0 NA NA 1 93 39,38 218,222 60,60 23 1.68 NA 13.54 NA FALSE 6.00 93 NA NA NA FALSE NA NA 63.56 18 62308236 HCC1395_HCC1395T 21 0.473 40 6,6 15,12 21,19 NA 0/1 NA NA NA NA 21,0,19,0 G/C PANCANCER NA FALSE KIF2A chr5:62308236:62308237:G:C SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 73909347 73909348 C G 108 108 1 MODIFIER ARHGEF28 ENSG00000214944 G intron_variant Transcript ENST00000296794 protein_coding 33/34 ENST00000296794.10:c.4162-65C>G NA 1 SNV HGNC HGNC:30322 5 CCDS93734.1 ENSP00000296794 Q8N1W1.160 UPI000048078F Q8N1W1-4 18 NA NA PASS SITE 87,41|80,28 NA NA 1 93 20,28 165,175 60,60 31 1.98 NA 28.15 NA FALSE 6.00 93 NA NA NA FALSE NA NA 335.35 18 73909347 HCC1395_HCC1395T 0 0.988 108 0,28 0,51 0,81 NA 0/1 NA NA NA NA 0,0,80,28 C/G PANCANCER NA FALSE ARHGEF28 chr5:73909347:73909348:C:G SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 77432423 77432424 G A 14 70 0.2 MODIFIER PDE8B ENSG00000113231 A downstream_gene_variant Transcript ENST00000264917 protein_coding NA 4167 1 SNV HGNC HGNC:8794 YES NM_003719.5 1 P1 CCDS4037.1 ENSP00000264917 O95263.200 UPI0000001BBE O95263-1 1 18 NA NA PASS SITE 88,47|8,6 NA NA 1 93 37,36 177,181 60,60 41 1.82 NA 18.65 NA FALSE 6.00 53 NA NA NA FALSE NA NA 33.93 18 77432423 HCC1395_HCC1395T 56 0.210 70 21,7 22,4 44,11 NA 0/1 NA NA NA NA 38,18,8,6 G/A PANCANCER NA FALSE PDE8B chr5:77432423:77432424:G:A SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 79752571 79752572 G C 7 11 0.636363636363636 MODIFIER CMYA5 ENSG00000164309 C intron_variant Transcript ENST00000446378 protein_coding 5/12 ENST00000446378.3:c.10992-105G>C NA 1 SNV HGNC HGNC:14305 YES NM_153610.5 5 P1 CCDS47238.1 ENSP00000394770 Q8N3K9.154 UPI00004F9478 18 NA NA PASS SITE 13,0|7,0 NA NA 1 27 41,39 199,182 60,60 13 1.02 NA 2.71 NA FALSE 6.00 61 NA NA NA FALSE NA NA 26.75 18 79752571 HCC1395_HCC1395T 4 0.616 11 2,5 2,2 4,7 NA 0/1 NA NA NA NA 4,0,7,0 G/C PANCANCER NA FALSE CMYA5 chr5:79752571:79752572:G:C SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 83061722 83061723 A G 3 12 0.25 MODIFIER SCARNA18 ENSG00000238835 G downstream_gene_variant Transcript ENST00000459004 snoRNA NA 2482 -1 SNV HGNC HGNC:32559 YES 18 NA NA PASS SITE 14,6|2,1 NA NA 1 32 37,20 181,150 60,60 47 1.06 NA 3.01 NA FALSE 6.00 28 NA NA NA FALSE NA NA 6.96 18 83061722 HCC1395_HCC1395T 9 0.298 12 3,1 3,1 6,2 NA 0/1 NA NA NA NA 5,4,2,1 A/G PANCANCER NA FALSE SCARNA18 chr5:83061722:83061723:A:G SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 90459010 90459011 T G 4 16 0.25 MODIFIER MBLAC2 ENSG00000176055 G 3_prime_UTR_variant Transcript ENST00000316610 protein_coding 2/2 ENST00000316610.7:c.*2157A>C NA 3476 -1 SNV HGNC HGNC:33711 YES NM_203406.2 1 P1 CCDS4067.1 ENSP00000314776 Q68D91.120 UPI00001975AC Q68D91-1 18 NA NA PASS SITE 30,1|4,0 NA NA 1 60 36,42 261,51 60,48 28 1.32 NA 5.72 NA FALSE 6.00 34 NA NA NA FALSE NA NA 13.61 18 90459010 HCC1395_HCC1395T 12 0.293 16 5,0 6,4 11,4 NA 0/1 NA NA NA NA 11,1,4,0 T/G PANCANCER NA FALSE MBLAC2 chr5:90459010:90459011:T:G SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 102236752 102236753 T G 15 33 0.454545454545455 MODIFIER SLCO4C1 ENSG00000173930 G 3_prime_UTR_variant Transcript ENST00000310954 protein_coding 13/13 ENST00000310954.7:c.*106A>C NA 2303 -1 SNV HGNC HGNC:23612 YES NM_180991.5 1 P1 CCDS34205.1 ENSP00000309741 Q6ZQN7.159 UPI00001C10B6 18 NA NA PASS SITE 39,17|12,3 NA NA 1 90 33,40 187,197 60,60 10 1.50 NA 9.03 NA FALSE 6.00 49 NA NA NA FALSE NA NA 54.88 18 102236752 HCC1395_HCC1395T 18 0.500 33 4,2 9,12 15,15 NA 0/1 NA NA NA NA 12,6,12,3 T/G PANCANCER NA FALSE SLCO4C1 chr5:102236752:102236753:T:G SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 103129447 103129448 C G 202 202 1 MODIFIER PPIP5K2 ENSG00000145725 G 5_prime_UTR_variant Transcript ENST00000321521 protein_coding 2/30 ENST00000321521.13:c.-143C>G NA 431 rs989208980 1 SNV HGNC HGNC:29035 5 A1 CCDS34207.1 ENSP00000313070 O43314.167 UPI000006E414 O43314-2 1 18 NA NA PASS SITE 123,99|103,99 NA NA 1 93 20,20 158,167 60,60 40 2.14 NA 41.14 NA FALSE 6.00 93 NA NA NA FALSE NA NA 597.34 18 103129447 HCC1395_HCC1395T 0 0.992 202 0,44 0,75 0,128 NA 0/1 NA NA NA NA 0,0,103,99 C/G PANCANCER NA FALSE PPIP5K2 chr5:103129447:103129448:C:G SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 115130597 115130598 ACTAACTG A 64 64 1 HIGH TRIM36 ENSG00000152503 - frameshift_variant Transcript ENST00000282369 protein_coding 9/10 ENST00000282369.7:c.1820_1826del ENSP00000282369.3:p.A607Vfs*27 ENSP00000282369.3 p.A607Vfs*27 1942-1948 1820-1826 607-609 AVS/X gCAGTTAGt/gt -1 deletion HGNC HGNC:16280 1 P1 CCDS4115.1 ENSP00000282369 Q9NQ86.189 UPI000013DCD9 Q9NQ86-1 1 PDB-ENSP_mappings:7qs4.A&PDB-ENSP_mappings:7qs4.B&PDB-ENSP_mappings:7qs4.C&PDB-ENSP_mappings:7qs4.D&CDD:cd12894&Gene3D:2.60.120.920&Superfamily:SSF49899&PROSITE_profiles:PS50188&PANTHER:PTHR24099&AlphaFold_DB_import:AF-Q9NQ86-F1 18 NA NA PASS SITE 45,12|48,16 NA NA 1 93 31,35 180,189 60,60 27 1.67 NA 13.51 NA FALSE 6.00 93 NA NA NA FALSE NA NA 282.36 18 115130597 HCC1395_HCC1395T 0 0.982 64 0,12 0,35 0,51 NA 0/1 NA NA NA NA 0,0,48,16 ACTAACTG/A PANCANCER NA FALSE TRIM36_p.A607Vfs*27 chr5:115130597:115130598:ACTAACTG:A indel 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 122388613 122388614 G C 29 29 1 MODIFIER SNCAIP ENSG00000064692 C 5_prime_UTR_variant Transcript ENST00000261367 protein_coding 2/14 ENST00000261367.11:c.-1304G>C NA 125 1 SNV HGNC HGNC:11139 1 CCDS78054.1 ENSP00000261367 Q9Y6H5.187 UPI000023272B Q9Y6H5-3 1 18 NA NA PASS SITE 32,18|20,9 NA NA 1 93 20,34 170,198 60,60 36 1.57 NA 10.83 NA FALSE 6.00 93 NA NA NA FALSE NA NA 97.52 18 122388613 HCC1395_HCC1395T 0 0.962 29 0,6 0,15 0,23 NA 0/1 NA NA NA NA 0,0,20,9 G/C PANCANCER NA FALSE SNCAIP chr5:122388613:122388614:G:C SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 122431925 122431926 G C 65 65 1 MODIFIER SNCAIP ENSG00000064692 C intron_variant Transcript ENST00000261367 protein_coding 7/13 ENST00000261367.11:c.1324-44G>C NA 1 SNV HGNC HGNC:11139 1 CCDS78054.1 ENSP00000261367 Q9Y6H5.187 UPI000023272B Q9Y6H5-3 1 18 NA NA PASS SITE 45,14|49,16 NA NA 1 93 36,29 161,168 60,60 26 1.69 NA 13.85 NA FALSE 6.00 93 NA NA NA FALSE NA NA 217.85 18 122431925 HCC1395_HCC1395T 0 0.980 65 0,10 0,37 0,49 NA 0/1 NA NA NA NA 0,0,49,16 G/C PANCANCER NA FALSE SNCAIP chr5:122431925:122431926:G:C SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 133103959 133103960 T C 95 95 1 MODERATE HSPA4 ENSG00000170606 C missense_variant Transcript ENST00000304858 protein_coding 18/19 ENST00000304858.7:c.2252T>C ENSP00000302961.2:p.L751P ENSP00000302961.2 p.L751P 2490 2252 751 L/P cTg/cCg COSV59183196 1 SNV HGNC HGNC:5237 YES NM_002154.4 1 P1 CCDS4166.1 ENSP00000302961 P34932.213 UPI000013E9D5 P34932-1 deleterious_low_confidence(0.03) benign(0.377) Low_complexity_(Seg):seg&PANTHER:PTHR45639&Gene3D:1.20.1270.10&Superfamily:SSF100934&Coiled-coils_(Ncoils):Coil&AlphaFold_DB_import:AF-P34932-F1 1 1 18 NA NA PASS SITE 25,60|28,67 NA NA 1 93 32,22 171,174 60,60 29 1.83 NA 19.56 NA FALSE 6.00 93 NA NA NA FALSE NA NA 291.42 18 133103959 HCC1395_HCC1395T 0 0.987 95 0,26 0,39 0,71 NA 0/1 NA NA NA NA 0,0,28,67 T/C PANCANCER NA FALSE HSPA4_p.L751P chr5:133103959:133103960:T:C SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 134606262 134606263 C T 76 77 0.987012987012987 MODIFIER SAR1B ENSG00000152700 T 3_prime_UTR_variant Transcript ENST00000402673 protein_coding 7/7 ENST00000402673.7:c.*688G>A NA 1404 -1 SNV HGNC HGNC:10535 YES NM_016103.4 1 P1 CCDS4177.1 ENSP00000385432 Q9Y6B6.195 UPI0000135569 1 18 NA NA PASS SITE 55,18|58,18 NA NA 1 93 38,37 191,205 60,60 36 1.81 NA 18.62 NA FALSE 6.00 93 NA NA NA FALSE NA NA 269.00 18 134606262 HCC1395_HCC1395T 1 0.970 77 1,26 0,36 1,64 NA 0/1 NA NA NA NA 1,0,58,18 C/T PANCANCER NA FALSE SAR1B chr5:134606262:134606263:C:T SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 134893642 134893643 T C 92 93 0.989247311827957 MODERATE TXNDC15 ENSG00000113621 C missense_variant Transcript ENST00000358387 protein_coding 3/5 ENST00000358387.9:c.742T>C ENSP00000351157.5:p.S248P ENSP00000351157.5 p.S248P 799 742 248 S/P Tct/Cct COSV64380303 1 SNV HGNC HGNC:20652 YES NM_024715.4 1 P1 CCDS4180.1 ENSP00000351157 Q96J42.167 UPI00000359EE Q96J42-1 1 deleterious(0) probably_damaging(0.999) Gene3D:3.40.30.10&AlphaFold_DB_import:AF-Q96J42-F1&Pfam:PF00085&PROSITE_profiles:PS51352&PANTHER:PTHR14684&Superfamily:SSF52833&CDD:cd02999 1 1 18 NA NA PASS SITE 14,65|14,78 NA NA 1 93 33,38 190,174 60,60 26 1.82 NA 19.26 NA FALSE 6.00 93 NA NA NA FALSE NA NA 334.63 18 134893642 HCC1395_HCC1395T 1 0.975 93 1,27 0,38 1,78 NA 0/1 NA NA NA NA 0,1,14,78 T/C PANCANCER NA FALSE TXNDC15_p.S248P chr5:134893642:134893643:T:C SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 135448915 135448916 G A 47 47 1 MODIFIER DCANP1 ENSG00000251380 A upstream_gene_variant Transcript ENST00000503143 protein_coding NA rs941933495 1567 -1 SNV HGNC HGNC:24459 YES NM_130848.3 P1 CCDS4186.1 ENSP00000421871 Q8TF63.123 UPI000006FF8B 1.315e-05 2.415e-05 0 0 0 0 0 0 1.47e-05 0 0 2.415e-05 gnomADg_AFR 18 NA NA PASS SITE 30,32|26,23 NA NA 1 93 20,20 174,160 60,60 34 -1.998e-01 NA 8.94 NA FALSE 4.31 93 NA NA NA FALSE NA NA 132.98 18 135448915 HCC1395_HCC1395T 0 0.969 47 0,14 0,16 0,30 NA 0/1 NA NA NA NA 0,0,26,21 G/A PANCANCER NA FALSE DCANP1 chr5:135448915:135448916:G:A SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 136274699 136274700 C T 34 79 0.430379746835443 MODIFIER TRPC7 ENSG00000069018 T intron_variant Transcript ENST00000352189 protein_coding 2/9 ENST00000352189.8:c.781-8263G>A NA -1 SNV HGNC HGNC:20754 5 CCDS54905.1 ENSP00000330322 Q9HCX4.173 UPI000007449C Q9HCX4-2 18 NA NA PASS SITE 68,60|17,17 NA NA 1 93 20,20 164,173 60,60 42 1.77 NA 16.86 NA FALSE 6.00 61 NA NA NA FALSE NA NA 80.60 18 136274699 HCC1395_HCC1395T 45 0.393 79 14,6 18,13 33,21 NA 0/1 NA NA NA NA 25,20,17,17 C/T PANCANCER NA FALSE TRPC7 chr5:136274699:136274700:C:T SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 138182226 138182227 G A 3 3 1 MODIFIER BRD8 ENSG00000112983 A upstream_gene_variant Transcript ENST00000230901 protein_coding NA 3596 -1 SNV HGNC HGNC:19874 1 CCDS34241.1 ENSP00000230901 Q9H0E9.179 UPI00001C0367 Q9H0E9-2 18 NA NA PASS SITE 15,0|3,0 NA NA 1 53 40,39 230,207 60,60 22 1.20 NA 4.42 NA FALSE 6.00 26 NA NA NA FALSE NA NA 12.49 18 138182226 HCC1395_HCC1395T 0 0.811 3 0,0 0,3 0,3 NA 0/1 NA NA NA NA 0,0,3,0 G/A PANCANCER NA FALSE BRD8 chr5:138182226:138182227:G:A SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 138187645 138187646 A T 2 10 0.2 MODIFIER CDC23 ENSG00000094880 T downstream_gene_variant Transcript ENST00000394886 protein_coding NA 5 -1 SNV HGNC HGNC:1724 YES NM_004661.4 1 P1 CCDS4200.2 ENSP00000378350 Q9UJX2.206 UPI000020C69D Q9UJX2-1 18 NA NA PASS SITE 15,5|0,2 NA NA 1 39 37,39 235,143 60,60 42 1.11 NA 3.61 NA FALSE 6.00 19 NA NA NA FALSE NA NA 6.04 18 138187645 HCC1395_HCC1395T 8 0.248 10 5,2 3,0 8,2 NA 0/1 NA NA NA NA 6,2,0,2 A/T PANCANCER NA FALSE CDC23 chr5:138187645:138187646:A:T SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 138561034 138561035 C T 124 124 1 MODIFIER HSPA9 ENSG00000113013 T intron_variant Transcript ENST00000297185 protein_coding 10/16 ENST00000297185.9:c.1182+546G>A NA -1 SNV HGNC HGNC:5244 YES NM_004134.7 1 P1 CCDS4208.1 ENSP00000297185 P38646.231 A0A384P5G6.22 UPI000012BA4E 1 18 NA NA PASS SITE 82,88|61,63 NA NA 1 93 20,20 161,153 60,60 39 2.03 NA 31.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 344.18 18 138561034 HCC1395_HCC1395T 0 0.987 124 0,36 0,38 0,77 NA 0/1 NA NA NA NA 0,0,61,63 C/T PANCANCER NA FALSE HSPA9 chr5:138561034:138561035:C:T SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 139648359 139648360 G C 59 93 0.634408602150538 MODIFIER CXXC5 ENSG00000171604 C 5_prime_UTR_variant Transcript ENST00000302517 protein_coding 1/3 ENST00000302517.8:c.-647G>C NA 11 1 SNV HGNC HGNC:26943 YES NM_016463.9 1 P1 CCDS43370.1 ENSP00000302543 Q7LFL8.125 UPI000003779E Q7LFL8-1 18 NA NA PASS SITE 94,66|35,24 NA NA 1 93 20,20 149,153 60,60 29 1.59 NA 22.57 NA FALSE 6.00 93 NA NA NA FALSE NA NA 149.20 18 139648359 HCC1395_HCC1395T 34 0.633 93 11,12 10,23 21,37 NA 0/1 NA NA NA NA 21,13,35,24 G/C PANCANCER NA FALSE CXXC5 chr5:139648359:139648360:G:C SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 140795698 140795699 C G 44 148 0.297297297297297 HIGH PCDHA2 ENSG00000204969 G stop_gained Transcript ENST00000378132 protein_coding 1/1 ENST00000378132.2:c.734C>G ENSP00000367372.1:p.S245* ENSP00000367372.1 p.S245* 847 734 245 S/* tCa/tGa COSV65369592 1 SNV HGNC HGNC:8668 ENSP00000367372 Q9Y5H9.184 UPI000002A612 Q9Y5H9-2 Gene3D:2.60.40.60&Superfamily:SSF49313&PROSITE_profiles:PS50268&PANTHER:PTHR24028&Prints:PR00205&AlphaFold_DB_import:AF-Q9Y5H9-F1 1 1 18 NA NA PASS SITE 107,89|24,20 NA NA 1 93 20,34 169,169 60,60 30 1.82 NA 18.96 NA FALSE 6.00 93 NA NA NA FALSE NA NA 122.53 18 140795698 HCC1395_HCC1395T 104 0.321 148 26,13 43,19 73,34 NA 0/1 NA NA NA NA 55,49,24,20 C/G PANCANCER NA FALSE PCDHA2_p.S245* chr5:140795698:140795699:C:G SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 141123693 141123694 G C 86 283 0.303886925795053 MODERATE PCDHB4 ENSG00000081818 C missense_variant Transcript ENST00000194152 protein_coding 1/1 ENST00000194152.4:c.1695G>C ENSP00000194152.1:p.Q565H ENSP00000194152.1 p.Q565H 1876 1695 565 Q/H caG/caC COSV52022325 1 SNV HGNC HGNC:8689 YES NM_018938.4 P1 CCDS4246.1 ENSP00000194152 Q9Y5E5.173 UPI00001273DF tolerated_low_confidence(0.06) Gene3D:2.60.40.60&Superfamily:SSF49313&Superfamily:SSF49313&PANTHER:PTHR24028&AlphaFold_DB_import:AF-Q9Y5E5-F1 1 1 18 NA NA PASS SITE 236,223|41,45 NA NA 1 93 20,20 171,174 49,46 34 2.25 NA 52.36 NA FALSE 6.00 93 NA NA NA FALSE NA NA 227.87 18 141123693 HCC1395_HCC1395T 197 0.323 283 60,27 71,31 135,64 NA 0/1 NA NA NA NA 96,101,41,45 G/C PANCANCER NA FALSE PCDHB4_p.Q565H chr5:141123693:141123694:G:C SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 141182171 141182172 C T 130 467 0.278372591006424 MODIFIER PCDHB8 ENSG00000120322 T downstream_gene_variant Transcript ENST00000239444 protein_coding NA 1632 1 SNV HGNC HGNC:8693 YES NM_019120.5 P1 CCDS4250.1 ENSP00000239444 Q9UN66.175 UPI000192C41A 18 NA NA PASS SITE 366,333|68,62 NA NA 1 93 20,20 164,173 60,60 39 2.36 NA 68.33 NA FALSE 6.00 93 NA NA NA FALSE NA NA 300.97 18 141182171 HCC1395_HCC1395T 337 0.278 467 79,31 130,51 223,85 NA 0/1 NA NA NA NA 177,160,68,62 C/T PANCANCER NA FALSE PCDHB8 chr5:141182171:141182172:C:T SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 141332648 141332649 C T 106 153 0.69281045751634 MODERATE PCDHGA1 ENSG00000204956 T missense_variant Transcript ENST00000378105 protein_coding 1/1 ENST00000378105.4:c.1964C>T ENSP00000367345.3:p.S655F ENSP00000367345.3 p.S655F 2078 1964 655 S/F tCc/tTc COSV65295971 1 SNV HGNC HGNC:8696 ENSP00000367345 Q9Y5H4.172 UPI000006CF78 Q9Y5H4-2 deleterious_low_confidence(0) probably_damaging(0.996) Gene3D:2.60.40.60&AlphaFold_DB_import:AF-Q9Y5H4-F1&Pfam:PF00028&PROSITE_profiles:PS50268&PANTHER:PTHR24028&SMART:SM00112&Superfamily:SSF49313&CDD:cd11304 1 1 18 NA NA PASS SITE 99,87|50,56 NA NA 1 93 20,20 157,165 60,58 23 2.01 NA 29.50 NA FALSE 6.00 93 NA NA NA FALSE NA NA 291.47 18 141332648 HCC1395_HCC1395T 47 0.687 153 8,23 23,41 34,76 NA 0/1 NA NA NA NA 27,20,50,56 C/T PANCANCER NA FALSE PCDHGA1_p.S655F chr5:141332648:141332649:C:T SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 141351877 141351878 C T 393 566 0.69434628975265 MODIFIER PCDHGA3 ENSG00000254245 T intron_variant Transcript ENST00000253812 protein_coding 1/3 ENST00000253812.8:c.2424+5420C>T NA rs932577945&COSV53921076 1 SNV HGNC HGNC:8701 YES NM_018916.4 1 P1 CCDS47290.1 ENSP00000253812 Q9Y5H0.170 UPI0000161C1A Q9Y5H0-1 4.037e-06 0 0 0 0 0 8.922e-06 0 0 8.922e-06 gnomADe_NFE 0&1 0&1 18 NA NA PASS SITE 404,341|220,173 NA NA 1 93 20,20 157,160 60,60 34 2.57 NA 108.22 NA FALSE 6.00 93 NA NA NA FALSE NA NA 1020.21 18 141351877 HCC1395_HCC1395T 173 0.701 566 42,105 60,131 106,249 NA 0/1 NA NA NA NA 87,86,220,173 C/T PANCANCER NA FALSE PCDHGA3 chr5:141351877:141351878:C:T SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 142152302 142152303 C G 49 49 1 MODIFIER NDFIP1 ENSG00000131507 G 3_prime_UTR_variant Transcript ENST00000253814 protein_coding 8/8 ENST00000253814.6:c.*574C>G NA 1436 rs1202335036 1 SNV HGNC HGNC:17592 YES NM_030571.4 1 P1 CCDS4273.1 ENSP00000253814 Q9BT67.148 UPI0000037796 Q9BT67-1 6.576e-06 2.416e-05 0 0 0 0 0 0 0 0 0 2.416e-05 gnomADg_AFR 18 NA NA PASS SITE 18,10|37,12 NA NA 1 93 39,39 196,183 60,60 29 1.43 NA 7.52 NA FALSE 4.61 93 NA NA NA FALSE NA NA 177.26 18 142152302 HCC1395_HCC1395T 0 0.977 49 0,21 0,19 0,40 NA 0/1 NA NA NA NA 0,0,37,12 C/G PANCANCER NA FALSE NDFIP1 chr5:142152302:142152303:C:G SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 143229015 143229016 G C 74 213 0.347417840375587 MODIFIER ARHGAP26 ENSG00000145819 C downstream_gene_variant Transcript ENST00000274498 protein_coding NA 4 1 SNV HGNC HGNC:17073 1 CCDS4277.1 ENSP00000274498 Q9UNA1.205 UPI0000130D6B Q9UNA1-1 1 18 NA NA PASS SITE 90,241|19,55 NA NA 1 93 34,29 180,184 60,60 25 2.16 NA 42.74 NA FALSE 6.00 93 NA NA NA FALSE NA NA 203.55 18 143229015 HCC1395_HCC1395T 139 0.332 213 33,18 64,28 113,56 NA 0/1 NA NA NA NA 32,107,19,55 G/C PANCANCER NA FALSE ARHGAP26 chr5:143229015:143229016:G:C SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 146478669 146478670 G C 27 27 1 MODIFIER TCERG1 ENSG00000113649 C intron_variant Transcript ENST00000296702 protein_coding 10/21 ENST00000296702.9:c.1762+16G>C NA 1 SNV HGNC HGNC:15630 1 P4 CCDS4282.1 ENSP00000296702 O14776.193 UPI000013E374 O14776-1 18 NA NA PASS SITE 4,18|3,24 NA NA 1 93 38,34 155,192 60,60 28 1.29 NA 5.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 95.27 18 146478669 HCC1395_HCC1395T 0 0.963 27 0,9 0,11 0,24 NA 0/1 NA NA NA NA 0,0,3,24 G/C PANCANCER NA FALSE TCERG1 chr5:146478669:146478670:G:C SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 146513439 146513440 C G 6 431 0.0139211136890951 MODIFIER TCERG1 ENSG00000113649 G downstream_gene_variant Transcript ENST00000296702 protein_coding NA 1478 1 SNV HGNC HGNC:15630 1 P4 CCDS4282.1 ENSP00000296702 O14776.193 UPI000013E374 O14776-1 18 NA NA PASS SITE 347,315|3,3 NA NA 1 93 20,40 165,78 60,60 23 2.23 NA 50.52 NA FALSE 6.00 13 NA NA NA FALSE NA NA 17.53 18 146513439 HCC1395_HCC1395T 425 0.014 431 109,3 159,0 288,3 NA 0/1 NA NA NA NA 231,194,3,3 C/G PANCANCER NA FALSE TCERG1 chr5:146513439:146513440:C:G SNV 2:0 chr5:50397624:146650492:2:0:1 TRUE NA 0.96 +chr5 150080891 150080892 G A 65 65 1 LOW CSF1R ENSG00000182578 A synonymous_variant Transcript ENST00000286301 protein_coding 3/22 ENST00000286301.7:c.183C>T ENSP00000286301.3:p.Y61= ENSP00000286301.3 p.Y61= 475 183 61 Y taC/taT rs1561940574&COSV53846800 -1 SNV HGNC HGNC:2433 1 P1 CCDS4302.1 ENSP00000286301 P07333.237 UPI000004984A P07333-1 1 Gene3D:2.60.40.10&PDB-ENSP_mappings:4dkd.C&PDB-ENSP_mappings:4liq.E&PDB-ENSP_mappings:4wrl.A&PDB-ENSP_mappings:4wrl.C&PDB-ENSP_mappings:4wrm.A&AlphaFold_DB_import:AF-P07333-F1&PIRSF:PIRSF000615&PIRSF:PIRSF500947&PROSITE_profiles:PS50835&SMART:SM00409&Superfamily:SSF48726 0&1 0&1 18 NA NA PASS SITE 34,37|29,36 NA NA 1 93 20,20 170,173 60,60 30 1.69 NA 14.10 NA FALSE 6.00 93 NA NA NA FALSE NA NA 209.91 18 150080891 HCC1395_HCC1395T 0 0.980 65 0,19 0,29 0,48 NA 0/1 NA NA NA NA 0,0,29,36 G/A PANCANCER NA FALSE CSF1R_p.Y61= chr5:150080891:150080892:G:A SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 150204585 150204586 G C 82 118 0.694915254237288 LOW SLC6A7 ENSG00000011083 C synonymous_variant Transcript ENST00000230671 protein_coding 11/14 ENST00000230671.7:c.1386G>C ENSP00000230671.2:p.L462= ENSP00000230671.2 p.L462= 1652 1386 462 L ctG/ctC 1 SNV HGNC HGNC:11054 YES NM_014228.5 1 P1 CCDS4305.1 ENSP00000230671 Q99884.161 UPI000013C93C AlphaFold_DB_import:AF-Q99884-F1&Pfam:PF00209&Prints:PR00176&PROSITE_profiles:PS50267&PANTHER:PTHR11616&Superfamily:SSF161070&Transmembrane_helices:TMhelix&CDD:cd11500 18 NA NA PASS SITE 68,98|33,49 NA NA 1 93 20,20 155,150 60,60 30 1.94 NA 25.89 NA FALSE 6.00 93 NA NA NA FALSE NA NA 217.66 18 150204585 HCC1395_HCC1395T 36 0.684 118 10,25 10,23 23,51 NA 0/1 NA NA NA NA 16,20,33,49 G/C PANCANCER NA FALSE SLC6A7_p.L462= chr5:150204585:150204586:G:C SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 150554757 150554758 G T 60 86 0.697674418604651 MODIFIER NDST1 ENSG00000070614 T 3_prime_UTR_variant Transcript ENST00000261797 protein_coding 15/15 ENST00000261797.7:c.*1425G>T NA 4557 1 SNV HGNC HGNC:7680 YES NM_001543.5 1 P1 CCDS34277.1 ENSP00000261797 P52848.189 UPI000012CDA5 P52848-1 1 18 NA NA PASS SITE 49,39|29,31 NA NA 1 93 20,20 168,171 60,60 33 1.64 NA 12.94 NA FALSE 6.00 93 NA NA NA FALSE NA NA 165.62 18 150554757 HCC1395_HCC1395T 26 0.700 86 4,22 11,17 17,41 NA 0/1 NA NA NA NA 16,10,29,31 G/T PANCANCER NA FALSE NDST1 chr5:150554757:150554758:G:T SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 154453835 154453836 TG T 12 18 0.666666666666667 MODIFIER SAP30L ENSG00000164576 - intron_variant Transcript ENST00000297109 protein_coding 3/3 ENST00000297109.11:c.423+336del NA 1 deletion HGNC HGNC:25663 YES NM_024632.6 1 P1 CCDS4326.1 ENSP00000297109 Q9HAJ7.161 UPI000007275D Q9HAJ7-1 18 NA NA PASS SITE 4,15|1,11 NA NA 1 22 36,39 176,193 60,60 23 1.14 NA 3.60 NA FALSE 6.00 93 NA NA NA FALSE NA NA 35.65 18 154453835 HCC1395_HCC1395T 6 0.667 18 1,0 0,1 5,11 NA 0/1 NA NA NA NA 1,5,1,11 TG/T PANCANCER NA FALSE SAP30L chr5:154453835:154453836:TG:T indel 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 157473516 157473517 G T 10 51 0.196078431372549 MODIFIER ADAM19 ENSG00000135074 T downstream_gene_variant Transcript ENST00000257527 protein_coding NA 3788 -1 SNV HGNC HGNC:197 YES NM_033274.5 1 P1 CCDS4338.1 ENSP00000257527 Q9H013.196 UPI000013CF6A Q9H013-2 18 NA NA PASS SITE 54,49|6,4 NA NA 1 93 20,32 162,175 60,60 31 1.66 NA 13.55 NA FALSE 6.00 46 NA NA NA FALSE NA NA 23.83 18 157473516 HCC1395_HCC1395T 41 0.230 51 12,4 17,4 29,8 NA 0/1 NA NA NA NA 22,19,6,4 G/T PANCANCER NA FALSE ADAM19 chr5:157473516:157473517:G:T SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 157743914 157743915 A C 157 502 0.312749003984064 MODIFIER THG1L ENSG00000113272 C downstream_gene_variant Transcript ENST00000231198 protein_coding NA 2465 1 SNV HGNC HGNC:26053 YES NM_017872.5 1 P1 CCDS4341.1 ENSP00000231198 Q9NWX6.164 UPI0000073782 1 18 NA NA PASS SITE 440,484|76,83 NA NA 1 93 20,20 151,154 60,60 36 2.56 NA 107.67 NA FALSE 6.00 93 NA NA NA FALSE NA NA 371.02 18 157743914 HCC1395_HCC1395T 345 0.312 502 107,44 105,52 224,101 NA 0/1 NA NA NA NA 165,180,76,81 A/C PANCANCER NA FALSE THG1L chr5:157743914:157743915:A:C SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 158712060 158712061 C G 34 47 0.723404255319149 MODIFIER EBF1 ENSG00000164330 G intron_variant Transcript ENST00000313708 protein_coding 14/15 ENST00000313708.11:c.1549+94G>C NA -1 SNV HGNC HGNC:3126 YES NM_024007.5 1 P1 CCDS4343.1 ENSP00000322898 Q9UH73.178 UPI000000D95E Q9UH73-1 1 18 NA NA PASS SITE 35,41|17,17 NA NA 1 93 37,20 169,161 60,60 35 1.68 NA 13.85 NA FALSE 6.00 63 NA NA NA FALSE NA NA 99.60 18 158712060 HCC1395_HCC1395T 13 0.676 47 2,4 7,19 11,24 NA 0/1 NA NA NA NA 6,7,17,17 C/G PANCANCER NA FALSE EBF1 chr5:158712060:158712061:C:G SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 160354994 160354995 G A 64 194 0.329896907216495 LOW C1QTNF2 ENSG00000145861 A synonymous_variant Transcript ENST00000393975 protein_coding 2/3 ENST00000393975.4:c.153C>T ENSP00000377545.3:p.L51= ENSP00000377545.3 p.L51= 157 153 51 L ctC/ctT rs377762554 -1 SNV HGNC HGNC:14325 1 ENSP00000377545 A0A499FIM1.19 UPI0000D4B9D3 AlphaFold_DB_import:AF-A0A499FIM1-F1&Low_complexity_(Seg):seg 1.009e-05 0.0001508 0 0 0 0 0 0 0 0.0001314 0.0004585 0 6.545e-05 0 0 0 0 0 0 0 0.0004585 gnomADg_AFR 18 NA NA PASS SITE 123,166|21,43 NA NA 1 93 20,20 160,168 60,60 34 2.05 NA 32.80 NA FALSE 4.31 93 NA NA NA FALSE NA NA 161.09 18 160354994 HCC1395_HCC1395T 130 0.356 194 34,18 42,25 84,46 NA 0/1 NA NA NA NA 55,75,21,43 G/A PANCANCER NA FALSE C1QTNF2_p.L51= chr5:160354994:160354995:G:A SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 168262872 168262873 T C 13 76 0.171052631578947 MODIFIER TENM2 ENSG00000145934 C 3_prime_UTR_variant Transcript ENST00000518659 protein_coding 31/31 ENST00000518659.6:c.*62T>C NA 9071 1 SNV HGNC HGNC:29943 YES NM_001395460.1 5 P1 CCDS93818.1 ENSP00000429430 Q9NT68.159 UPI0001C48FC2 Q9NT68-1 18 NA NA PASS SITE 43,65|6,7 NA NA 1 93 29,36 184,182 60,60 29 1.56 NA 10.53 NA FALSE 6.00 34 NA NA NA FALSE NA NA 32.80 18 168262872 HCC1395_HCC1395T 63 0.184 76 22,3 25,7 48,10 NA 0/1 NA NA NA NA 25,38,6,7 T/C PANCANCER NA FALSE TENM2 chr5:168262872:168262873:T:C SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 172683319 172683320 C T 6 12 0.5 MODIFIER NEURL1B ENSG00000214357 T intron_variant Transcript ENST00000369800 protein_coding 2/4 ENST00000369800.6:c.578-100C>T NA 1 SNV HGNC HGNC:35422 YES NM_001142651.3 1 P1 CCDS47342.1 ENSP00000358815 A8MQ27.115 UPI0000D6E5EA A8MQ27-1 18 NA NA PASS SITE 13,3|6,0 NA NA 1 27 38,36 238,206 60,60 24 1.05 NA 2.71 NA FALSE 6.00 27 NA NA NA FALSE NA NA 20.90 18 172683319 HCC1395_HCC1395T 6 0.583 12 2,5 2,1 4,6 NA 0/1 NA NA NA NA 4,2,6,0 C/T PANCANCER NA FALSE NEURL1B chr5:172683319:172683320:C:T SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 175528598 175528599 GA G 40 288 0.138888888888889 MODIFIER SFXN1 ENSG00000164466 - 3_prime_UTR_variant Transcript ENST00000321442 protein_coding 11/11 ENST00000321442.10:c.*1870del NA 2923 1 deletion HGNC HGNC:16085 YES NM_022754.7 1 P1 CCDS4394.1 ENSP00000316905 Q9H9B4.180 UPI0000044799 5 18 NA NA PASS SITE 209,227|19,21 NA NA 2 93 20,20 166,160 60,60 27 2.11 NA 37.41 NA FALSE 6.00 93 6,5 A NA TRUE NA 93 128.32 18 175528598 HCC1395_HCC1395T 248 0.143 288 53,4 73,16 167,27 NA 0|1 0|1 175528598_GA_G NA 175528598 119,129,19,21 GA|G PANCANCER NA FALSE SFXN1 chr5:175528598:175528599:GA:G indel 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 175528605 175528606 T C 41 298 0.13758389261745 MODIFIER SFXN1 ENSG00000164466 C 3_prime_UTR_variant Transcript ENST00000321442 protein_coding 11/11 ENST00000321442.10:c.*1871T>C NA 2929 1 SNV HGNC HGNC:16085 YES NM_022754.7 1 P1 CCDS4394.1 ENSP00000316905 Q9H9B4.180 UPI0000044799 18 NA NA PASS SITE 215,234|19,22 NA NA 2 93 20,20 166,159 60,60 29 2.11 NA 38.01 NA FALSE 6.00 29 NA NA NA FALSE NA NA 127.99 18 175528605 HCC1395_HCC1395T 257 0.139 298 51,4 79,16 172,27 NA 0|1 0|1 175528598_GA_G NA 175528598 123,134,19,22 T|C PANCANCER NA FALSE SFXN1 chr5:175528605:175528606:T:C SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 177460555 177460557 CC TA 73 232 0.314655172413793 HIGH DBN1 ENSG00000113758 TA splice_acceptor_variant&coding_sequence_variant Transcript ENST00000292385 protein_coding 11/15 10/14 ENST00000292385.9:c.838-1_838delinsTA NA ?-1448 ?-838 ?-280 -1 substitution HGNC HGNC:2695 1 CCDS4421.1 ENSP00000292385 Q16643.209 UPI0000457395 Q16643-2 18 NA NA PASS SITE 224,144|51,22 NA NA 1 93 20,20 167,166 60,60 24 2.18 NA 44.85 NA FALSE 6.00 93 NA NA NA FALSE NA NA 281.93 18 177460555 HCC1395_HCC1395T 159 0.317 232 56,22 51,30 113,52 NA 0/1 NA NA NA NA 100,59,51,22 CC/TA PANCANCER NA FALSE DBN1 chr5:177460555:177460557:CC:TA indel 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 179733119 179733120 C G 26 72 0.361111111111111 MODIFIER CANX ENSG00000127022 G downstream_gene_variant Transcript ENST00000247461 protein_coding NA 1478 1 SNV HGNC HGNC:1473 YES NM_001746.4 1 P3 CCDS4447.1 ENSP00000247461 P27824.237 UPI000000D9F9 P27824-1 18 NA NA PASS SITE 66,51|17,9 NA NA 1 93 20,36 156,171 60,60 27 1.71 NA 15.05 NA FALSE 6.00 84 NA NA NA FALSE NA NA 73.82 18 179733119 HCC1395_HCC1395T 46 0.404 72 7,6 23,14 30,20 NA 0/1 NA NA NA NA 24,22,17,9 C/G PANCANCER NA FALSE CANX chr5:179733119:179733120:C:G SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 179820845 179820846 C T 46 126 0.365079365079365 MODIFIER SQSTM1 ENSG00000161011 T upstream_gene_variant Transcript ENST00000360718 protein_coding NA rs368244826 1640 1 SNV HGNC HGNC:11280 1 CCDS47355.1 ENSP00000353944 Q13501.222 UPI000007291E Q13501-2 1 18 NA NA PASS SITE 107,82|28,18 NA NA 1 93 33,20 176,152 60,60 26 1.92 NA 24.98 NA FALSE 6.00 71 NA NA NA FALSE NA NA 117.82 18 179820845 HCC1395_HCC1395T 80 0.351 126 23,9 36,23 60,32 NA 0/1 NA NA NA NA 45,35,28,18 C/T PANCANCER NA FALSE SQSTM1 chr5:179820845:179820846:C:T SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 179913895 179913896 GGCTCACGCTTT G 74 74 1 MODIFIER RNF130 ENSG00000113269 - 3_prime_UTR_variant Transcript ENST00000522208 protein_coding 8/8 ENST00000522208.6:c.*6411_*6421del NA 7690-7700 -1 deletion HGNC HGNC:18280 5 A1 CCDS93841.1 ENSP00000429509 E5RI87.87 UPI0001E8F14E 18 NA NA PASS SITE 39,29|40,34 NA NA 1 93 20,21 168,180 60,60 33 1.69 NA 14.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 327.98 18 179913895 HCC1395_HCC1395T 0 0.983 74 0,18 0,24 0,55 NA 0/1 NA NA NA NA 0,0,40,34 GGCTCACGCTTT/G PANCANCER NA FALSE RNF130 chr5:179913895:179913896:GGCTCACGCTTT:G indel 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 180100974 180100975 G A 76 106 0.716981132075472 MODIFIER RASGEF1C ENSG00000146090 A 3_prime_UTR_variant Transcript ENST00000361132 protein_coding 14/14 ENST00000361132.9:c.*527C>T NA 2118 -1 SNV HGNC HGNC:27400 YES NM_175062.4 1 P1 CCDS4452.1 ENSP00000354963 Q8N431.133 UPI0000037308 Q8N431-1 18 NA NA PASS SITE 63,64|39,37 NA NA 1 93 20,20 157,159 60,60 31 1.84 NA 20.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 208.86 18 180100974 HCC1395_HCC1395T 30 0.693 106 10,19 9,27 22,51 NA 0/1 NA NA NA NA 12,18,39,37 G/A PANCANCER NA FALSE RASGEF1C chr5:180100974:180100975:G:A SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 180101704 180101705 G A 4 8 0.5 MODIFIER RASGEF1C ENSG00000146090 A intron_variant Transcript ENST00000361132 protein_coding 13/13 ENST00000361132.9:c.1377-179C>T NA rs182843034 -1 SNV HGNC HGNC:27400 YES NM_175062.4 1 P1 CCDS4452.1 ENSP00000354963 Q8N431.133 UPI0000037308 Q8N431-1 0.0004 0.0015 0 0 0 0 0.0001577 0.0002895 0 0.0005886 0 0 0 0 4.41e-05 0 0 0.0015 AFR 18 NA NA PASS SITE 0,13|0,4 NA NA 1 6 38,36 226,223 60,60 21 1.000 NA 2.71 NA FALSE 3.71 34 NA NA NA FALSE NA NA 13.67 18 180101704 HCC1395_HCC1395T 4 0.500 8 1,3 3,1 4,4 NA 0/1 NA NA NA NA 0,4,0,4 G/A PANCANCER NA FALSE RASGEF1C chr5:180101704:180101705:G:A SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 180330640 180330641 A G 70 70 1 MODIFIER GFPT2 ENSG00000131459 G intron_variant Transcript ENST00000253778 protein_coding 6/18 ENST00000253778.13:c.534+60T>C NA -1 SNV HGNC HGNC:4242 YES NM_005110.4 1 P1 CCDS43411.1 ENSP00000253778 O94808.179 A0A0S2Z4X9.44 UPI000014F5AC 18 NA NA PASS SITE 41,15|53,17 NA NA 1 93 20,33 172,165 60,60 18 1.63 NA 12.34 NA FALSE 6.00 93 NA NA NA FALSE NA NA 237.97 18 180330640 HCC1395_HCC1395T 0 0.983 70 0,19 0,35 0,54 NA 0/1 NA NA NA NA 0,0,53,17 A/G PANCANCER NA FALSE GFPT2 chr5:180330640:180330641:A:G SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr5 180947416 180947417 T A 3 15 0.2 MODIFIER BTNL8 ENSG00000113303 A intron_variant Transcript ENST00000231229 protein_coding 3/7 ENST00000231229.8:c.674-96T>A NA 1 SNV HGNC HGNC:26131 1 CCDS4459.1 ENSP00000231229 Q6UX41.153 UPI000006DFD7 Q6UX41-5 18 NA NA PASS SITE 33,0|3,0 NA NA 1 66 36,35 210,267 60,60 28 1.35 NA 6.32 NA FALSE 6.00 31 NA NA NA FALSE NA NA 7.74 18 180947416 HCC1395_HCC1395T 12 0.234 15 2,1 10,2 12,3 NA 0/1 NA NA NA NA 12,0,3,0 T/A PANCANCER NA FALSE BTNL8 chr5:180947416:180947417:T:A SNV 3:0 chr5:149858353:181155980:3:0:1 NA NA 0.96 +chr6 367481 367482 T G 88 234 0.376068376068376 MODIFIER G intergenic_variant NA rs7738368 SNV 0.2542 0.2474 0.3213 0.2227 0.2434 0.3093 0.2546 0.3377 0.2542 0.2965 0.3244 0.3377 gnomADg_MID 19 NA NA PASS SITE 89,146|33,55 NA NA 1 93 20,20 169,165 60,60 30 1.79 NA 18.36 NA FALSE 0.569 93 NA NA NA FALSE NA NA 217.36 19 367481 HCC1395_HCC1395T 146 0.367 234 37,23 49,34 101,58 NA 0/1 NA NA NA NA 56,90,33,55 T/G PANCANCER NA FALSE chr6:367481:367482:T:G SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 406714 406715 G C 54 94 0.574468085106383 MODIFIER IRF4 ENSG00000137265 C intron_variant Transcript ENST00000380956 protein_coding 8/8 ENST00000380956.9:c.1213-741G>C NA rs113279656 1 SNV HGNC HGNC:6119 YES NM_002460.4 1 P3 CCDS4469.1 ENSP00000370343 Q15306.212 UPI000012D88B Q15306-1 1 0.0076 0.0257 0.0043 0 0.001 0 0.007791 0.02669 0 0.003012 0 0 0 0.003165 0.0002499 0.007163 0.0002074 0.02669 gnomADg_AFR 19 NA NA PASS SITE 32,41|22,32 NA NA 1 28 20,20 173,184 60,60 30 1.38 NA 6.92 NA FALSE 2.23 93 NA NA NA FALSE NA NA 159.49 19 406714 HCC1395_HCC1395T 40 0.556 94 7,9 9,13 32,40 NA 0/1 NA NA NA NA 17,23,22,32 G/C PANCANCER TRUE FALSE IRF4 chr6:406714:406715:G:C SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 693180 693181 G C 37 52 0.711538461538462 MODIFIER EXOC2 ENSG00000112685 C upstream_gene_variant Transcript ENST00000230449 protein_coding NA rs542770065 41 -1 SNV HGNC HGNC:24968 YES NM_018303.6 1 P1 CCDS34327.1 ENSP00000230449 Q96KP1.186 A0A024QZT2.62 UPI000003E7E3 1 0.0032 0.0121 0 0 0 0 0.002668 0.009479 0 0.000327 0 0 0 0 7.349e-05 0.001438 0 0.0121 AFR 19 NA NA PASS SITE 10,29|13,24 NA NA 1 25 30,20 172,156 60,60 36 1.30 NA 5.42 NA FALSE 2.55 87 NA NA NA FALSE NA NA 105.97 19 693180 HCC1395_HCC1395T 15 0.659 52 6,6 7,18 13,26 NA 0/1 NA NA NA NA 3,12,13,24 G/C PANCANCER NA FALSE EXOC2 chr6:693180:693181:G:C SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 1394902 1394903 C T 37 254 0.145669291338583 MODIFIER MIR6720 ENSG00000275859 T upstream_gene_variant Transcript ENST00000611664 miRNA NA 4491 -1 SNV HGNC HGNC:50032 YES 19 NA NA PASS SITE 124,177|11,26 NA NA 1 93 20,38 169,179 60,60 27 1.79 NA 17.75 NA FALSE 6.00 93 NA NA NA FALSE NA NA 100.36 19 1394902 HCC1395_HCC1395T 217 0.175 254 50,12 91,16 150,31 NA 0/1 NA NA NA NA 91,126,11,26 C/T PANCANCER NA FALSE MIR6720 chr6:1394902:1394903:C:T SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 1611782 1611786 A ACGG 126 211 0.597156398104265 MODERATE FOXC1 ENSG00000054598 CGG inframe_insertion Transcript ENST00000645831 protein_coding 1/1 ENST00000645831.2:c.1359_1361dup ENSP00000493906.1:p.Gly455dup ENSP00000493906.1 p.Gly455dup 1868-1869 1337-1338 446 H/HG cac/caCGGc rs398123612 1 insertion HGNC HGNC:3800 YES NM_001453.3 P1 CCDS4473.1 ENSP00000493906 Q12948.209 W6CJ52.68 UPI000012ADC5 1 Low_complexity_(Seg):seg&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-Q12948-F1 24 0.2401 0.2789 0.3366 0.2002 0.3154 0.1812 0.2067 0.2353 0.2422 0.2831 0.327 0.171 0.3377 0.2179 0.4153 0.2252 0.1739 0.2454 0.2747 0.3319 0.4153 gnomADg_EAS 1 19 NA NA PASS SITE 57,78|52,74 NA NA 1 19 20,20 154,166 60,60 39 1.62 NA 10.32 NA FALSE 0.595 93 8,9 CGG NA TRUE NA 93 361.73 19 1611782 HCC1395_HCC1395T 85 0.602 211 24,36 23,32 62,95 NA 0/1 NA NA NA NA 33,52,52,74 A/ACGG PANCANCER NA FALSE FOXC1_p.Gly455dup chr6:1611782:1611786:A:ACGG indel 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 1623755 1623756 C T 101 188 0.537234042553192 MODIFIER GMDS ENSG00000112699 T downstream_gene_variant Transcript ENST00000380805 retained_intron NA rs9501746 52 -1 SNV HGNC HGNC:4369 2 0.2788 0.6324 0.1974 0.1002 0.1511 0.1738 0.2675 0.5651 0.1645 0.2362 0.1086 0.1041 0.131 0.2437 0.1429 0.2572 0.189 0.6324 AFR 19 NA NA PASS SITE 109,38|77,24 NA NA 2 66 20,37 164,171 60,60 23 1.63 NA 12.34 NA FALSE 0.618 93 NA NA NA FALSE NA NA 302.38 19 1623755 HCC1395_HCC1395T 87 0.536 188 29,33 40,45 69,80 NA 0/1 NA NA NA NA 68,19,77,24 C/T PANCANCER NA FALSE GMDS chr6:1623755:1623756:C:T SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 1623794 1623795 T A 192 355 0.540845070422535 MODIFIER GMDS ENSG00000112699 A downstream_gene_variant Transcript ENST00000380805 retained_intron NA rs113534680 13 -1 SNV HGNC HGNC:4369 2 0.0068 0.0257 0 0 0 0 0.005735 0.02 0 0.002159 0 0 0 0.003165 4.409e-05 0.003346 0 0.0257 AFR 19 NA NA PASS SITE 168,104|126,66 NA NA 2 93 20,20 165,168 60,60 32 1.86 NA 21.37 NA FALSE 2.29 93 NA NA NA FALSE NA NA 543.32 19 1623794 HCC1395_HCC1395T 163 0.555 355 38,47 64,81 109,136 NA 0/1 NA NA NA NA 101,62,126,66 T/A PANCANCER NA FALSE GMDS chr6:1623794:1623795:T:A SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 2664218 2664219 C T 167 302 0.552980132450331 MODIFIER MYLK4 ENSG00000145949 T 3_prime_UTR_variant Transcript ENST00000274643 protein_coding 13/13 ENST00000274643.9:c.*3707G>A NA 5173 rs111399695 -1 SNV HGNC HGNC:27972 YES NM_001012418.5 1 A2 CCDS34330.1 ENSP00000274643 Q86YV6.140 UPI00000498AE Q86YV6-1 0.0336 0.1248 0.0043 0 0 0 0.03334 0.1159 0 0.01285 0 0 0 0 0.0003823 0.02392 0.0004146 0.1248 AFR 19 NA NA PASS SITE 105,134|73,94 NA NA 1 93 20,20 163,164 60,60 39 1.83 NA 19.82 NA FALSE 1.55 93 NA NA NA FALSE NA NA 396.35 19 2664218 HCC1395_HCC1395T 135 0.534 302 39,38 42,54 90,103 NA 0/1 NA NA NA NA 60,75,73,94 C/T PANCANCER NA FALSE MYLK4 chr6:2664218:2664219:C:T SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 2665879 2665880 G A 131 253 0.517786561264822 MODIFIER MYLK4 ENSG00000145949 A 3_prime_UTR_variant Transcript ENST00000274643 protein_coding 13/13 ENST00000274643.9:c.*2046C>T NA 3512 rs115412487 -1 SNV HGNC HGNC:27972 YES NM_001012418.5 1 A2 CCDS34330.1 ENSP00000274643 Q86YV6.140 UPI00000498AE Q86YV6-1 0.0038 0.0144 0 0 0 0 0.00526 0.01831 0 0.002094 0 0 0 0 4.412e-05 0.003349 0 0.01831 gnomADg_AFR 19 NA NA PASS SITE 69,127|52,79 NA NA 1 93 20,20 161,154 60,60 23 1.73 NA 15.65 NA FALSE 2.40 93 NA NA NA FALSE NA NA 330.55 19 2665879 HCC1395_HCC1395T 122 0.503 253 30,32 24,30 86,87 NA 0/1 NA NA NA NA 44,78,52,79 G/A PANCANCER NA FALSE MYLK4 chr6:2665879:2665880:G:A SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 2674999 2675000 A C 54 87 0.620689655172414 MODIFIER MYLK4 ENSG00000145949 C intron_variant Transcript ENST00000274643 protein_coding 11/12 ENST00000274643.9:c.1119+48T>G NA rs56013759&COSV51157686 -1 SNV HGNC HGNC:27972 YES NM_001012418.5 1 A2 CCDS34330.1 ENSP00000274643 Q86YV6.140 UPI00000498AE Q86YV6-1 0.0028 0.0106 0 0 0 0 0.001186 0.01633 0.0007318 0 0 0 2.705e-05 0.0005078 0 0.004881 0.01705 0 0.001897 0 0 0 0 1.47e-05 0.002395 0.000207 0.01705 gnomADg_AFR 0&1 0&1 19 NA NA PASS SITE 42,23|38,16 NA NA 1 30 20,30 174,165 60,60 34 1.39 NA 6.92 NA FALSE 2.40 93 NA NA NA FALSE NA NA 162.03 19 2674999 HCC1395_HCC1395T 33 0.612 87 5,11 20,27 25,40 NA 0/1 NA NA NA NA 22,11,38,16 A/C PANCANCER NA FALSE MYLK4 chr6:2674999:2675000:A:C SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 2834013 2834014 C G 114 223 0.511210762331839 HIGH SERPINB1 ENSG00000021355 G splice_acceptor_variant Transcript ENST00000380739 protein_coding 6/6 ENST00000380739.6:c.736-1G>C NA COSV66313938 -1 SNV HGNC HGNC:3311 YES NM_030666.4 1 P1 CCDS4477.1 ENSP00000370115 P30740.204 V9HWH1.74 UPI000012D514 P30740-1 1 1 19 NA NA PASS SITE 47,108|39,75 NA NA 1 93 20,20 166,162 60,60 27 1.55 NA 10.19 NA FALSE 6.00 93 NA NA NA FALSE NA NA 306.22 19 2834013 HCC1395_HCC1395T 109 0.505 223 25,22 39,44 78,80 NA 0/1 NA NA NA NA 35,74,39,75 C/G PANCANCER NA FALSE SERPINB1 chr6:2834013:2834014:C:G SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 2840548 2840549 C T 219 402 0.544776119402985 LOW SERPINB1 ENSG00000021355 T synonymous_variant Transcript ENST00000380739 protein_coding 2/7 ENST00000380739.6:c.39G>A ENSP00000370115.5:p.L13= ENSP00000370115.5 p.L13= 99 39 13 L ttG/ttA rs34249702&COSV66313964 -1 SNV HGNC HGNC:3311 YES NM_030666.4 1 P1 CCDS4477.1 ENSP00000370115 P30740.204 V9HWH1.74 UPI000012D514 P30740-1 Gene3D:3.30.497.10&PDB-ENSP_mappings:4ga7.A&PDB-ENSP_mappings:4ga7.B&AlphaFold_DB_import:AF-P30740-F1&Pfam:PF00079&PANTHER:PTHR11461&SMART:SM00093&Superfamily:SSF56574&CDD:cd19560 0.0134 0.0469 0.0043 0 0.002 0 0.003579 0.04283 0.002642 0.002284 0 0 0.0006068 0.003266 0 0.01234 0.04248 0 0.004318 0.002594 0 0 0.006329 0.0003675 0.007191 0.0002072 0.0469 AFR benign 0&1 1&1 19 NA NA PASS SITE 119,174|89,130 NA NA 1 93 20,20 155,156 60,60 33 1.87 NA 21.67 NA FALSE 2.01 93 NA NA NA FALSE NA NA 563.05 19 2840548 HCC1395_HCC1395T 183 0.548 402 49,57 51,76 118,143 NA 0/1 NA NA NA NA 75,108,89,130 C/T PANCANCER NA FALSE SERPINB1_p.L13= chr6:2840548:2840549:C:T SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 2840643 2840644 G A 81 134 0.604477611940298 MODIFIER SERPINB1 ENSG00000021355 A intron_variant Transcript ENST00000380739 protein_coding 1/6 ENST00000380739.6:c.-8-49C>T NA rs76406190 -1 SNV HGNC HGNC:3311 YES NM_030666.4 1 P1 CCDS4477.1 ENSP00000370115 P30740.204 V9HWH1.74 UPI000012D514 P30740-1 0.0134 0.0469 0.0043 0 0.002 0 0.01228 0.04227 0 0.004316 0.002592 0 0 0.006329 0.0003675 0.007177 0.0002069 0.0469 AFR 19 NA NA PASS SITE 25,61|29,52 NA NA 1 33 34,20 162,169 60,60 35 1.43 NA 7.83 NA FALSE 2.01 93 NA NA NA FALSE NA NA 231.91 19 2840643 HCC1395_HCC1395T 53 0.585 134 11,24 22,25 41,58 NA 0/1 NA NA NA NA 17,36,29,52 G/A PANCANCER NA FALSE SERPINB1 chr6:2840643:2840644:G:A SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 2842016 2842017 G A 58 107 0.542056074766355 MODIFIER SERPINB1 ENSG00000021355 A upstream_gene_variant Transcript ENST00000380739 protein_coding NA rs552588610 153 -1 SNV HGNC HGNC:3311 YES NM_030666.4 1 P1 CCDS4477.1 ENSP00000370115 P30740.204 V9HWH1.74 UPI000012D514 P30740-1 0.0062 0.0227 0.0014 0 0 0 0.00597 0.02127 0 0.001309 0 0 0 0 0 0.003365 0 0.0227 AFR 19 NA NA PASS SITE 29,57|17,41 NA NA 1 41 20,20 158,168 60,60 22 1.46 NA 8.13 NA FALSE 2.32 51 NA NA NA FALSE NA NA 171.28 19 2842016 HCC1395_HCC1395T 49 0.560 107 8,7 19,29 33,42 NA 0/1 NA NA NA NA 17,32,17,41 G/A PANCANCER NA FALSE SERPINB1 chr6:2842016:2842017:G:A SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 3000069 3000070 A C 122 213 0.572769953051643 MODIFIER NQO2 ENSG00000124588 C 5_prime_UTR_variant Transcript ENST00000338130 protein_coding 1/10 ENST00000338130.7:c.-617A>C NA 96 rs2071002&CR093469 1 SNV HGNC HGNC:7856 2 P1 CCDS4481.1 ENSP00000337773 P16083.224 UPI000020E40D 1 0.3249 0.3865 0.3199 0.3413 0.2932 0.2607 0.3225 0.3711 0.1923 0.329 0.2082 0.347 0.295 0.2215 0.3053 0.3069 0.2815 0.3865 AFR 0&1 19 NA NA PASS SITE 90,67|71,51 NA NA 1 73 20,20 161,147 60,60 39 1.66 NA 13.54 NA FALSE 0.502 93 NA NA NA FALSE NA NA 319.71 19 3000069 HCC1395_HCC1395T 91 0.579 213 19,35 31,40 57,79 NA 0/1 NA NA NA NA 49,42,71,51 A/C PANCANCER NA FALSE NQO2 chr6:3000069:3000070:A:C SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 3177289 3177290 A C 11 602 0.0182724252491694 MODIFIER TUBB2BP1 ENSG00000216819 C non_coding_transcript_exon_variant Transcript ENST00000404155 unprocessed_pseudogene 3/3 ENST00000404155.1:n.626T>G NA 626 -1 SNV HGNC HGNC:42332 YES 19 NA NA PASS SITE 331,394|5,6 NA NA 1 93 20,20 163,175 53,39 40 1.94 NA 25.28 NA FALSE 6.00 57 NA NA NA FALSE NA NA 16.25 19 3177289 HCC1395_HCC1395T 591 0.023 602 170,3 181,4 377,8 NA 0/1 NA NA NA NA 270,321,5,6 A/C PANCANCER NA FALSE TUBB2BP1 chr6:3177289:3177290:A:C SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 3723708 3723709 C G 249 432 0.576388888888889 MODERATE PXDC1 ENSG00000168994 G missense_variant Transcript ENST00000380277 protein_coding 5/5 ENST00000380277.6:c.451G>C ENSP00000369630.2:p.E151Q ENSP00000369630.2 p.E151Q 450 451 151 E/Q Gag/Cag rs368727869&COSV66662225 -1 cds_start_NF SNV HGNC HGNC:21361 3 ENSP00000369630 H0Y3G1.55 UPI000059D88E deleterious(0.04) benign(0.011) PANTHER:PTHR31433 4.014e-06 0 0 0 0 0 8.974e-06 0 0 6.571e-06 0 0 0 0 0 0 0 1.47e-05 0 0 1.47e-05 gnomADg_NFE 0&1 0&1 19 NA NA PASS SITE 161,143|129,120 NA NA 1 93 20,20 157,165 60,60 34 1.90 NA 22.87 NA FALSE 6.00 93 NA NA NA FALSE NA NA 641.78 19 3723708 HCC1395_HCC1395T 183 0.574 432 46,61 63,89 115,155 NA 0/1 NA NA NA NA 96,87,129,120 C/G PANCANCER NA FALSE PXDC1_p.E151Q chr6:3723708:3723709:C:G SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 5042499 5042500 T C 135 239 0.564853556485356 MODIFIER ENSG00000271978 C intron_variant&non_coding_transcript_variant Transcript ENST00000606227 lncRNA 1/1 ENST00000606227.1:n.347-7817A>G NA rs73365181 -1 SNV YES 2 0.0365 0.0076 0.0173 0.0069 0.0437 0.1125 0.02651 0.01576 0.002198 0.01564 0.01962 0.002502 0.05272 0.03165 0.02908 0.03152 0.09253 0.1125 SAS 19 NA NA PASS SITE 95,58|75,60 NA NA 1 49 20,20 157,155 60,60 34 1.54 NA 9.93 NA FALSE 1.54 93 NA NA NA FALSE NA NA 343.84 19 5042499 HCC1395_HCC1395T 104 0.547 239 27,30 42,55 71,86 NA 0/1 NA NA NA NA 64,40,75,60 T/C PANCANCER NA FALSE chr6:5042499:5042500:T:C SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 6250887 6250888 T A 242 442 0.547511312217195 MODERATE F13A1 ENSG00000124491 A missense_variant Transcript ENST00000264870 protein_coding 5/15 ENST00000264870.8:c.614A>T ENSP00000264870.3:p.Y205F ENSP00000264870.3 p.Y205F 708 614 205 Y/F tAt/tTt rs3024477&CM994628&COSV99079976 -1 SNV HGNC HGNC:3531 YES NM_000129.4 1 P1 CCDS4496.1 ENSP00000264870 P00488.244 UPI000013D585 1 tolerated(0.45) probably_damaging(0.981) PDB-ENSP_mappings:1evu.A&PDB-ENSP_mappings:1evu.B&PDB-ENSP_mappings:1ex0.A&PDB-ENSP_mappings:1ex0.B&PDB-ENSP_mappings:1f13.A&PDB-ENSP_mappings:1f13.B&PDB-ENSP_mappings:1fie.A&PDB-ENSP_mappings:1fie.B&PDB-ENSP_mappings:1ggt.A&PDB-ENSP_mappings:1ggt.B&PDB-ENSP_mappings:1ggu.A&PDB-ENSP_mappings:1ggu.B&PDB-ENSP_mappings:1ggy.A&PDB-ENSP_mappings:1ggy.B&PDB-ENSP_mappings:1qrk.A&PDB-ENSP_mappings:1qrk.B&PDB-ENSP_mappings:4kty.A&PDB-ENSP_mappings:4kty.B&PDB-ENSP_mappings:5mhl.A&PDB-ENSP_mappings:5mhl.B&PDB-ENSP_mappings:5mhm.A&PDB-ENSP_mappings:5mhm.B&PDB-ENSP_mappings:5mhn.A&PDB-ENSP_mappings:5mhn.B&PDB-ENSP_mappings:5mho.A&PDB-ENSP_mappings:5mho.B&PANTHER:PTHR11590&Gene3D:3.90.260.10&PIRSF:PIRSF000459&Superfamily:SSF54001&AlphaFold_DB_import:AF-P00488-F1 0.0082 0.0008 0.0101 0 0.0298 0.0031 0.01792 0.004614 0.00613 0.02075 0.0001632 0.03525 0.02691 0.01617 0.002875 0.01867 0.005404 0.05263 0.006678 0.01729 0.0001922 0.03639 0.003165 0.02918 0.00956 0.002897 0.05263 gnomADg_AMI likely_benign 0&0&1 1&1&1 19 NA NA PASS SITE 155,152|122,121 NA NA 1 93 20,20 161,165 60,60 35 0.233 NA 17.89 NA FALSE 1.66 93 NA NA NA FALSE NA NA 641.59 19 6250887 HCC1395_HCC1395T 200 0.559 442 45,57 81,98 127,161 NA 0/1 NA NA NA NA 100,100,121,121 T/A PANCANCER NA FALSE F13A1_p.Y205F chr6:6250887:6250888:T:A SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 7268321 7268322 A G 82 147 0.557823129251701 MODIFIER SSR1 ENSG00000124783 G 3_prime_UTR_variant Transcript ENST00000474597 protein_coding 10/10 ENST00000474597.5:c.*809T>C NA 1793 rs142136740 -1 SNV HGNC HGNC:11323 5 ENSP00000418617 C9IZQ1.78 UPI0001B793E4 0.0020 0 0.0043 0 0.007 0 0.002648 0.0009409 0 0.002552 0.0008646 0 0.0007536 0.003165 0.004438 0.005253 0 0.007 EUR 19 NA NA PASS SITE 68,39|58,24 NA NA 1 43 20,34 165,167 60,60 31 1.46 NA 8.13 NA FALSE 2.66 93 NA NA NA FALSE NA NA 248.22 19 7268321 HCC1395_HCC1395T 65 0.582 147 15,24 29,35 45,63 NA 0/1 NA NA NA NA 42,23,58,24 A/G PANCANCER NA FALSE SSR1 chr6:7268321:7268322:A:G SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 7285918 7285919 A G 61 109 0.559633027522936 MODIFIER SSR1 ENSG00000124783 G 3_prime_UTR_variant Transcript ENST00000244763 protein_coding 8/8 ENST00000244763.9:c.*3946T>C NA 4886 rs72818943 -1 SNV HGNC HGNC:11323 YES NM_003144.5 1 P2 CCDS4499.1 ENSP00000244763 P43307.192 UPI0000135FFE P43307-1 0.0112 0.0023 0.0216 0 0.0358 0.002 0.02244 0.006464 0.07127 0.0269 0.04441 0 0.01357 0.02215 0.03337 0.03547 0.004758 0.07127 gnomADg_AMI 19 NA NA PASS SITE 49,38|32,29 NA NA 1 57 34,39 223,236 60,60 22 1.57 NA 10.49 NA FALSE 1.66 93 NA NA NA FALSE NA NA 213.48 19 7285918 HCC1395_HCC1395T 48 0.548 109 20,17 26,38 46,56 NA 0/1 NA NA NA NA 24,24,32,29 A/G PANCANCER NA FALSE SSR1 chr6:7285918:7285919:A:G SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 7585458 7585459 C T 50 172 0.290697674418605 MODIFIER SNRNP48 ENSG00000168566 T upstream_gene_variant Transcript ENST00000342415 protein_coding NA 4740 1 SNV HGNC HGNC:21368 YES NM_152551.4 1 P1 CCDS4502.1 ENSP00000339834 Q6IEG0.148 UPI000020E4AD Q6IEG0-1 19 NA NA PASS SITE 97,82|22,28 NA NA 1 93 20,20 176,169 60,60 26 1.60 NA 11.74 NA FALSE 6.00 38 NA NA NA FALSE NA NA 118.00 19 7585458 HCC1395_HCC1395T 122 0.279 172 36,6 49,27 92,35 NA 0/1 NA NA NA NA 63,59,22,28 C/T PANCANCER NA FALSE SNRNP48 chr6:7585458:7585459:C:T SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 7883281 7883282 GAA G 134 253 0.529644268774704 MODIFIER BMP6 ENSG00000153162 - downstream_gene_variant Transcript ENST00000283147 protein_coding NA rs545105682 1554 1 deletion HGNC HGNC:1073 YES NM_001718.6 1 P1 CCDS4503.1 ENSP00000283147 P22004.201 UPI0000126A2D 1 0.0098 0.0015 0.0202 0 0.0278 0.0051 0.01597 0.004327 0.01266 0.0307 0 0.006569 0.02342 0.01652 0.009872 0.01614 0.005023 0.01645 0.0173 0.03199 0.0003846 0.00614 0.03165 0.02495 0.02061 0.008299 0.03199 gnomADg_ASJ 19 NA NA PASS SITE 76,95|55,79 NA NA 1 40 20,20 160,168 60,60 30 1.55 NA 10.23 NA FALSE 1.82 93 6,4 A NA TRUE NA 93 349.63 19 7883281 HCC1395_HCC1395T 119 0.540 253 26,27 36,35 80,94 NA 0/1 NA NA NA NA 55,64,55,79 GAA/G PANCANCER NA FALSE BMP6 chr6:7883281:7883282:GAA:G indel 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 8054329 8054330 T C 146 242 0.603305785123967 MODIFIER BLOC1S5 ENSG00000188428 C intron_variant&NMD_transcript_variant Transcript ENST00000244777 nonsense_mediated_decay 2/5 ENST00000244777.6:c.195+8205A>G NA rs9505348 -1 SNV HGNC HGNC:18561 1 ENSP00000244777 G5E931.78 UPI000022CD4D 1 0.1799 0.3079 0.1628 0.0714 0.1998 0.1104 0.2071 0.2826 0.4364 0.1854 0.1478 0.07176 0.186 0.1646 0.1867 0.1936 0.1157 0.4364 gnomADg_AMI 19 NA NA PASS SITE 58,91|58,88 NA NA 1 42 20,20 168,154 60,60 39 1.54 NA 10.23 NA FALSE 0.676 93 NA NA NA FALSE NA NA 369.75 19 8054329 HCC1395_HCC1395T 96 0.601 242 19,41 38,49 64,97 NA 0/1 NA NA NA NA 36,60,58,88 T/C PANCANCER NA FALSE BLOC1S5 chr6:8054329:8054330:T:C SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 8652438 8652439 C G 166 277 0.59927797833935 MODIFIER HULC ENSG00000285219 G intron_variant&non_coding_transcript_variant Transcript ENST00000503668 lncRNA 1/1 ENST00000503668.2:n.254+48C>G NA rs2038540 1 SNV HGNC HGNC:34232 1 0.1695 0.0144 0.2536 0.2609 0.2187 0.1748 0.1824 0.04699 0.4156 0.2412 0.2496 0.2507 0.139 0.2089 0.2446 0.1783 0.2124 0.4156 gnomADg_AMI 19 NA NA PASS SITE 77,101|66,100 NA NA 1 73 20,20 157,160 60,60 31 1.65 NA 13.24 NA FALSE 0.750 93 NA NA NA FALSE NA NA 444.74 19 8652438 HCC1395_HCC1395T 111 0.621 277 30,49 35,49 66,109 NA 0/1 NA NA NA NA 50,61,66,100 C/G PANCANCER NA FALSE HULC chr6:8652438:8652439:C:G SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 10397660 10397662 T TA 66 119 0.554621848739496 MODIFIER TFAP2A ENSG00000137203 A downstream_gene_variant Transcript ENST00000319516 protein_coding NA rs61569279 211 -1 insertion HGNC HGNC:11742 5 A1 CCDS43422.1 ENSP00000316516 P05549.214 UPI000022CA11 P05549-6 1 0.2913 0.5499 0.2349 0.2679 0.1998 0.1002 0.3307 0.5678 0.1259 0.2808 0.3267 0.3171 0.2707 0.2862 0.2218 0.3204 0.1393 0.5678 gnomADg_AFR 19 NA NA PASS SITE 66,43|37,29 NA NA 1 81 34,34 205,212 60,60 33 1.45 NA 15.65 NA FALSE 0.535 93 11,12 A NA TRUE NA 93 138.66 19 10397660 HCC1395_HCC1395T 53 0.563 119 14,10 23,29 51,64 NA 0/1 NA NA NA NA 31,22,37,29 T/TA PANCANCER NA FALSE TFAP2A chr6:10397660:10397662:T:TA indel 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 10398435 10398436 C T 157 235 0.668085106382979 LOW TFAP2A ENSG00000137203 T synonymous_variant Transcript ENST00000319516 protein_coding 7/7 ENST00000319516.8:c.1284G>A ENSP00000316516.4:p.E428= ENSP00000316516.4 p.E428= 1472 1284 428 E gaG/gaA rs374310228 -1 SNV HGNC HGNC:11742 5 A1 CCDS43422.1 ENSP00000316516 P05549.214 UPI000022CA11 P05549-6 1 PANTHER:PTHR10812&MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-P05549-F1 1.602e-05 0 0 0 0 0 2.677e-05 0.000163 0 3.942e-05 0 0 0 0 0 0 0 7.349e-05 0.000478 0 0.000478 gnomADg_OTH 19 NA NA PASS SITE 99,73|89,68 NA NA 1 93 20,20 158,157 60,60 36 1.80 NA 18.36 NA FALSE 6.00 93 NA NA NA FALSE NA NA 434.99 19 10398435 HCC1395_HCC1395T 78 0.660 235 20,44 31,58 55,107 NA 0/1 NA NA NA NA 46,32,89,68 C/T PANCANCER NA FALSE TFAP2A_p.E428= chr6:10398435:10398436:C:T SNV 9:0 chr6:152749:10647039:9:0:1 NA NA 0.96 +chr6 10801908 10801909 C G 66 282 0.234042553191489 MODERATE MAK ENSG00000111837 G missense_variant Transcript ENST00000313243 protein_coding 8/14 ENST00000313243.6:c.815G>C ENSP00000313021.2:p.R272P ENSP00000313021.2 p.R272P 1198 815 272 R/P cGa/cCa COSV57568710 -1 SNV HGNC HGNC:6816 5 A1 CCDS4516.1 ENSP00000313021 P20794.195 A0A140VK28.30 UPI0000001BCD P20794-1 1 deleterious(0) probably_damaging(1) Gene3D:1.10.510.10&AlphaFold_DB_import:AF-P20794-F1&Pfam:PF00069&PROSITE_profiles:PS50011&PANTHER:PTHR24055&SMART:SM00220&Superfamily:SSF56112&CDD:cd07830 1 1 19 NA NA PASS SITE 180,127|39,27 NA NA 1 93 20,20 165,170 60,60 36 1.80 NA 18.31 NA FALSE 6.00 91 NA NA NA FALSE NA NA 161.88 19 10801908 HCC1395_HCC1395T 216 0.236 282 47,13 96,30 148,45 NA 0/1 NA NA NA NA 127,89,39,27 C/G PANCANCER NA FALSE MAK_p.R272P chr6:10801908:10801909:C:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 10989772 10989773 G A 36 269 0.133828996282528 LOW ELOVL2 ENSG00000197977 A synonymous_variant Transcript ENST00000354666 protein_coding 7/8 ENST00000354666.4:c.696C>T ENSP00000346693.3:p.F232= ENSP00000346693.3 p.F232= 771 696 232 F ttC/ttT rs747355132&COSV61153667 -1 SNV HGNC HGNC:14416 YES NM_017770.4 1 P1 CCDS4518.1 ENSP00000346693 Q9NXB9.156 A0A024QZV3.52 UPI0000051C66 AlphaFold_DB_import:AF-Q9NXB9-F1&HAMAP:MF_03202&Pfam:PF01151&PANTHER:PTHR11157 3.978e-06 0 0 0 0 0 0 0 3.266e-05 6.571e-06 2.414e-05 0 0 0 0 0 0 0 0 0 3.266e-05 gnomADe_SAS 0&1 0&1 19 NA NA PASS SITE 165,158|23,13 NA NA 1 93 20,20 158,157 60,60 36 1.76 NA 16.85 NA FALSE 4.61 9 NA NA NA FALSE NA NA 75.88 19 10989772 HCC1395_HCC1395T 233 0.153 269 71,3 61,21 137,24 NA 0/1 NA NA NA NA 119,114,23,13 G/A PANCANCER NA FALSE ELOVL2_p.F232= chr6:10989772:10989773:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 11183354 11183355 C T 137 230 0.595652173913043 MODIFIER NEDD9 ENSG00000111859 T 3_prime_UTR_variant Transcript ENST00000379446 protein_coding 7/7 ENST00000379446.10:c.*1808G>A NA 4466 rs1044417 -1 SNV HGNC HGNC:7733 YES NM_006403.4 1 P4 CCDS4520.1 ENSP00000368759 Q14511.220 UPI000000D981 Q14511-1 0.5094 0.6884 0.4308 0.3522 0.5517 0.4417 0.5555 0.6572 0.5551 0.4563 0.5332 0.3612 0.517 0.4747 0.5485 0.5321 0.4214 0.6884 AFR 19 NA NA PASS SITE 134,52|107,30 NA NA 1 93 26,35 176,195 60,60 22 1.87 NA 21.97 NA FALSE 0.255 93 NA NA NA FALSE NA NA 421.24 19 11183354 HCC1395_HCC1395T 93 0.618 230 18,41 49,68 68,110 NA 0/1 NA NA NA NA 66,27,107,30 C/T PANCANCER NA FALSE NEDD9 chr6:11183354:11183355:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 11183647 11183649 A AT 77 103 0.747572815533981 MODIFIER NEDD9 ENSG00000111859 T 3_prime_UTR_variant Transcript ENST00000379446 protein_coding 7/7 ENST00000379446.10:c.*1514_*1515insA NA 4172-4173 rs34467611 -1 insertion HGNC HGNC:7733 YES NM_006403.4 1 P4 CCDS4520.1 ENSP00000368759 Q14511.220 UPI000000D981 Q14511-1 0.2057 0.1974 0.1715 0.2986 0.1551 0.1973 0.162 0.1912 0.1225 0.1927 0.214 0.3173 0.07859 0.207 0.1357 0.1756 0.1615 0.3173 gnomADg_EAS 19 NA NA PASS SITE 15,47|20,57 NA NA 1 75 35,36 203,218 60,60 26 1.55 NA 9.25 NA FALSE 0.833 93 9,10 T NA TRUE NA 93 178.13 19 11183647 HCC1395_HCC1395T 26 0.735 103 2,12 4,23 26,73 NA 0/1 NA NA NA NA 3,23,20,57 A/AT PANCANCER NA FALSE NEDD9 chr6:11183647:11183649:A:AT indel 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 11183857 11183858 G A 61 85 0.717647058823529 MODIFIER NEDD9 ENSG00000111859 A 3_prime_UTR_variant Transcript ENST00000379446 protein_coding 7/7 ENST00000379446.10:c.*1305C>T NA 3963 rs1570372 -1 SNV HGNC HGNC:7733 YES NM_006403.4 1 P4 CCDS4520.1 ENSP00000368759 Q14511.220 UPI000000D981 Q14511-1 0.5094 0.6876 0.4308 0.3532 0.5517 0.4417 0.5555 0.6571 0.5538 0.456 0.5329 0.3631 0.5158 0.4747 0.5486 0.534 0.4206 0.6876 AFR 19 NA NA PASS SITE 26,41|30,31 NA NA 1 71 26,20 183,191 60,60 27 1.55 NA 10.23 NA FALSE 0.254 93 NA NA NA FALSE NA NA 177.12 19 11183857 HCC1395_HCC1395T 24 0.708 85 2,16 13,27 18,45 NA 0/1 NA NA NA NA 8,16,30,31 G/A PANCANCER NA FALSE NEDD9 chr6:11183857:11183858:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 11198530 11198531 T C 90 144 0.625 MODIFIER NEDD9 ENSG00000111859 C 3_prime_UTR_variant Transcript ENST00000379433 protein_coding 3/3 ENST00000379433.5:c.*2451A>G NA 3119 rs9393968 -1 SNV HGNC HGNC:7733 1 CCDS34340.1 ENSP00000368745 Q14511.220 UPI000014144A Q14511-2 0.3175 0.2458 0.3415 0.3601 0.339 0.3313 0.3239 0.2668 0.5562 0.3223 0.3902 0.3516 0.295 0.4268 0.3532 0.3552 0.3269 0.5562 gnomADg_AMI 19 NA NA PASS SITE 54,49|51,40 NA NA 1 59 20,20 166,182 60,60 34 1.45 NA 8.59 NA FALSE 0.499 93 NA NA NA FALSE NA NA 259.50 19 11198530 HCC1395_HCC1395T 54 0.624 144 17,23 18,38 37,62 NA 0/1 NA NA NA NA 28,26,51,39 T/C PANCANCER NA FALSE NEDD9 chr6:11198530:11198531:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 12297249 12297250 C T 24 39 0.615384615384615 MODIFIER EDN1 ENSG00000078401 T downstream_gene_variant Transcript ENST00000379375 protein_coding NA rs4714383 55 1 SNV HGNC HGNC:3176 YES NM_001955.5 1 P1 CCDS4522.1 ENSP00000368683 P05305.224 Q6FH53.137 UPI000012A217 1 0.5397 0.7731 0.3905 0.6528 0.3748 0.3834 0.4863 0.7334 0.3385 0.4247 0.3124 0.6505 0.4519 0.3703 0.361 0.4416 0.407 0.7731 AFR 19 NA NA PASS SITE 12,27|8,16 NA NA 1 5 34,20 192,152 60,60 14 1.28 NA 5.42 NA FALSE 0.320 71 NA NA NA FALSE NA NA 61.32 19 12297249 HCC1395_HCC1395T 15 0.567 39 4,5 7,9 12,16 NA 0/1 NA NA NA NA 4,11,8,16 C/T PANCANCER NA FALSE EDN1 chr6:12297249:12297250:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 13328419 13328420 G C 87 124 0.701612903225806 MODIFIER TBC1D7 ENSG00000145979 C intron_variant Transcript ENST00000343141 protein_coding 1/6 ENST00000343141.8:c.-9+37C>G NA rs13212123 -1 SNV HGNC HGNC:21066 1 CCDS58995.1 ENSP00000343100 Q9P0N9.169 UPI000067C9EA Q9P0N9-4 1 0.1468 0.0991 0.0749 0.2808 0.1103 0.1616 0.1134 0.1087 0.1853 0.08082 0.1336 0.2942 0.1819 0.08599 0.09367 0.1232 0.1598 0.2942 gnomADg_EAS 19 NA NA PASS SITE 45,46|38,49 NA NA 2 66 20,20 175,160 60,60 29 1.60 NA 11.44 NA FALSE 0.928 93 NA NA NA FALSE NA NA 238.76 19 13328419 HCC1395_HCC1395T 37 0.687 124 9,13 13,36 25,56 NA 0/1 NA NA NA NA 17,20,38,49 G/C PANCANCER NA FALSE TBC1D7 chr6:13328419:13328420:G:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 13328485 13328486 C G 63 98 0.642857142857143 MODIFIER TBC1D7 ENSG00000145979 G 5_prime_UTR_variant Transcript ENST00000343141 protein_coding 1/7 ENST00000343141.8:c.-38G>C NA 99 rs11557360 -1 SNV HGNC HGNC:21066 1 CCDS58995.1 ENSP00000343100 Q9P0N9.169 UPI000067C9EA Q9P0N9-4 1 0.1779 0.205 0.0908 0.2817 0.1123 0.1636 0.149 0.2215 0.1903 0.09487 0.1423 0.2955 0.1842 0.0894 0.09793 0.1486 0.1688 0.2955 gnomADg_EAS 19 NA NA PASS SITE 35,51|24,39 NA NA 2 63 20,20 159,160 60,60 36 1.54 NA 10.14 NA FALSE 0.842 93 NA NA NA FALSE NA NA 166.21 19 13328485 HCC1395_HCC1395T 35 0.635 98 9,11 6,15 24,42 NA 0/1 NA NA NA NA 13,22,24,39 C/G PANCANCER NA FALSE TBC1D7 chr6:13328485:13328486:C:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 13579676 13579677 T G 124 147 0.843537414965986 MODIFIER SIRT5 ENSG00000124523 G intron_variant Transcript ENST00000359782 protein_coding 2/8 ENST00000359782.8:c.-36+67T>G NA rs2804912 1 SNV HGNC HGNC:14933 2 CCDS54966.1 ENSP00000352830 Q9NXA8.181 UPI0001DD21BE Q9NXA8-3 0.5699 0.5696 0.7089 0.3562 0.6133 0.6472 0.596 0.5745 0.7697 0.6796 0.5188 0.3331 0.6062 0.5892 0.6084 0.6183 0.6155 0.7697 gnomADg_AMI 19 NA NA PASS SITE 15,45|40,84 NA NA 1 31 29,20 180,174 60,60 26 1.48 NA 8.73 NA FALSE 0.230 93 NA NA NA FALSE NA NA 374.67 19 13579676 HCC1395_HCC1395T 23 0.829 147 7,21 8,55 17,86 NA 0/1 NA NA NA NA 6,17,40,84 T/G PANCANCER NA FALSE SIRT5 chr6:13579676:13579677:T:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 16147945 16147946 G A 194 296 0.655405405405405 MODIFIER MYLIP ENSG00000007944 A 3_prime_UTR_variant Transcript ENST00000349606 protein_coding 6/6 ENST00000349606.4:c.*1194G>A NA 2493 rs2205794&COSV62767921 1 SNV HGNC HGNC:21155 1 ENSP00000008686 Q5TIA5.159 UPI0000E5ACB8 1 0.0663 0.0106 0.0303 0.1944 0.0368 0.0654 0.0337 0.01636 0.01096 0.0247 0.04498 0.1865 0.01681 0.01582 0.03539 0.0364 0.05597 0.1944 EAS 0&1 0&1 19 NA NA PASS SITE 101,90|111,83 NA NA 1 93 20,20 164,178 60,60 33 1.77 NA 17.46 NA FALSE 1.46 93 NA NA NA FALSE NA NA 539.25 19 16147945 HCC1395_HCC1395T 102 0.663 296 24,36 39,92 66,130 NA 0/1 NA NA NA NA 56,46,111,83 G/A PANCANCER NA FALSE MYLIP chr6:16147945:16147946:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 16522643 16522644 G A 166 236 0.703389830508475 MODIFIER ATXN1 ENSG00000124788 A 5_prime_UTR_variant Transcript ENST00000244769 protein_coding 6/9 ENST00000244769.8:c.-315C>T NA 623 rs75873938 -1 SNV HGNC HGNC:10548 1 P1 CCDS34342.1 ENSP00000244769 P54253.208 UPI000013CB8B P54253-1 1 0.0066 0 0.0086 0 0.0239 0.0031 0.01396 0.003068 0.002193 0.008312 0.03633 0.0001925 0.0332 0.003165 0.01988 0.01337 0.001658 0.03633 gnomADg_ASJ 19 NA NA PASS SITE 63,94|65,102 NA NA 1 93 20,20 156,161 60,60 28 1.79 NA 17.76 NA FALSE 1.80 93 NA NA NA FALSE NA NA 480.33 19 16522643 HCC1395_HCC1395T 70 0.707 236 13,38 31,67 49,120 NA 0/1 NA NA NA NA 25,45,65,101 G/A PANCANCER NA FALSE ATXN1 chr6:16522643:16522644:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 17828388 17828389 A G 38 55 0.690909090909091 MODIFIER KIF13A ENSG00000137177 G intron_variant Transcript ENST00000259711 protein_coding 13/38 ENST00000259711.11:c.1402-18T>C NA rs201054184 -1 SNV HGNC HGNC:14566 YES NM_022113.6 1 CCDS47381.1 ENSP00000259711 Q9H1H9.175 UPI0000E20DA3 Q9H1H9-1 0.0003446 0 9.915e-05 0 0 4.705e-05 0.0007082 0 0 0.0005189 0.0001689 0 0.0001308 0 0 0 0 0.001029 0 0 0.001029 gnomADg_NFE 19 NA NA PASS SITE 3,25|6,32 NA NA 1 8 38,39 221,197 60,60 23 1.06 NA 3.01 NA FALSE 3.57 93 NA NA NA FALSE NA NA 126.38 19 17828388 HCC1395_HCC1395T 17 0.679 55 3,12 9,19 15,33 NA 0/1 NA NA NA NA 2,15,6,32 A/G PANCANCER NA FALSE KIF13A chr6:17828388:17828389:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 18222149 18222150 C G 22 85 0.258823529411765 MODIFIER DEK ENSG00000124795 G downstream_gene_variant Transcript ENST00000244776 protein_coding NA rs1234320289 3321 -1 SNV HGNC HGNC:2768 2 CCDS47382.1 ENSP00000244776 P35659.207 UPI00017A79CB P35659-2 1 6.588e-06 0 0 0 0 0 0 0 4.251e-05 4.251e-05 gnomADe_SAS 19 NA NA PASS SITE 54,38|11,11 NA NA 1 64 23,20 183,192 60,60 35 1.39 NA 6.92 NA FALSE 6.00 82 NA NA NA FALSE NA NA 57.69 19 18222149 HCC1395_HCC1395T 63 0.262 85 15,6 29,8 47,16 NA 0/1 NA NA NA NA 39,24,11,11 C/G PANCANCER NA FALSE DEK chr6:18222149:18222150:C:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 21232232 21232233 C G 40 105 0.380952380952381 MODIFIER CDKAL1 ENSG00000145996 G 3_prime_UTR_variant Transcript ENST00000274695 protein_coding 16/16 ENST00000274695.8:c.*1193C>G NA 3100 1 SNV HGNC HGNC:21050 YES NM_017774.3 1 P1 CCDS4546.1 ENSP00000274695 Q5VV42.160 UPI000013DA21 Q5VV42-1 19 NA NA PASS SITE 86,15|33,7 NA NA 1 93 38,39 194,184 60,60 19 1.45 NA 8.13 NA FALSE 6.00 93 NA NA NA FALSE NA NA 120.85 19 21232232 HCC1395_HCC1395T 65 0.364 105 23,11 32,22 59,33 NA 0/1 NA NA NA NA 59,6,33,7 C/G PANCANCER NA FALSE CDKAL1 chr6:21232232:21232233:C:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 21232384 21232385 A G 191 243 0.786008230452675 MODIFIER CDKAL1 ENSG00000145996 G 3_prime_UTR_variant Transcript ENST00000274695 protein_coding 16/16 ENST00000274695.8:c.*1345A>G NA 3252 rs1137970 1 SNV HGNC HGNC:21050 YES NM_017774.3 1 P1 CCDS4546.1 ENSP00000274695 Q5VV42.160 UPI000013DA21 Q5VV42-1 0.4030 0.1331 0.4942 0.3899 0.6352 0.4775 0.509 0.211 0.8257 0.5434 0.6391 0.369 0.6759 0.4937 0.6566 0.5206 0.5056 0.8257 gnomADg_AMI 19 NA NA PASS SITE 53,77|67,124 NA NA 1 93 20,20 176,177 60,60 27 1.73 NA 15.91 NA FALSE 0.267 93 NA NA NA FALSE NA NA 596.52 19 21232384 HCC1395_HCC1395T 52 0.792 243 14,46 20,78 36,140 NA 0/1 NA NA NA NA 21,31,67,124 A/G PANCANCER NA FALSE CDKAL1 chr6:21232384:21232385:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24173154 24173155 T C 380 437 0.869565217391304 MODIFIER DCDC2 ENSG00000146038 C 3_prime_UTR_variant Transcript ENST00000378450 protein_coding 3/3 ENST00000378450.6:c.*1576A>G NA 2286 rs9467062 -1 SNV HGNC HGNC:18141 1 ENSP00000367711 Q9UHG0.170 UPI0000458AA9 Q9UHG0-2 1 0.1434 0.4955 0.0548 0 0.0249 0 0.1427 0.4375 0 0.08309 0.02683 0.0001924 0.003508 0.06646 0.02835 0.1248 0.002896 0.4955 AFR 19 NA NA PASS SITE 66,83|183,197 NA NA 1 93 20,20 154,160 60,60 33 1.76 NA 16.85 NA FALSE 0.917 93 NA NA NA FALSE NA NA 985.62 19 24173154 HCC1395_HCC1395T 57 0.860 437 7,76 20,128 36,226 NA 0/1 NA NA NA NA 24,33,183,197 T/C PANCANCER NA FALSE DCDC2 chr6:24173154:24173155:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24173958 24173959 G A 95 123 0.772357723577236 MODIFIER DCDC2 ENSG00000146038 A 3_prime_UTR_variant Transcript ENST00000378450 protein_coding 3/3 ENST00000378450.6:c.*772C>T NA 1482 rs6901696 -1 SNV HGNC HGNC:18141 1 ENSP00000367711 Q9UHG0.170 UPI0000458AA9 Q9UHG0-2 1 0.1432 0.4947 0.0548 0 0.0249 0 0.1427 0.4383 0 0.08242 0.02707 0.0001927 0.003577 0.06329 0.02812 0.1244 0.002902 0.4947 AFR 19 NA NA PASS SITE 47,28|58,37 NA NA 1 38 20,20 167,191 60,60 30 1.51 NA 9.33 NA FALSE 0.917 93 NA NA NA FALSE NA NA 270.07 19 24173958 HCC1395_HCC1395T 28 0.777 123 8,24 10,40 18,65 NA 0/1 NA NA NA NA 17,11,58,37 G/A PANCANCER NA FALSE DCDC2 chr6:24173958:24173959:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24174161 24174163 GC AA 304 402 0.756218905472637 MODIFIER DCDC2 ENSG00000146038 AA 3_prime_UTR_variant Transcript ENST00000378450 protein_coding 3/3 ENST00000378450.6:c.*568_*569delinsTT NA 1278-1279 rs386698068 -1 substitution HGNC HGNC:18141 1 ENSP00000367711 Q9UHG0.170 UPI0000458AA9 Q9UHG0-2 1 19 NA NA PASS SITE 138,83|200,104 NA NA 1 93 20,20 164,169 60,60 31 1.94 NA 25.59 NA FALSE 6.00 93 NA NA NA FALSE NA NA 1283.84 19 24174161 HCC1395_HCC1395T 98 0.757 402 35,88 29,122 68,214 NA 0/1 NA NA NA NA 59,39,200,104 GC/AA PANCANCER NA FALSE DCDC2 chr6:24174161:24174163:GC:AA indel 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24301935 24301936 T C 323 395 0.817721518987342 MODIFIER DCDC2 ENSG00000146038 C intron_variant Transcript ENST00000378454 protein_coding 3/9 ENST00000378454.8:c.425+33A>G NA rs35029429 -1 SNV HGNC HGNC:18141 YES NM_016356.5 1 P1 CCDS4550.1 ENSP00000367715 Q9UHG0.170 UPI000013DA24 Q9UHG0-1 1 0.0068 0.0212 0.0014 0 0.005 0 0.009923 0.01723 0.004161 0.00171 0 0.003148 0.01689 0.0094 3.295e-05 0.01344 0.01518 0 0.00766 0.002017 0 0.003206 0.006329 0.01814 0.01053 0 0.0212 AFR likely_benign 1 19 NA NA PASS SITE 88,81|169,154 NA NA 1 93 20,20 155,163 60,60 35 1.79 NA 18.01 NA FALSE 1.92 93 NA NA NA FALSE NA NA 915.79 19 24301935 HCC1395_HCC1395T 72 0.820 395 22,80 23,124 46,213 NA 0/1 NA NA NA NA 38,34,169,154 T/C PANCANCER NA FALSE DCDC2 chr6:24301935:24301936:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24476174 24476175 C T 109 127 0.858267716535433 LOW GPLD1 ENSG00000112293 T splice_region_variant&intron_variant Transcript ENST00000230036 protein_coding 4/24 ENST00000230036.2:c.330+7G>A NA rs75119852&COSV57753845 -1 SNV HGNC HGNC:4459 YES NM_001503.4 1 P1 CCDS4553.1 ENSP00000230036 P80108.176 UPI000013C91C P80108-1 0.0214 0.0726 0.0058 0 0.007 0 0.01488 0.07243 0.01046 0.001561 0.001042 0.002643 0.01984 0.011 0.001547 0.03025 0.07055 0 0.01376 0.002594 0.0003849 0.003208 0.03165 0.01987 0.02679 0.001658 0.0726 AFR 0&1 0&1 19 NA NA PASS SITE 35,10|69,40 NA NA 1 34 36,20 191,169 60,60 29 1.38 NA 6.92 NA FALSE 1.59 93 NA NA NA FALSE NA NA 304.09 19 24476174 HCC1395_HCC1395T 18 0.820 127 7,20 8,52 15,72 NA 0/1 NA NA NA NA 15,3,69,40 C/T PANCANCER NA FALSE GPLD1 chr6:24476174:24476175:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24494776 24494777 C T 49 67 0.73134328358209 MODIFIER ALDH5A1 ENSG00000112294 T upstream_gene_variant Transcript ENST00000348925 protein_coding NA rs4646829 193 1 SNV HGNC HGNC:408 1 CCDS4556.1 ENSP00000314649 P51649.205 X5D299.50 UPI00001619D2 P51649-2 1 0.0323 0.0832 0.0072 0.006 0.0119 0.0297 0.03576 0.07851 0 0.01643 0.01757 0.007529 0.004706 0.03797 0.0229 0.032 0.03102 0.0832 AFR benign 1 19 NA NA PASS SITE 43,20|29,20 NA NA 2 44 20,20 158,158 60,60 31 1.50 NA 9.03 NA FALSE 1.51 93 NA NA NA FALSE NA NA 143.84 19 24494776 HCC1395_HCC1395T 18 0.700 67 1,13 13,21 14,34 NA 0/1 NA NA NA NA 14,4,29,20 C/T PANCANCER NA FALSE ALDH5A1 chr6:24494776:24494777:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24494950 24494951 C T 187 270 0.692592592592593 MODIFIER ALDH5A1 ENSG00000112294 T upstream_gene_variant Transcript ENST00000348925 protein_coding NA rs200776997 19 1 SNV HGNC HGNC:408 1 CCDS4556.1 ENSP00000314649 P51649.205 X5D299.50 UPI00001619D2 P51649-2 1 0.0010 0 0 0 0.005 0 0.01044 0.003282 0.001927 0.00503 0 0.003403 0.01631 0.01119 0 0.009979 0.002798 0 0.004842 0.002595 0 0.003209 0 0.01869 0.006692 0 0.01869 gnomADg_NFE 19 NA NA PASS SITE 94,98|98,89 NA NA 1 93 20,20 156,155 60,60 35 1.85 NA 21.07 NA FALSE 2.02 93 NA NA NA FALSE NA NA 485.19 19 24494950 HCC1395_HCC1395T 83 0.675 270 22,49 27,65 57,119 NA 0/1 NA NA NA NA 41,42,98,89 C/T PANCANCER NA FALSE ALDH5A1 chr6:24494950:24494951:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24544254 24544255 C G 335 437 0.766590389016018 MODIFIER KIAA0319 ENSG00000137261 G 3_prime_UTR_variant Transcript ENST00000378214 protein_coding 21/21 ENST00000378214.8:c.*2911G>C NA 6691 rs807528 -1 SNV HGNC HGNC:21580 YES NM_014809.4 1 P2 CCDS34348.1 ENSP00000367459 Q5VV43.162 UPI000020D61A Q5VV43-1 0.2392 0.32 0.1902 0.12 0.2406 0.2863 0.2642 0.3233 0.4397 0.2038 0.1377 0.1306 0.2277 0.1994 0.2627 0.2428 0.2657 0.4397 gnomADg_AMI 19 NA NA PASS SITE 100,82|181,154 NA NA 1 93 20,20 164,154 60,60 36 1.74 NA 16.25 NA FALSE 0.580 93 NA NA NA FALSE NA NA 909.82 19 24544254 HCC1395_HCC1395T 102 0.757 437 22,76 41,122 66,208 NA 0/1 NA NA NA NA 55,47,181,154 C/G PANCANCER NA FALSE KIAA0319 chr6:24544254:24544255:C:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24545711 24545712 G C 65 95 0.684210526315789 MODIFIER KIAA0319 ENSG00000137261 C 3_prime_UTR_variant Transcript ENST00000378214 protein_coding 21/21 ENST00000378214.8:c.*1454C>G NA 5234 rs807530 -1 SNV HGNC HGNC:21580 YES NM_014809.4 1 P2 CCDS34348.1 ENSP00000367459 Q5VV43.162 UPI000020D61A Q5VV43-1 0.4840 0.7693 0.3573 0.2282 0.4473 0.4898 0.5047 0.7304 0.5066 0.3804 0.3544 0.2372 0.4642 0.4399 0.433 0.4847 0.4693 0.7693 AFR 19 NA NA PASS SITE 12,61|15,50 NA NA 1 56 39,39 200,198 60,60 27 1.60 NA 11.14 NA FALSE 0.303 93 NA NA NA FALSE NA NA 216.04 19 24545711 HCC1395_HCC1395T 30 0.663 95 7,16 19,36 27,54 NA 0/1 NA NA NA NA 6,24,15,50 G/C PANCANCER NA FALSE KIAA0319 chr6:24545711:24545712:G:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24546281 24546282 C A 342 447 0.76510067114094 MODIFIER KIAA0319 ENSG00000137261 A 3_prime_UTR_variant Transcript ENST00000378214 protein_coding 21/21 ENST00000378214.8:c.*884G>T NA 4664 rs7744621 -1 SNV HGNC HGNC:21580 YES NM_014809.4 1 P2 CCDS34348.1 ENSP00000367459 Q5VV43.162 UPI000020D61A Q5VV43-1 0.0419 0.1475 0.0115 0 0.007 0 0.05054 0.1386 0 0.02341 0.004614 0.0001926 0.003214 0.0414 0.02121 0.03732 0.002079 0.1475 AFR 19 NA NA PASS SITE 115,94|177,165 NA NA 2 93 20,20 172,164 60,60 32 1.90 NA 23.18 NA FALSE 1.35 93 NA NA NA FALSE NA NA 958.86 19 24546281 HCC1395_HCC1395T 105 0.759 447 32,82 36,144 76,242 NA 0/1 NA NA NA NA 54,51,177,165 C/A PANCANCER NA FALSE KIAA0319 chr6:24546281:24546282:C:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24546356 24546357 T C 295 380 0.776315789473684 MODIFIER KIAA0319 ENSG00000137261 C 3_prime_UTR_variant Transcript ENST00000378214 protein_coding 21/21 ENST00000378214.8:c.*809A>G NA 4589 rs7764860 -1 SNV HGNC HGNC:21580 YES NM_014809.4 1 P2 CCDS34348.1 ENSP00000367459 Q5VV43.162 UPI000020D61A Q5VV43-1 0.0419 0.1475 0.0115 0 0.007 0 0.05049 0.1384 0 0.02344 0.004611 0.0003848 0.003206 0.04114 0.02125 0.03633 0.002077 0.1475 AFR 19 NA NA PASS SITE 90,107|140,155 NA NA 2 93 20,20 169,167 60,60 31 1.87 NA 21.67 NA FALSE 1.35 93 NA NA NA FALSE NA NA 836.26 19 24546356 HCC1395_HCC1395T 85 0.752 380 12,53 25,99 65,199 NA 0/1 NA NA NA NA 34,51,140,155 T/C PANCANCER NA FALSE KIAA0319 chr6:24546356:24546357:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24546480 24546481 C T 131 169 0.775147928994083 MODIFIER KIAA0319 ENSG00000137261 T 3_prime_UTR_variant Transcript ENST00000378214 protein_coding 21/21 ENST00000378214.8:c.*685G>A NA 4465 rs7744939 -1 SNV HGNC HGNC:21580 YES NM_014809.4 1 P2 CCDS34348.1 ENSP00000367459 Q5VV43.162 UPI000020D61A Q5VV43-1 0.0423 0.149 0.0115 0 0.007 0 0.05125 0.1405 0 0.0237 0.004611 0.000386 0.003211 0.0443 0.02146 0.03931 0.002699 0.149 AFR 19 NA NA PASS SITE 30,55|49,82 NA NA 1 54 20,34 180,176 60,60 28 1.56 NA 10.53 NA FALSE 1.34 93 NA NA NA FALSE NA NA 405.10 19 24546480 HCC1395_HCC1395T 38 0.769 169 6,28 20,60 29,99 NA 0/1 NA NA NA NA 13,25,49,82 C/T PANCANCER NA FALSE KIAA0319 chr6:24546480:24546481:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24579828 24579829 G C 19 150 0.126666666666667 MODIFIER KIAA0319 ENSG00000137261 C intron_variant Transcript ENST00000378214 protein_coding 8/20 ENST00000378214.8:c.1372+30C>G NA -1 SNV HGNC HGNC:21580 YES NM_014809.4 1 P2 CCDS34348.1 ENSP00000367459 Q5VV43.162 UPI000020D61A Q5VV43-1 19 NA NA PASS SITE 106,67|12,7 NA NA 1 93 20,38 161,193 60,60 29 1.48 NA 8.73 NA FALSE 6.00 75 NA NA NA FALSE NA NA 48.11 19 24579828 HCC1395_HCC1395T 131 0.154 150 36,5 48,8 84,15 NA 0/1 NA NA NA NA 77,54,12,7 G/C PANCANCER NA FALSE KIAA0319 chr6:24579828:24579829:G:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24601012 24601013 G A 239 303 0.788778877887789 MODIFIER KIAA0319 ENSG00000137261 A intron_variant Transcript ENST00000378214 protein_coding 2/20 ENST00000378214.8:c.55+37C>T NA rs4472344 -1 SNV HGNC HGNC:21580 YES NM_014809.4 1 P2 CCDS34348.1 ENSP00000367459 Q5VV43.162 UPI000020D61A Q5VV43-1 0.0341 0.1203 0.0058 0 0.008 0 0.01799 0.1005 0.0118 0.001985 0.001033 0.003372 0.01986 0.01436 0.000784 0.03813 0.09626 0 0.01815 0.002882 0.0003855 0.003394 0.009494 0.02074 0.03462 0.001453 0.1203 AFR 19 NA NA PASS SITE 93,75|128,111 NA NA 1 93 20,20 152,162 60,60 30 1.81 NA 18.92 NA FALSE 1.49 93 NA NA NA FALSE NA NA 690.84 19 24601012 HCC1395_HCC1395T 64 0.806 303 15,69 20,82 38,161 NA 0/1 NA NA NA NA 34,30,128,111 G/A PANCANCER NA FALSE KIAA0319 chr6:24601012:24601013:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24805598 24805599 GA G 261 353 0.739376770538244 MODIFIER RIPOR2 ENSG00000111913 - 3_prime_UTR_variant Transcript ENST00000259698 protein_coding 23/23 ENST00000259698.9:c.*774del NA 4238 rs10713602&COSV52416620 -1 deletion HGNC HGNC:13872 1 A2 CCDS47383.1 ENSP00000259698 Q9Y4F9.155 A0A024QZY9.63 UPI0000EE554D Q9Y4F9-1 1 0.3562 0.267 0.428 0.1865 0.5219 0.4305 0.4448 0.3102 0.4978 0.4405 0.532 0.198 0.5171 0.4968 0.5325 0.4243 0.4157 0.5325 gnomADg_NFE 0&1 0&1 19 NA NA PASS SITE 110,91|146,115 NA NA 1 93 20,20 164,162 60,60 36 1.84 NA 19.85 NA FALSE 0.340 93 NA NA NA FALSE NA NA 607.53 19 24805598 HCC1395_HCC1395T 92 0.728 353 25,67 29,86 61,165 NA 0/1 NA NA NA NA 55,37,146,115 GA/G PANCANCER NA FALSE RIPOR2 chr6:24805598:24805599:GA:G indel 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24805820 24805821 T C 119 135 0.881481481481482 MODIFIER RIPOR2 ENSG00000111913 C 3_prime_UTR_variant Transcript ENST00000259698 protein_coding 23/23 ENST00000259698.9:c.*553A>G NA 4017 rs3730 -1 SNV HGNC HGNC:13872 1 A2 CCDS47383.1 ENSP00000259698 Q9Y4F9.155 A0A024QZY9.63 UPI0000EE554D Q9Y4F9-1 1 0.3570 0.267 0.4294 0.1865 0.5229 0.4325 0.4437 0.3091 0.5011 0.4407 0.532 0.1979 0.5048 0.5 0.5326 0.426 0.4179 0.5326 gnomADg_NFE 1 19 NA NA PASS SITE 31,23|56,63 NA NA 2 62 35,37 222,203 60,60 26 1.54 NA 10.23 NA FALSE 0.342 93 NA NA NA FALSE NA NA 517.63 19 24805820 HCC1395_HCC1395T 16 0.865 135 6,31 7,61 14,95 NA 0|1 0|1 24805820_T_C NA 24805820 9,7,56,63 T|C PANCANCER NA FALSE RIPOR2 chr6:24805820:24805821:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24805842 24805843 A C 121 136 0.889705882352941 MODIFIER RIPOR2 ENSG00000111913 C 3_prime_UTR_variant Transcript ENST00000259698 protein_coding 23/23 ENST00000259698.9:c.*531T>G NA 3995 rs1132352 -1 SNV HGNC HGNC:13872 1 A2 CCDS47383.1 ENSP00000259698 Q9Y4F9.155 A0A024QZY9.63 UPI0000EE554D Q9Y4F9-1 1 0.3576 0.2685 0.428 0.1865 0.5258 0.4315 0.4448 0.3095 0.4967 0.4411 0.532 0.1981 0.5169 0.5 0.5329 0.4262 0.4177 0.5329 gnomADg_NFE 19 NA NA PASS SITE 33,28|64,57 NA NA 2 75 33,37 206,192 60,60 33 1.58 NA 11.14 NA FALSE 0.340 93 NA NA NA FALSE NA NA 521.25 19 24805842 HCC1395_HCC1395T 15 0.882 136 5,29 7,61 12,96 NA 0|1 0|1 24805820_T_C NA 24805820 9,6,64,57 A|C PANCANCER NA FALSE RIPOR2 chr6:24805842:24805843:A:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 24870803 24870804 C T 174 207 0.840579710144927 MODIFIER RIPOR2 ENSG00000111913 T intron_variant Transcript ENST00000259698 protein_coding 5/22 ENST00000259698.9:c.360+63G>A NA rs112061020 -1 SNV HGNC HGNC:13872 1 A2 CCDS47383.1 ENSP00000259698 Q9Y4F9.155 A0A024QZY9.63 UPI0000EE554D Q9Y4F9-1 1 0.0252 0.0802 0.0058 0.001 0.0149 0 0.03226 0.06742 0.005482 0.01413 0.005767 0.0003852 0.004807 0.009494 0.02593 0.02677 0 0.0802 AFR benign 1 19 NA NA PASS SITE 54,39|103,71 NA NA 1 86 20,20 142,166 60,60 30 1.63 NA 12.34 NA FALSE 1.54 93 NA NA NA FALSE NA NA 492.20 19 24870803 HCC1395_HCC1395T 33 0.825 207 9,42 13,65 23,112 NA 0/1 NA NA NA NA 21,12,103,71 C/T PANCANCER NA FALSE RIPOR2 chr6:24870803:24870804:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 25488355 25488356 C T 60 82 0.731707317073171 MODIFIER CARMIL1 ENSG00000079691 T intron_variant Transcript ENST00000329474 protein_coding 12/36 ENST00000329474.7:c.962-127C>T NA rs2274089 1 SNV HGNC HGNC:21581 YES NM_017640.6 1 P1 CCDS54973.1 ENSP00000331983 Q5VZK9.158 UPI00004588AB Q5VZK9-1 0.0323 0.0038 0.0519 0.0288 0.0765 0.0153 0.05879 0.01561 0.04167 0.05428 0.02248 0.02772 0.09466 0.02848 0.08816 0.05651 0.017 0.09466 gnomADg_FIN 1 19 NA NA PASS SITE 33,13|45,15 NA NA 1 3 20,35 155,190 60,60 28 1.26 NA 5.12 NA FALSE 1.17 93 NA NA NA FALSE NA NA 188.40 19 25488355 HCC1395_HCC1395T 22 0.739 82 4,18 12,28 16,47 NA 0/1 NA NA NA NA 16,6,45,15 C/T PANCANCER NA FALSE CARMIL1 chr6:25488355:25488356:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 25777954 25777955 C T 161 214 0.752336448598131 MODIFIER SLC17A1 ENSG00000124568 T downstream_gene_variant Transcript ENST00000244527 protein_coding NA rs2328894 4961 -1 SNV HGNC HGNC:10929 YES NM_005074.5 5 P1 CCDS4565.1 ENSP00000244527 Q14916.171 UPI00000719C0 Q14916-1 0.0048 0 0.0072 0 0.0159 0.0031 0.01061 0.002339 0.004663 0.00566 0.0003263 0.0246 0.01505 0.01063 0.003302 0.009703 0.002534 0 0.005305 0.006055 0.0007698 0.02678 0.009494 0.01397 0.007656 0.002484 0.02678 gnomADg_FIN 19 NA NA PASS SITE 48,58|69,92 NA NA 1 57 20,20 171,168 60,60 31 1.55 NA 10.23 NA FALSE 1.89 93 NA NA NA FALSE NA NA 434.31 19 25777954 HCC1395_HCC1395T 53 0.760 214 11,42 17,58 34,109 NA 0/1 NA NA NA NA 24,29,69,92 C/T PANCANCER NA FALSE SLC17A1 chr6:25777954:25777955:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 25780104 25780105 C T 118 157 0.751592356687898 MODIFIER SLC17A1 ENSG00000124568 T downstream_gene_variant Transcript ENST00000244527 protein_coding NA rs1141034 2811 -1 SNV HGNC HGNC:10929 YES NM_005074.5 5 P1 CCDS4565.1 ENSP00000244527 Q14916.171 UPI00000719C0 Q14916-1 0.3427 0.0923 0.4337 0.6706 0.2922 0.3303 0.2727 0.1291 0.2874 0.3631 0.1734 0.679 0.4219 0.1361 0.2874 0.2586 0.3337 0.679 gnomADg_EAS 19 NA NA PASS SITE 43,23|76,42 NA NA 1 12 37,36 170,192 60,60 23 1.41 NA 7.22 NA FALSE 0.533 93 NA NA NA FALSE NA NA 402.63 19 25780104 HCC1395_HCC1395T 39 0.764 157 8,37 22,58 31,103 NA 0/1 NA NA NA NA 25,14,76,42 C/T PANCANCER NA FALSE SLC17A1 chr6:25780104:25780105:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 25780911 25780912 G A 30 46 0.652173913043478 MODIFIER SLC17A1 ENSG00000124568 A downstream_gene_variant Transcript ENST00000244527 protein_coding NA rs7749149&COSV55078900 2004 -1 SNV HGNC HGNC:10929 YES NM_005074.5 5 P1 CCDS4565.1 ENSP00000244527 Q14916.171 UPI00000719C0 Q14916-1 0.3932 0.2073 0.4438 0.7411 0.3082 0.3374 0.3113 0.2285 0.2874 0.3827 0.1796 0.7457 0.4589 0.1741 0.2959 0.29 0.3393 0.7457 gnomADg_EAS 0&1 0&1 19 NA NA PASS SITE 33,21|24,6 NA NA 1 29 20,36 178,206 60,60 25 1.45 NA 8.13 NA FALSE 0.484 93 NA NA NA FALSE NA NA 99.39 19 25780911 HCC1395_HCC1395T 16 0.667 46 4,11 9,16 13,27 NA 0/1 NA NA NA NA 10,6,24,6 G/A PANCANCER NA FALSE SLC17A1 chr6:25780911:25780912:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 26020708 26020709 C T 165 219 0.753424657534247 MODIFIER H1-1 ENSG00000124610 T upstream_gene_variant Transcript ENST00000244573 protein_coding NA rs2229766 2921 -1 SNV HGNC HGNC:4715 YES NM_005325.4 P1 CCDS4569.1 ENSP00000244573 Q02539.176 UPI0000001BD8 0.0120 0.0015 0.0187 0 0.0318 0.0133 0.02839 0.007694 0.01877 0.02749 0.0009243 0.01317 0.0443 0.03017 0.01832 0.02576 0.008295 0.009868 0.01871 0.02711 0.002119 0.01186 0.04114 0.0427 0.02436 0.01696 0.0443 gnomADe_NFE 19 NA NA PASS SITE 49,81|76,89 NA NA 1 93 27,20 172,167 60,60 30 1.78 NA 17.45 NA FALSE 1.57 93 NA NA NA FALSE NA NA 484.61 19 26020708 HCC1395_HCC1395T 54 0.735 219 20,55 19,60 43,121 NA 0/1 NA NA NA NA 18,36,76,89 C/T PANCANCER NA FALSE H1-1 chr6:26020708:26020709:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 26096966 26096967 G A 407 556 0.732014388489209 MODIFIER HFE ENSG00000010704 A downstream_gene_variant Transcript ENST00000309234 protein_coding NA rs17596719 2413 1 SNV HGNC HGNC:4886 2 CCDS75412.1 ENSP00000311698 F8W7W8.81 UPI0001B793D7 1 0.0929 0.0159 0.1182 0.0655 0.0974 0.2025 0.09456 0.02851 0.1414 0.1064 0.1951 0.06344 0.1016 0.1646 0.1192 0.1033 0.2051 0.2051 gnomADg_SAS 19 NA NA PASS SITE 177,132|255,152 NA NA 1 93 20,20 156,165 60,60 34 2.00 NA 29.75 NA FALSE 1.03 93 NA NA NA FALSE NA NA 1123.41 19 26096966 HCC1395_HCC1395T 149 0.736 556 32,97 59,164 95,267 NA 0/1 NA NA NA NA 86,63,255,152 G/A PANCANCER NA FALSE HFE chr6:26096966:26096967:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 26392015 26392016 G A 145 186 0.779569892473118 MODIFIER BTN2A2 ENSG00000124508 A intron_variant Transcript ENST00000352867 protein_coding 6/6 ENST00000352867.6:c.632-360G>A NA rs543642074 1 SNV HGNC HGNC:1137 2 CCDS4607.1 ENSP00000337117 Q8WVV5.166 UPI00001AA162 Q8WVV5-4 0.001202 0.0004585 0 0.0001309 0 0 0.0001885 0 0.002352 0 0 0.002352 gnomADg_NFE 19 NA NA PASS SITE 55,22|101,44 NA NA 1 45 34,31 185,188 60,60 30 1.46 NA 8.08 NA FALSE 2.92 93 NA NA NA FALSE NA NA 432.61 19 26392015 HCC1395_HCC1395T 41 0.769 186 7,34 25,72 32,109 NA 0/1 NA NA NA NA 29,12,101,44 G/A PANCANCER NA FALSE BTN2A2 chr6:26392015:26392016:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 26414230 26414231 T C 115 154 0.746753246753247 MODIFIER BTN3A1 ENSG00000026950 C non_coding_transcript_exon_variant Transcript ENST00000082468 retained_intron 9/9 ENST00000082468.11:n.2468T>C NA 2468 rs532225597 1 SNV HGNC HGNC:1138 2 0.001045 0.0004585 0 6.54e-05 0 0 0 0 0.002028 0 0.0002071 0.002028 gnomADg_NFE 19 NA NA PASS SITE 35,56|47,68 NA NA 1 90 33,20 192,172 60,60 35 1.63 NA 12.29 NA FALSE 3.00 93 NA NA NA FALSE NA NA 349.75 19 26414230 HCC1395_HCC1395T 39 0.726 154 8,28 20,42 31,84 NA 0/1 NA NA NA NA 14,25,47,68 T/C PANCANCER NA FALSE BTN3A1 chr6:26414230:26414231:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 26510336 26510337 T C 142 189 0.751322751322751 MODIFIER BTN1A1 ENSG00000124557 C 3_prime_UTR_variant Transcript ENST00000244513 protein_coding 7/7 ENST00000244513.10:c.*1162T>C NA 2809 rs1056667&COSV55066929 1 SNV HGNC HGNC:1135 1 P1 CCDS4614.1 ENSP00000244513 Q13410.179 UPI000006E521 0.5689 0.5159 0.5879 0.746 0.4423 0.5746 0.502 0.5208 0.3824 0.5619 0.5723 0.743 0.3959 0.5 0.469 0.512 0.5565 0.746 EAS 0&1 1&1 19 NA NA PASS SITE 46,61|63,79 NA NA 2 57 20,20 168,169 60,60 34 1.62 NA 12.04 NA FALSE 0.311 93 NA NA NA FALSE NA NA 363.41 19 26510336 HCC1395_HCC1395T 47 0.741 189 9,27 19,51 29,85 NA 0/1 NA NA NA NA 21,26,63,79 T/C PANCANCER NA FALSE BTN1A1 chr6:26510336:26510337:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 26510377 26510378 C T 87 124 0.701612903225806 MODIFIER BTN1A1 ENSG00000124557 T 3_prime_UTR_variant Transcript ENST00000244513 protein_coding 7/7 ENST00000244513.10:c.*1203C>T NA 2850 rs1056668&COSV55066938 1 SNV HGNC HGNC:1135 1 P1 CCDS4614.1 ENSP00000244513 Q13410.179 UPI000006E521 0.4159 0.0461 0.5086 0.7034 0.4225 0.547 0.3632 0.1026 0.3838 0.4595 0.5176 0.6872 0.3961 0.3987 0.4512 0.3799 0.513 0.7034 EAS 0&1 0&1 19 NA NA PASS SITE 26,51|23,64 NA NA 2 23 20,20 170,173 60,60 28 1.44 NA 7.83 NA FALSE 0.426 93 NA NA NA FALSE NA NA 266.04 19 26510377 HCC1395_HCC1395T 37 0.707 124 7,10 9,19 26,64 NA 0/1 NA NA NA NA 11,26,23,64 C/T PANCANCER NA FALSE BTN1A1 chr6:26510377:26510378:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 27133144 27133145 C T 114 678 0.168141592920354 MODIFIER H2BC11 ENSG00000124635 T upstream_gene_variant Transcript ENST00000339812 protein_coding NA rs376267515 349 -1 SNV HGNC HGNC:4761 YES NM_021058.4 P1 CCDS4618.1 ENSP00000342886 P06899.211 A0A024RCJ2.55 UPI0000001BD5 1.597e-05 0.0001268 0 0 0 0 0 0 6.534e-05 1.971e-05 2.413e-05 0 0 0 0 0 0 1.47e-05 0 0.0002071 0.0002071 gnomADg_SAS 19 NA NA PASS SITE 358,424|51,63 NA NA 1 93 20,20 159,170 60,60 38 2.14 NA 40.94 NA FALSE 6.00 93 NA NA NA FALSE NA NA 241.25 19 27133144 HCC1395_HCC1395T 564 0.169 678 150,28 183,42 365,74 NA 0/1 NA NA NA NA 249,315,51,63 C/T PANCANCER NA FALSE H2BC11 chr6:27133144:27133145:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 27310287 27310288 T C 30 266 0.112781954887218 MODIFIER POM121L2 ENSG00000158553 C intron_variant Transcript ENST00000429945 protein_coding 1/1 ENST00000429945.1:c.216+810A>G NA -1 cds_start_NF SNV HGNC HGNC:13973 3 ENSP00000415181 H7C418.46 UPI000020D6D3 19 NA NA PASS SITE 166,139|17,13 NA NA 2 93 20,20 164,164 60,60 29 1.68 NA 14.15 NA FALSE 6.00 19 NA NA NA FALSE NA NA 101.70 19 27310287 HCC1395_HCC1395T 236 0.121 266 61,3 95,16 166,22 NA 0|1 0|1 27310287_T_C NA 27310287 129,107,17,13 T|C PANCANCER NA FALSE POM121L2 chr6:27310287:27310288:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 27310289 27310290 G A 30 266 0.112781954887218 MODIFIER POM121L2 ENSG00000158553 A intron_variant Transcript ENST00000429945 protein_coding 1/1 ENST00000429945.1:c.216+808C>T NA COSV66275925&COSV66275934 -1 cds_start_NF SNV HGNC HGNC:13973 3 ENSP00000415181 H7C418.46 UPI000020D6D3 1&1 1&1 19 NA NA PASS SITE 166,139|17,13 NA NA 2 93 20,20 164,164 60,60 30 1.68 NA 14.15 NA FALSE 6.00 16 NA NA NA FALSE NA NA 101.69 19 27310289 HCC1395_HCC1395T 236 0.121 266 59,3 94,17 166,22 NA 0|1 0|1 27310287_T_C NA 27310287 129,107,17,13 G|A PANCANCER NA FALSE POM121L2 chr6:27310289:27310290:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 27402267 27402268 T G 317 429 0.738927738927739 MODIFIER ZNF391 ENSG00000124613 G 3_prime_UTR_variant Transcript ENST00000244576 protein_coding 3/3 ENST00000244576.9:c.*820T>G NA 2401 rs6456778 1 SNV HGNC HGNC:18779 YES NM_001076781.3 2 P1 CCDS43429.1 ENSP00000244576 Q9UJN7.155 UPI00001D81D5 0.6859 0.6641 0.7305 0.5813 0.7445 0.7311 0.7116 0.6657 0.7176 0.7298 0.8233 0.5807 0.6026 0.8196 0.7529 0.7335 0.7458 0.8233 gnomADg_ASJ 19 NA NA PASS SITE 87,129|129,188 NA NA 1 93 20,20 172,171 60,60 31 1.85 NA 21.07 NA FALSE 0.153 93 NA NA NA FALSE NA NA 882.41 19 27402267 HCC1395_HCC1395T 112 0.742 429 24,82 48,100 72,209 NA 0/1 NA NA NA NA 43,69,129,188 T/G PANCANCER NA FALSE ZNF391 chr6:27402267:27402268:T:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 27403146 27403148 T TA 537 702 0.764957264957265 MODIFIER ZNF391 ENSG00000124613 A 3_prime_UTR_variant Transcript ENST00000244576 protein_coding 3/3 ENST00000244576.9:c.*1708dup NA 3280-3281 rs34885201 1 insertion HGNC HGNC:18779 YES NM_001076781.3 2 P1 CCDS43429.1 ENSP00000244576 Q9UJN7.155 UPI00001D81D5 9 0.6408 0.6309 0.6816 0.5744 0.6451 0.6892 0.6308 0.6274 0.5675 0.6679 0.7764 0.5682 0.4695 0.7785 0.6466 0.6602 0.621 0.7785 gnomADg_MID 19 NA NA PASS SITE 157,191|227,310 NA NA 1 93 20,20 168,166 60,60 34 2.11 NA 36.68 NA FALSE 0.209 93 9,10 A NA TRUE NA 93 773.67 19 27403146 HCC1395_HCC1395T 165 0.780 702 37,108 54,170 110,380 NA 0/1 NA NA NA NA 79,86,227,310 T/TA PANCANCER NA FALSE ZNF391 chr6:27403146:27403148:T:TA indel 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 28225328 28225329 C A 58 193 0.300518134715026 MODIFIER ZSCAN9 ENSG00000137185 A 5_prime_UTR_variant Transcript ENST00000252207 protein_coding 1/4 ENST00000252207.10:c.-112C>A NA 54 1 SNV HGNC HGNC:12984 YES NM_006299.5 1 P2 CCDS4646.1 ENSP00000252207 O15535.201 A0A024RCK9.54 UPI000013C315 O15535-1 19 NA NA PASS SITE 87,115|25,33 NA NA 1 93 20,20 152,152 60,60 24 1.66 NA 12.94 NA FALSE 6.00 70 NA NA NA FALSE NA NA 127.25 19 28225328 HCC1395_HCC1395T 135 0.269 193 33,11 52,19 97,35 NA 0/1 NA NA NA NA 56,79,25,33 C/A PANCANCER NA FALSE ZSCAN9 chr6:28225328:28225329:C:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 28227743 28227744 A G 75 107 0.700934579439252 LOW ZSCAN9 ENSG00000137185 G synonymous_variant Transcript ENST00000252207 protein_coding 3/4 ENST00000252207.10:c.474A>G ENSP00000252207.5:p.L158= ENSP00000252207.5 p.L158= 639 474 158 L ctA/ctG rs12197427 1 SNV HGNC HGNC:12984 YES NM_006299.5 1 P2 CCDS4646.1 ENSP00000252207 O15535.201 A0A024RCK9.54 UPI000013C315 O15535-1 PANTHER:PTHR23226&SMART:SM00431&AlphaFold_DB_import:AF-O15535-F1 0.0156 0 0.0274 0.0129 0.0278 0.0184 0.03135 0.005055 0.02549 0.1259 0.0154 0.02682 0.03354 0.04526 0.0228 0.0264 0.004848 0.05702 0.03776 0.1446 0.0125 0.02448 0.08861 0.03165 0.03629 0.02151 0.1446 gnomADg_ASJ 19 NA NA PASS SITE 32,30|42,33 NA NA 1 21 20,20 168,158 60,60 33 1.35 NA 6.32 NA FALSE 1.59 93 NA NA NA FALSE NA NA 209.22 19 28227743 HCC1395_HCC1395T 32 0.690 107 8,16 14,32 23,52 NA 0/1 NA NA NA NA 15,17,42,33 A/G PANCANCER NA FALSE ZSCAN9_p.L158= chr6:28227743:28227744:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 29174126 29174127 C T 262 1135 0.230837004405286 MODERATE OR2J2 ENSG00000204700 T missense_variant Transcript ENST00000377167 protein_coding 1/1 ENST00000377167.3:c.491C>T ENSP00000366372.2:p.T164I ENSP00000366372.2 p.T164I 824 491 164 T/I aCt/aTt 1 SNV HGNC HGNC:8260 P1 CCDS43434.1 ENSP00000366372 O76002.178 UPI000004B9D1 tolerated(0.18) benign(0.045) PROSITE_profiles:PS50262&CDD:cd15947&PANTHER:PTHR26453&Pfam:PF13853&Gene3D:1.20.1070.10&Superfamily:SSF81321&AlphaFold_DB_import:AF-O76002-F1 19 NA NA PASS SITE 585,605|133,129 NA NA 1 93 20,20 161,172 60,60 32 2.32 NA 61.30 NA FALSE 6.00 93 NA NA NA FALSE NA NA 620.30 19 29174126 HCC1395_HCC1395T 873 0.235 1135 200,63 351,106 585,180 NA 0/1 NA NA NA NA 431,442,133,129 C/T PANCANCER NA FALSE OR2J2_p.T164I chr6:29174126:29174127:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 29373672 29373673 A G 125 147 0.850340136054422 MODIFIER OR5V1 ENSG00000243729 G intron_variant Transcript ENST00000377154 protein_coding 3/3 ENST00000377154.1:c.-82-17395T>C NA rs10456372 -1 SNV HGNC HGNC:13972 P1 CCDS4657.1 ENSP00000366359 Q9UGF6.178 A0A126GV99.42 UPI000004186B 0.2897 0.0651 0.3646 0.255 0.493 0.3671 0.3636 0.1149 0.3733 0.3431 0.3639 0.2623 0.6251 0.443 0.4864 0.3453 0.3745 0.6251 gnomADg_FIN 19 NA NA PASS SITE 11,47|30,95 NA NA 1 43 34,30 176,179 60,60 25 1.52 NA 9.33 NA FALSE 0.395 93 NA NA NA FALSE NA NA 401.44 19 29373672 HCC1395_HCC1395T 22 0.851 147 7,28 7,59 16,96 NA 0/1 NA NA NA NA 6,16,30,95 A/G PANCANCER NA FALSE OR5V1 chr6:29373672:29373673:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 29374538 29374539 G C 89 224 0.397321428571429 MODIFIER OR5V1 ENSG00000243729 C intron_variant Transcript ENST00000377154 protein_coding 3/3 ENST00000377154.1:c.-82-18261C>G NA COSV105318084&COSV105318152&COSV65830945 -1 SNV HGNC HGNC:13972 P1 CCDS4657.1 ENSP00000366359 Q9UGF6.178 A0A126GV99.42 UPI000004186B 1&1&1 1&1&1 19 NA NA PASS SITE 92,106|44,45 NA NA 1 93 20,20 166,152 60,60 34 1.63 NA 12.34 NA FALSE 6.00 89 NA NA NA FALSE NA NA 233.65 19 29374538 HCC1395_HCC1395T 135 0.391 224 38,14 49,45 94,60 NA 0/1 NA NA NA NA 64,71,44,45 G/C PANCANCER NA FALSE OR5V1 chr6:29374538:29374539:G:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 29603064 29603065 A G 106 135 0.785185185185185 MODIFIER GABBR1 ENSG00000204681 G intron_variant Transcript ENST00000355973 protein_coding 18/18 ENST00000355973.7:c.*2+477T>C NA rs2267633 -1 SNV HGNC HGNC:4070 2 CCDS4665.1 ENSP00000348248 Q9UBS5.209 Q5SUJ9.153 UPI000000D9EB Q9UBS5-2 1 0.1839 0.1051 0.1628 0.249 0.1064 0.318 0.1574 0.1134 0.1231 0.1629 0.2441 0.05335 0.1248 0.1552 0.2708 0.1253 0.1076 0.1206 0.12 0.166 0.2529 0.06259 0.2102 0.1218 0.1539 0.2969 0.318 SAS 1 19 NA NA PASS SITE 35,36|53,53 NA NA 1 29 20,20 156,155 60,60 30 1.46 NA 8.43 NA FALSE 0.947 93 NA NA NA FALSE NA NA 308.92 19 29603064 HCC1395_HCC1395T 29 0.768 135 5,28 12,42 21,72 NA 0/1 NA NA NA NA 11,18,53,53 A/G PANCANCER NA FALSE GABBR1 chr6:29603064:29603065:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 29664788 29664789 G C 55 63 0.873015873015873 MODIFIER MOG ENSG00000204655 C intron_variant Transcript ENST00000376888 protein_coding 1/6 ENST00000376888.6:c.89-1364G>C NA rs2907895&COSV65321572 1 SNV HGNC HGNC:7197 1 CCDS47395.2 ENSP00000366085 Q16653.188 UPI0000470268 Q16653-4 1 0.0753 0.0008 0.0375 0.1567 0.0577 0.137 0.04988 0.01187 0.09802 0.04131 0.05594 0.1657 0.03888 0.04747 0.06062 0.04846 0.1387 0.1657 gnomADg_EAS 0&1 0&1 19 NA NA PASS SITE 14,20|26,29 NA NA 1 8 20,20 139,151 60,60 41 1.24 NA 4.82 NA FALSE 1.29 93 NA NA NA FALSE NA NA 146.65 19 29664788 HCC1395_HCC1395T 8 0.833 63 4,14 2,17 6,34 NA 0/1 NA NA NA NA 3,5,26,29 G/C PANCANCER NA FALSE MOG chr6:29664788:29664789:G:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 29681157 29681158 C T 50 62 0.806451612903226 MODIFIER ZFP57 ENSG00000204644 T upstream_gene_variant Transcript ENST00000376883 protein_coding NA rs62392956 5 -1 SNV HGNC HGNC:18791 YES NM_001109809.5 5 P1 CCDS43436.2 ENSP00000366080 Q9NU63.165 A0A1U9X8V5.33 UPI0001951170 Q9NU63-3 1 0.0751 0.0008 0.0375 0.1567 0.0577 0.136 0.04924 0.0114 0.09582 0.04091 0.05546 0.1635 0.03763 0.04777 0.06029 0.04668 0.1374 0.1635 gnomADg_EAS 19 NA NA PASS SITE 15,29|18,32 NA NA 1 20 20,20 174,170 60,60 22 1.38 NA 6.92 NA FALSE 1.29 93 NA NA NA FALSE NA NA 144.14 19 29681157 HCC1395_HCC1395T 12 0.783 62 5,15 4,18 9,35 NA 0/1 NA NA NA NA 3,9,18,32 C/T PANCANCER NA FALSE ZFP57 chr6:29681157:29681158:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 29888769 29888770 G T 307 381 0.805774278215223 MODIFIER HLA-H ENSG00000206341 T intron_variant&non_coding_transcript_variant Transcript ENST00000383620 unprocessed_pseudogene 3/6 ENST00000383620.4:n.625+27G>T NA rs55682221 1 SNV HGNC HGNC:4965 YES 0.1046 0.0023 0.0476 0.2411 0.0636 0.1851 0.08665 0.01477 0.04541 0.06894 0.2489 0.04203 0.06617 0.08336 0.1839 0.06078 0.01526 0.1045 0.05364 0.06396 0.2492 0.04217 0.06552 0.06835 0.06231 0.202 0.2492 gnomADg_EAS 19 NA NA PASS SITE 120,119|160,147 NA NA 1 93 20,20 160,163 60,60 38 2.05 NA 33.05 NA FALSE 1.21 93 NA NA NA FALSE NA NA 892.77 19 29888769 HCC1395_HCC1395T 74 0.808 381 11,72 34,122 49,208 NA 0/1 NA NA NA NA 38,36,160,147 G/T PANCANCER NA FALSE HLA-H chr6:29888769:29888770:G:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 30185586 30185587 G A 117 153 0.764705882352941 MODIFIER TRIM26 ENSG00000234127 A 3_prime_UTR_variant Transcript ENST00000437089 protein_coding 9/9 ENST00000437089.5:c.*290C>T NA 2119 rs2106072 -1 SNV HGNC HGNC:12962 1 P1 CCDS4678.1 ENSP00000395491 Q12899.202 A0A024RCP3.67 UPI0000001C20 0.0220 0.0159 0.0187 0 0.0755 0 0.06326 0.02905 0.1656 0.02515 0.03026 0 0.06713 0.003165 0.1026 0.04115 0.0004142 0.1656 gnomADg_AMI 1 19 NA NA PASS SITE 36,50|48,69 NA NA 1 46 20,27 158,177 60,60 25 1.53 NA 9.93 NA FALSE 1.13 93 NA NA NA FALSE NA NA 360.46 19 30185586 HCC1395_HCC1395T 36 0.769 153 11,38 13,42 26,89 NA 0/1 NA NA NA NA 16,20,48,69 G/A PANCANCER NA FALSE TRIM26 chr6:30185586:30185587:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 30213340 30213341 A G 289 364 0.793956043956044 MODIFIER TRIM26 ENSG00000234127 G 5_prime_UTR_variant Transcript ENST00000416596 protein_coding 1/6 ENST00000416596.5:c.-300T>C NA 80 rs3094615 -1 cds_end_NF SNV HGNC HGNC:12962 5 ENSP00000413673 A2AE48.130 UPI0000E5ACBD 0.3974 0.4319 0.4597 0.3026 0.4304 0.3701 0.4233 0.4098 0.5121 0.411 0.3642 0.3116 0.4172 0.3196 0.4489 0.388 0.3985 0.5121 gnomADg_AMI 19 NA NA PASS SITE 100,97|145,144 NA NA 1 93 20,20 149,151 60,60 35 1.84 NA 20.47 NA FALSE 0.374 93 NA NA NA FALSE NA NA 742.43 19 30213340 HCC1395_HCC1395T 75 0.777 364 24,60 24,105 49,173 NA 0/1 NA NA NA NA 36,39,145,144 A/G PANCANCER NA FALSE TRIM26 chr6:30213340:30213341:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 30586823 30586824 C G 7 32 0.21875 MODIFIER ABCF1 ENSG00000204574 G intron_variant Transcript ENST00000326195 protein_coding 20/24 ENST00000326195.13:c.2031+112C>G NA 1 SNV HGNC HGNC:70 YES NM_001025091.2 1 A1 CCDS34380.1 ENSP00000313603 Q8NE71.185 A0A1U9X609.36 UPI0000141876 Q8NE71-1 19 NA NA PASS SITE 14,24|3,4 NA NA 1 20 20,20 169,142 60,60 26 0.954 NA 2.41 NA FALSE 6.00 56 NA NA NA FALSE NA NA 13.62 19 30586823 HCC1395_HCC1395T 25 0.208 32 7,2 9,2 18,4 NA 0/1 NA NA NA NA 9,16,3,4 C/G PANCANCER NA FALSE ABCF1 chr6:30586823:30586824:C:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 30616918 30616919 C G 42 199 0.21105527638191 MODIFIER MRPS18B ENSG00000204568 G upstream_gene_variant Transcript ENST00000259873 protein_coding NA 922 1 SNV HGNC HGNC:14516 YES NM_014046.4 1 P1 CCDS4682.1 ENSP00000259873 Q9Y676.177 B0S7P4.102 UPI0000132F37 19 NA NA PASS SITE 113,116|20,22 NA NA 1 93 20,20 161,148 60,60 36 1.68 NA 14.15 NA FALSE 6.00 93 NA NA NA FALSE NA NA 86.60 19 30616918 HCC1395_HCC1395T 157 0.205 199 38,11 53,13 102,26 NA 0/1 NA NA NA NA 78,79,20,22 C/G PANCANCER NA FALSE MRPS18B chr6:30616918:30616919:C:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 30814225 30814226 C T 291 373 0.780160857908847 MODIFIER LINC00243 ENSG00000214894 T non_coding_transcript_exon_variant Transcript ENST00000399196 lncRNA 2/2 ENST00000399196.1:n.693G>A NA 693 rs886424 -1 SNV HGNC HGNC:30956 2 0.0405 0.0507 0.0389 0.003 0.0915 0.0143 0.07076 0.06103 0.03027 0.06193 0.0002857 0.07207 0.1252 0.07943 0.02081 0.08487 0.05898 0.1473 0.04163 0.06286 0.001347 0.06981 0.0538 0.1247 0.07354 0.01697 0.1473 gnomADg_AMI 1 19 NA NA PASS SITE 131,71|186,105 NA NA 1 93 20,20 166,160 60,60 34 1.93 NA 24.64 NA FALSE 1.04 93 NA NA NA FALSE NA NA 808.98 19 30814225 HCC1395_HCC1395T 82 0.772 373 25,74 31,116 56,192 NA 0/1 NA NA NA NA 54,28,186,105 C/T PANCANCER NA FALSE LINC00243 chr6:30814225:30814226:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 30814428 30814429 G C 389 489 0.795501022494888 MODIFIER LINC00243 ENSG00000214894 C non_coding_transcript_exon_variant Transcript ENST00000399196 lncRNA 2/2 ENST00000399196.1:n.490C>G NA 490 rs886423 -1 SNV HGNC HGNC:30956 2 0.1250 0.2352 0.0836 0.0675 0.1312 0.0583 0.1162 0.2276 0.06812 0.08327 0.09912 0.0845 0.1547 0.1171 0.07084 0.1582 0.2253 0.1685 0.09343 0.08338 0.07408 0.0854 0.1266 0.1589 0.1505 0.07291 0.2352 AFR 1 19 NA NA PASS SITE 97,128|161,228 NA NA 1 93 20,20 155,168 60,60 30 1.90 NA 23.48 NA FALSE 0.807 93 NA NA NA FALSE NA NA 1094.39 19 30814428 HCC1395_HCC1395T 100 0.801 489 28,93 34,153 67,271 NA 0/1 NA NA NA NA 45,55,161,228 G/C PANCANCER NA FALSE LINC00243 chr6:30814428:30814429:G:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 30884132 30884133 C A 196 250 0.784 MODIFIER DDR1 ENSG00000204580 A intron_variant Transcript ENST00000324771 protein_coding 1/19 ENST00000324771.12:c.-271-406C>A NA rs1264326 1 SNV HGNC HGNC:2730 5 P1 CCDS34385.1 ENSP00000318217 Q08345.231 A0A024RCL1.67 UPI000000D740 Q08345-1 0.0343 0.0242 0.0216 0.004 0.0795 0.0419 0.07441 0.03242 0.1458 0.02932 0.04412 0.004054 0.07023 0.01582 0.1192 0.05359 0.05362 0.1458 gnomADg_AMI 19 NA NA PASS SITE 73,91|85,111 NA NA 2 93 20,20 151,155 60,60 37 1.86 NA 21.07 NA FALSE 1.08 93 NA NA NA FALSE NA NA 501.77 19 30884132 HCC1395_HCC1395T 54 0.770 250 16,50 18,59 35,120 NA 0/1 NA NA NA NA 22,32,85,111 C/A PANCANCER NA FALSE DDR1 chr6:30884132:30884133:C:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 30884212 30884213 G A 51 69 0.739130434782609 MODIFIER DDR1 ENSG00000204580 A intron_variant Transcript ENST00000324771 protein_coding 1/19 ENST00000324771.12:c.-271-326G>A NA rs1264325 1 SNV HGNC HGNC:2730 5 P1 CCDS34385.1 ENSP00000318217 Q08345.231 A0A024RCL1.67 UPI000000D740 Q08345-1 0.0343 0.0242 0.0216 0.004 0.0795 0.0419 0.07414 0.03232 0.1465 0.02902 0.04443 0.00409 0.06726 0.01592 0.1191 0.05331 0.05346 0.1465 gnomADg_AMI 19 NA NA PASS SITE 19,36|11,40 NA NA 2 21 20,36 165,185 60,60 26 1.40 NA 7.22 NA FALSE 1.09 93 NA NA NA FALSE NA NA 155.99 19 30884212 HCC1395_HCC1395T 18 0.749 69 4,8 3,8 13,41 NA 0/1 NA NA NA NA 6,12,11,40 G/A PANCANCER NA FALSE DDR1 chr6:30884212:30884213:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 31025536 31025537 C T 216 277 0.779783393501805 LOW MUC22 ENSG00000261272 T synonymous_variant Transcript ENST00000561890 protein_coding 2/4 ENST00000561890.1:c.105C>T ENSP00000455906.1:p.S35= ENSP00000455906.1 p.S35= 338 105 35 S tcC/tcT rs1419664 1 SNV HGNC HGNC:39755 YES NM_001395414.1 2 P1 CCDS59003.1 ENSP00000455906 E2RYF6.70 UPI0001E92A31 AlphaFold_DB_import:AF-E2RYF6-F1 0.1206 0.0998 0.1297 0.0952 0.1302 0.1585 0.1348 0.1159 0.09681 0.1263 0.05581 0.1601 0.1615 0.1391 0.1633 0.1342 0.1129 0.1667 0.101 0.1215 0.08813 0.1531 0.05696 0.1547 0.1258 0.152 0.1667 gnomADg_AMI 1 19 NA NA PASS SITE 84,59|133,83 NA NA 1 93 20,20 167,157 60,60 35 1.75 NA 16.51 NA FALSE 0.857 93 NA NA NA FALSE NA NA 613.16 19 31025536 HCC1395_HCC1395T 61 0.769 277 15,52 27,88 42,142 NA 0/1 NA NA NA NA 37,24,133,83 C/T PANCANCER NA FALSE MUC22_p.S35= chr6:31025536:31025537:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 31158201 31158202 A T 107 143 0.748251748251748 MODIFIER TCF19 ENSG00000137310 T upstream_gene_variant Transcript ENST00000376255 protein_coding NA rs3130455 346 1 SNV HGNC HGNC:11629 1 P1 CCDS43446.1 ENSP00000365431 Q9Y242.176 A0A1U9X8M7.38 UPI0000071646 0.1236 0.1301 0.0893 0.0377 0.1909 0.1585 0.1788 0.1518 0.3456 0.1123 0.1788 0.04223 0.1502 0.2308 0.2243 0.1625 0.1318 0.3456 gnomADg_AMI 19 NA NA PASS SITE 41,43|50,57 NA NA 1 29 20,20 144,158 60,60 33 1.48 NA 8.59 NA FALSE 0.757 93 NA NA NA FALSE NA NA 277.62 19 31158201 HCC1395_HCC1395T 36 0.732 143 7,32 16,31 26,71 NA 0/1 NA NA NA NA 20,16,50,57 A/T PANCANCER NA FALSE TCF19 chr6:31158201:31158202:A:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 31640582 31640583 C A 24 123 0.195121951219512 MODIFIER BAG6 ENSG00000204463 A intron_variant Transcript ENST00000211379 protein_coding 21/24 ENST00000211379.9:c.2887-54G>T NA -1 SNV HGNC HGNC:13919 1 P2 CCDS4709.1 ENSP00000211379 P46379.207 A0A1U9X7A6.35 UPI000008A3C8 P46379-2 19 NA NA PASS SITE 87,60|12,12 NA NA 1 91 20,27 175,168 60,60 36 1.54 NA 9.93 NA FALSE 6.00 73 NA NA NA FALSE NA NA 58.01 19 31640582 HCC1395_HCC1395T 99 0.200 123 26,11 46,7 75,18 NA 0/1 NA NA NA NA 57,42,12,12 C/A PANCANCER NA FALSE BAG6 chr6:31640582:31640583:C:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 31770190 31770191 G T 18 73 0.246575342465753 MODIFIER VWA7 ENSG00000204396 T intron_variant Transcript ENST00000375688 protein_coding 7/16 ENST00000375688.5:c.1088-77C>A NA -1 SNV HGNC HGNC:13939 YES NM_025258.3 5 P1 CCDS4721.2 ENSP00000364840 Q9Y334.146 A0A1U9X8T7.26 UPI0000E5AD19 Q9Y334-1 19 NA NA PASS SITE 22,57|7,11 NA NA 1 52 36,20 175,167 60,60 29 1.31 NA 5.72 NA FALSE 6.00 63 NA NA NA FALSE NA NA 42.52 19 31770190 HCC1395_HCC1395T 55 0.232 73 19,5 19,6 42,12 NA 0/1 NA NA NA NA 16,39,7,11 G/T PANCANCER NA FALSE VWA7 chr6:31770190:31770191:G:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32038540 32038541 C T 210 384 0.546875 MODIFIER TNXB ENSG00000168477 T downstream_gene_variant Transcript ENST00000375244 protein_coding NA rs6468&COSV64473789 2614 -1 SNV HGNC HGNC:11976 5 CCDS93886.1 ENSP00000364393 P22105.232 UPI0001B798E9 P22105-3 1 0.7944 0.8847 0.8423 0.8739 0.71 0.7914 0.7687 0.7899 0.8135 0.8328 0.9085 0.9159 0.8464 0.8925 0.7511 0.8162 0.8903 0.7886 0.8461 0.8229 0.9159 gnomADg_AMI benign 0&1 1&1 19 NA NA PASS SITE 226,220|105,107 NA NA 1 93 20,20 156,154 44,45 42 -4.484e-01 NA 44.18 NA FALSE 0.090 93 NA NA NA FALSE NA NA 473.18 19 32038540 HCC1395_HCC1395T 174 0.528 384 42,47 59,71 109,122 NA 0/1 NA NA NA NA 90,84,104,106 C/T PANCANCER NA FALSE TNXB chr6:32038540:32038541:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32058086 32058087 C T 351 469 0.748400852878465 LOW TNXB ENSG00000168477 T synonymous_variant Transcript ENST00000375244 protein_coding 22/44 ENST00000375244.7:c.7797G>A ENSP00000364393.3:p.L2599= ENSP00000364393.3 p.L2599= 7999 7797 2599 L ctG/ctA rs369637&COSV64479032 -1 SNV HGNC HGNC:11976 5 CCDS93886.1 ENSP00000364393 P22105.232 UPI0001B798E9 P22105-3 1 Gene3D:2.60.40.10&PROSITE_profiles:PS50853&SMART:SM00060&Superfamily:SSF49265 0.0495 0.0469 0.0432 0.0169 0.1113 0.0276 0.09082 0.05347 0.04137 0.05313 0.01441 0.1112 0.1402 0.09179 0.02931 0.09886 0.05591 0.08443 0.05587 0.05392 0.01833 0.1105 0.04114 0.1475 0.07799 0.0275 0.1475 gnomADg_NFE benign 0&1 1&1 19 NA NA PASS SITE 139,169|157,194 NA NA 1 93 20,20 154,155 60,60 32 2.09 NA 36.12 NA FALSE 0.959 93 NA NA NA FALSE NA NA 931.35 19 32058086 HCC1395_HCC1395T 118 0.745 469 31,68 31,134 76,224 NA 0/1 NA NA NA NA 49,69,157,194 C/T PANCANCER NA FALSE TNXB_p.L2599= chr6:32058086:32058087:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32061428 32061429 G A 350 554 0.631768953068592 LOW TNXB ENSG00000168477 A synonymous_variant Transcript ENST00000375244 protein_coding 21/44 ENST00000375244.7:c.7461C>T ENSP00000364393.3:p.R2487= ENSP00000364393.3 p.R2487= 7663 7461 2487 R cgC/cgT rs1150757 -1 SNV HGNC HGNC:11976 5 CCDS93886.1 ENSP00000364393 P22105.232 UPI0001B798E9 P22105-3 1 Gene3D:2.60.40.10&PROSITE_profiles:PS50853&SMART:SM00060&Superfamily:SSF49265&CDD:cd00063 0.0190 0.0023 0.0231 0 0.0755 0 0.05867 0.0147 0.0217 0.03606 0.0001114 0.07833 0.1001 0.05965 6.54e-05 0.06236 0.01551 0.07033 0.02965 0.03864 0 0.07991 0.01899 0.1062 0.04685 0.0002071 0.1062 gnomADg_NFE benign 1 19 NA NA PASS SITE 191,235|152,198 NA NA 2 93 20,20 154,161 60,60 31 2.16 NA 42.14 NA FALSE 1.13 93 NA NA NA FALSE NA NA 886.95 19 32061428 HCC1395_HCC1395T 204 0.635 554 57,105 60,101 129,225 NA 0/1 NA NA NA NA 91,113,152,198 G/A PANCANCER NA FALSE TNXB_p.R2487= chr6:32061428:32061429:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32067917 32067918 C T 313 421 0.743467933491686 LOW TNXB ENSG00000168477 T synonymous_variant Transcript ENST00000375244 protein_coding 18/44 ENST00000375244.7:c.6288G>A ENSP00000364393.3:p.P2096= ENSP00000364393.3 p.P2096= 6490 6288 2096 P ccG/ccA rs1150756&COSV64479042 -1 SNV HGNC HGNC:11976 5 CCDS93886.1 ENSP00000364393 P22105.232 UPI0001B798E9 P22105-3 1 Gene3D:2.60.40.10&SMART:SM00060&Low_complexity_(Seg):seg 0.0192 0.0023 0.0231 0.001 0.0755 0 0.06021 0.01433 0.02234 0.04475 0.001619 0.07837 0.1018 0.06231 0.0003598 0.06277 0.01551 0.07127 0.03057 0.04842 0.0009649 0.07966 0.02215 0.1066 0.04741 0.0004149 0.1066 gnomADg_NFE benign 0&1 1&1 19 NA NA PASS SITE 169,148|175,138 NA NA 1 93 20,20 155,160 48,46 38 2.12 NA 38.78 NA FALSE 1.13 93 NA NA NA FALSE NA NA 809.00 19 32067917 HCC1395_HCC1395T 108 0.741 421 28,69 38,121 68,196 NA 0/1 NA NA NA NA 62,46,175,138 C/T PANCANCER NA FALSE TNXB_p.P2096= chr6:32067917:32067918:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32096949 32096950 T C 198 307 0.644951140065147 MODERATE TNXB ENSG00000168477 C missense_variant Transcript ENST00000375244 protein_coding 3/44 ENST00000375244.7:c.904A>G ENSP00000364393.3:p.T302A ENSP00000364393.3 p.T302A 1106 904 302 T/A Act/Gct rs1150752&COSV100926411&COSV105302285 -1 SNV HGNC HGNC:11976 5 CCDS93886.1 ENSP00000364393 P22105.232 UPI0001B798E9 P22105-3 1 tolerated(0.18) benign(0.039) Gene3D:2.10.25.10&Pfam:PF18720&SMART:SM00181&CDD:cd00054 0.0188 0.0023 0.0216 0 0.0755 0 0.05885 0.01414 0.02155 0.0369 5.589e-05 0.07794 0.1 0.06003 6.595e-05 0.06243 0.01556 0.07095 0.02919 0.03877 0 0.08064 0.01948 0.1062 0.04703 0 0.1062 gnomADg_NFE benign 0&1&1 1&1&1 19 NA NA PASS SITE 134,129|109,89 NA NA 1 93 20,20 152,160 60,60 27 2.00 NA 29.80 NA FALSE 1.14 93 NA NA NA FALSE NA NA 560.88 19 32096949 HCC1395_HCC1395T 109 0.654 307 25,50 41,82 74,139 NA 0/1 NA NA NA NA 56,53,109,89 T/C PANCANCER NA FALSE TNXB_p.T302A chr6:32096949:32096950:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32181196 32181197 G T 21 91 0.230769230769231 MODIFIER AGPAT1 ENSG00000204310 T upstream_gene_variant Transcript ENST00000336984 protein_coding NA COSV61249074 3100 -1 SNV HGNC HGNC:324 1 P1 CCDS4744.1 ENSP00000337463 Q99943.189 A0A024RCV5.57 UPI0000131BD2 1 1 19 NA NA PASS SITE 47,45|8,13 NA NA 1 40 20,36 164,161 60,60 31 1.23 NA 4.77 NA FALSE 6.00 54 NA NA NA FALSE NA NA 57.58 19 32181196 HCC1395_HCC1395T 70 0.246 91 19,4 31,9 51,16 NA 0/1 NA NA NA NA 35,35,8,13 G/T PANCANCER NA FALSE AGPAT1 chr6:32181196:32181197:G:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32184665 32184666 A G 112 161 0.695652173913043 MODIFIER PBX2 ENSG00000204304 G downstream_gene_variant Transcript ENST00000375050 protein_coding NA rs1800625&CR012231 68 -1 SNV HGNC HGNC:8633 YES NM_002586.5 1 P1 CCDS4748.1 ENSP00000364190 P40425.199 A0A024RCR3.56 UPI00001313B2 0.1366 0.1354 0.0836 0.0962 0.16 0.1933 0.1457 0.121 0.2319 0.08281 0.08757 0.1043 0.1373 0.0981 0.1803 0.1295 0.1565 0.2319 gnomADg_AMI 1&1 19 NA NA PASS SITE 59,57|60,52 NA NA 1 92 20,20 180,164 60,60 35 1.68 NA 13.80 NA FALSE 0.815 93 NA NA NA FALSE NA NA 313.94 19 32184665 HCC1395_HCC1395T 49 0.688 161 13,25 19,41 33,74 NA 0/1 NA NA NA NA 22,27,60,52 A/G PANCANCER NA FALSE PBX2 chr6:32184665:32184666:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32192450 32192451 C T 158 213 0.741784037558685 MODIFIER NOTCH4 ENSG00000204301 T downstream_gene_variant Transcript ENST00000375023 protein_coding NA rs767012126 2393 -1 SNV HGNC HGNC:7884 YES NM_004557.4 1 P1 CCDS34420.1 ENSP00000364163 Q99466.222 A0A1U9X983.34 UPI0000130571 Q99466-1 1.492e-05 8.463e-05 0 0 0 0 2.324e-05 0 0 1.972e-05 0 0 0 0 0 0 0 4.412e-05 0 0 8.463e-05 gnomADe_AFR 19 NA NA PASS SITE 53,69|62,96 NA NA 1 93 20,20 157,183 60,60 32 1.65 NA 12.94 NA FALSE 6.00 93 NA NA NA FALSE NA NA 450.47 19 32192450 HCC1395_HCC1395T 55 0.766 213 16,37 15,71 34,114 NA 0/1 NA NA NA NA 24,31,62,96 C/T PANCANCER NA FALSE NOTCH4 chr6:32192450:32192451:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32288641 32288642 T C 306 423 0.723404255319149 MODIFIER TSBP1 ENSG00000204296 C downstream_gene_variant Transcript ENST00000375015 protein_coding NA rs9268142 4057 -1 SNV HGNC HGNC:13922 5 A2 ENSP00000364155 Q5SRN2.135 UPI0000470278 Q5SRN2-2 0.2169 0.23 0.1282 0.2163 0.2326 0.2464 0.1958 0.2315 0.1283 0.2076 0.1984 0.2708 0.2197 0.2041 0.1833 0.2173 0.2226 0.2489 0.1434 0.2014 0.2022 0.2762 0.1392 0.2239 0.2199 0.2081 0.2762 gnomADg_FIN 19 NA NA PASS SITE 112,123|143,163 NA NA 2 93 20,20 158,159 60,60 37 1.89 NA 22.88 NA FALSE 0.638 93 NA NA NA FALSE NA NA 815.61 19 32288641 HCC1395_HCC1395T 117 0.714 423 24,56 45,121 76,191 NA 0/1 NA NA NA NA 58,59,143,163 T/C PANCANCER NA FALSE TSBP1 chr6:32288641:32288642:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32288696 32288697 A G 164 242 0.677685950413223 MODIFIER TSBP1 ENSG00000204296 G downstream_gene_variant Transcript ENST00000375015 protein_coding NA rs9268143 4002 -1 SNV HGNC HGNC:13922 5 A2 ENSP00000364155 Q5SRN2.135 UPI0000470278 Q5SRN2-2 0.2672 0.3654 0.1643 0.2371 0.2465 0.2597 0.2168 0.3635 0.1586 0.2094 0.2115 0.2918 0.2305 0.2219 0.197 0.2633 0.3477 0.2522 0.1733 0.2045 0.2225 0.3033 0.1592 0.2358 0.2608 0.2228 0.3654 AFR 19 NA NA PASS SITE 55,94|52,112 NA NA 2 93 20,20 171,170 60,60 30 1.68 NA 13.85 NA FALSE 0.570 93 NA NA NA FALSE NA NA 465.57 19 32288696 HCC1395_HCC1395T 78 0.682 242 11,20 21,47 53,115 NA 0/1 NA NA NA NA 28,50,52,112 A/G PANCANCER NA FALSE TSBP1 chr6:32288696:32288697:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32313583 32313584 T C 183 251 0.729083665338645 MODIFIER TSBP1 ENSG00000204296 C intron_variant Transcript ENST00000375015 protein_coding 22/25 ENST00000375015.8:c.577+2811A>G NA rs1018434&COSV66660368 -1 SNV HGNC HGNC:13922 5 A2 ENSP00000364155 Q5SRN2.135 UPI0000470278 Q5SRN2-2 0.2189 0.2201 0.1167 0.2381 0.2296 0.2587 0.2109 0.2105 0.2511 0.1269 0.1083 0.2235 0.302 0.1234 0.2196 0.1989 0.2211 0.302 gnomADg_FIN 0&1 0&1 19 NA NA PASS SITE 83,57|103,80 NA NA 1 90 20,20 170,164 60,60 37 1.69 NA 14.45 NA FALSE 0.644 93 NA NA NA FALSE NA NA 507.82 19 32313583 HCC1395_HCC1395T 68 0.722 251 21,39 24,78 46,121 NA 0/1 NA NA NA NA 40,28,103,80 T/C PANCANCER NA FALSE TSBP1 chr6:32313583:32313584:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32316331 32316332 T G 62 81 0.765432098765432 MODIFIER TSBP1 ENSG00000204296 G intron_variant Transcript ENST00000375015 protein_coding 22/25 ENST00000375015.8:c.577+63A>C NA rs9268219 -1 SNV HGNC HGNC:13922 5 A2 ENSP00000364155 Q5SRN2.135 UPI0000470278 Q5SRN2-2 0.0168 0.0023 0.013 0 0.0716 0 0.05825 0.01378 0.04515 0.01937 0.02535 0 0.08431 0 0.1014 0.03547 0 0.1014 gnomADg_NFE 1 19 NA NA PASS SITE 33,17|42,20 NA NA 1 9 20,20 164,176 60,60 34 1.33 NA 6.02 NA FALSE 1.15 93 NA NA NA FALSE NA NA 180.76 19 32316331 HCC1395_HCC1395T 19 0.750 81 5,13 9,30 14,44 NA 0/1 NA NA NA NA 14,5,42,20 T/G PANCANCER NA FALSE TSBP1 chr6:32316331:32316332:T:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32319977 32319978 T C 90 141 0.638297872340426 MODIFIER TSBP1 ENSG00000204296 C intron_variant Transcript ENST00000375015 protein_coding 21/25 ENST00000375015.8:c.556+2509A>G NA rs9268231 -1 SNV HGNC HGNC:13922 5 A2 ENSP00000364155 Q5SRN2.135 UPI0000470278 Q5SRN2-2 0.1022 0.1248 0.0692 0.0169 0.1481 0.136 0.1316 0.1084 0.2259 0.06998 0.05328 0.0144 0.1612 0.06646 0.1697 0.1181 0.1002 0.2259 gnomADg_AMI 19 NA NA PASS SITE 60,32|65,25 NA NA 1 61 20,34 161,181 60,60 28 1.50 NA 9.03 NA FALSE 0.848 93 NA NA NA FALSE NA NA 275.69 19 32319977 HCC1395_HCC1395T 51 0.667 141 13,22 19,47 34,69 NA 0/1 NA NA NA NA 33,18,65,25 T/C PANCANCER NA FALSE TSBP1 chr6:32319977:32319978:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32445032 32445033 T A 66 91 0.725274725274725 MODIFIER HLA-DRA ENSG00000204287 A 3_prime_UTR_variant Transcript ENST00000374982 protein_coding 5/5 ENST00000374982.5:c.*392T>A NA 1155 rs1041885 1 SNV HGNC HGNC:4947 ENSP00000364121 Q30118.182 UPI000008972A 1 0.1194 0.1263 0.1282 0.12 0.1471 0.0746 0.1516 0.1214 0.1143 0.1248 0.1035 0.125 0.2056 0.06329 0.1791 0.1473 0.06735 0.2056 gnomADg_FIN 19 NA NA PASS SITE 26,33|32,34 NA NA 1 21 20,20 173,179 60,60 31 1.41 NA 7.52 NA FALSE 0.788 93 NA NA NA FALSE NA NA 190.13 19 32445032 HCC1395_HCC1395T 25 0.719 91 8,22 9,19 18,48 NA 0/1 NA NA NA NA 11,14,32,34 T/A PANCANCER NA FALSE HLA-DRA chr6:32445032:32445033:T:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32581502 32581503 A G 9 28 0.321428571428571 MODIFIER HLA-DRB1 ENSG00000196126 G intron_variant Transcript ENST00000360004 protein_coding 3/5 ENST00000360004.6:c.652+55T>C NA rs111760370&COSV63511407 -1 SNV HGNC HGNC:4948 YES NM_002124.4 P1 CCDS47409.1 ENSP00000353099 P01911.178 X5DNQ0.49&D7RIH8.99 UPI000008A1F7 1 0.03344 0.04532 0.01873 0.02982 0.04521 0.03964 0.02427 0.0463 0.02925 0.04135 0.02512 0.0463 gnomADg_MID 0&1 0&1 19 NA NA PASS SITE 10,35|1,8 NA NA 1 76 38,40 182,0 60,38 39 1.40 NA 7.22 NA FALSE 6.00 17 NA NA NA FALSE NA NA 24.18 19 32581502 HCC1395_HCC1395T 19 0.346 28 1,1 12,7 16,8 NA 0/1 NA NA NA NA 5,14,1,8 A/G PANCANCER NA FALSE HLA-DRB1 chr6:32581502:32581503:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32668296 32668297 A G 16 22 0.727272727272727 MODIFIER HLA-DQB1 ENSG00000179344 G upstream_gene_variant Transcript ENST00000374943 protein_coding NA rs3828802 1612 -1 SNV HGNC HGNC:4944 A2 CCDS59006.1 ENSP00000364080 Q5SU54.131 UPI0000E5AD35 1 0.5425 0.6188 0.4986 0.4722 0.5696 0.5153 0.5604 0.5948 0.4879 0.5047 0.5872 0.4523 0.4659 0.712 0.5709 0.6036 0.5815 0.712 gnomADg_MID 19 NA NA PASS SITE 5,12|5,11 NA NA 2 24 20,38 175,188 60,60 32 0.954 NA 2.41 NA FALSE 6.00 47 NA NA NA FALSE NA NA 62.30 19 32668296 HCC1395_HCC1395T 6 0.714 22 2,2 1,5 5,14 NA 0/1 NA NA NA NA 1,5,5,11 A/G PANCANCER NA FALSE HLA-DQB1 chr6:32668296:32668297:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32745635 32745637 AG GA 28 80 0.35 MODIFIER HLA-DQA2 ENSG00000237541 GA intron_variant Transcript ENST00000374940 protein_coding 2/4 ENST00000374940.4:c.332-156_332-155delinsGA NA 1 substitution HGNC HGNC:4943 YES NM_020056.5 P1 CCDS4753.1 ENSP00000364076 P01906.192 Q76NI6.36 UPI0000001086 1 19 NA NA PASS SITE 62,9|26,2 NA NA 1 62 37,32 208,197 60,60 20 1.23 NA 4.82 NA FALSE 6.00 56 NA NA NA FALSE NA NA 97.33 19 32745635 HCC1395_HCC1395T 52 0.351 80 16,7 33,17 49,26 NA 0/1 NA NA NA NA 46,6,26,2 AG/GA PANCANCER NA FALSE HLA-DQA2 chr6:32745635:32745637:AG:GA indel 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32854307 32854308 G C 177 442 0.400452488687783 MODIFIER TAP1 ENSG00000168394 C upstream_gene_variant Transcript ENST00000354258 protein_coding NA 603 -1 SNV HGNC HGNC:43 YES NM_000593.6 1 P1 CCDS4758.2 ENSP00000346206 Q03518.226 X5CKB3.51 UPI00001368D6 Q03518-1 1 19 NA NA PASS SITE 252,253|83,94 NA NA 1 93 20,20 155,158 60,60 33 2.20 NA 46.61 NA FALSE 6.00 93 NA NA NA FALSE NA NA 456.24 19 32854307 HCC1395_HCC1395T 265 0.401 442 54,43 112,63 177,118 NA 0/1 NA NA NA NA 133,132,83,94 G/C PANCANCER NA FALSE TAP1 chr6:32854307:32854308:G:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 32968664 32968665 T C 71 93 0.763440860215054 MODIFIER BRD2 ENSG00000204256 C 5_prime_UTR_variant Transcript ENST00000374825 protein_coding 1/13 ENST00000374825.9:c.-1697T>C NA 71 rs9276935 1 SNV HGNC HGNC:1103 YES NM_005104.4 1 P2 CCDS4762.1 ENSP00000363958 P25440.213 A0A024RCR5.62 UPI0000126ACC P25440-1 0.0515 0.0068 0.0548 0.0397 0.0805 0.092 0.05758 0.01673 0.1535 0.04559 0.07229 0.03983 0.06076 0.06688 0.08143 0.0468 0.09768 0.1535 gnomADg_AMI 19 NA NA PASS SITE 50,26|48,23 NA NA 1 63 20,20 164,151 60,60 25 1.60 NA 11.44 NA FALSE 1.25 93 NA NA NA FALSE NA NA 212.59 19 32968664 HCC1395_HCC1395T 22 0.736 93 9,21 8,28 17,49 NA 0/1 NA NA NA NA 16,6,48,23 T/C PANCANCER NA FALSE BRD2 chr6:32968664:32968665:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 33064586 33064587 T A 44 68 0.647058823529412 MODIFIER HLA-DPA1 ENSG00000231389 A 3_prime_UTR_variant Transcript ENST00000419277 protein_coding 6/6 ENST00000419277.5:c.*774A>T NA 1687 rs9277338 -1 SNV HGNC HGNC:4938 YES P1 CCDS4764.1 ENSP00000393566 P20036.190 X5CKE2.70 UPI000012C03B 1 0.1156 0.0333 0.1081 0.1498 0.1203 0.1922 0.1004 0.03705 0.07895 0.1086 0.1457 0.1475 0.1374 0.207 0.1186 0.1201 0.1765 0.207 gnomADg_MID 19 NA NA PASS SITE 38,18|28,16 NA NA 1 21 20,20 177,169 60,60 29 1.34 NA 6.32 NA FALSE 0.987 93 NA NA NA FALSE NA NA 112.33 19 33064586 HCC1395_HCC1395T 24 0.620 68 9,9 9,19 18,30 NA 0/1 NA NA NA NA 18,6,28,16 T/A PANCANCER NA FALSE HLA-DPA1 chr6:33064586:33064587:T:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 33133569 33133570 C A 26 40 0.65 MODIFIER HLA-DPA3 ENSG00000237398 A intron_variant&non_coding_transcript_variant Transcript ENST00000454398 unprocessed_pseudogene 1/1 ENST00000454398.1:n.103-2227G>T NA rs4582368 -1 SNV HGNC HGNC:19393 YES 0.4265 0.1899 0.5648 0.755 0.3748 0.363 0.3619 0.2123 0.2396 0.4964 0.5193 0.7496 0.4068 0.4745 0.3788 0.3933 0.3559 0.755 EAS 19 NA NA PASS SITE 19,27|8,18 NA NA 2 8 20,20 156,158 60,60 34 1.32 NA 6.02 NA FALSE 0.440 68 NA NA NA FALSE NA NA 77.70 19 33133569 HCC1395_HCC1395T 14 0.645 40 6,6 4,11 10,19 NA 0/1 NA NA NA NA 6,8,8,18 C/A PANCANCER NA FALSE HLA-DPA3 chr6:33133569:33133570:C:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 33193883 33193885 T TG 82 115 0.71304347826087 MODIFIER COL11A2 ENSG00000204248 G upstream_gene_variant Transcript ENST00000341947 protein_coding NA rs576307070&COSV59498449 1416 -1 insertion HGNC HGNC:2187 YES NM_080680.3 5 P4 ENSP00000339915 A0A0C4DFS1.59 UPI000013CD48 1 0.1244 0.0129 0.17 0.1915 0.1054 0.1933 0.0954 0.02712 0.1214 0.121 0.1971 0.1655 0.07941 0.2089 0.1163 0.1177 0.1699 0.2089 gnomADg_MID 0&1 0&1 19 NA NA PASS SITE 42,47|34,48 NA NA 1 54 20,20 164,151 60,60 41 1.62 NA 11.84 NA FALSE 1.02 93 NA NA NA FALSE NA NA 116.09 19 33193883 HCC1395_HCC1395T 33 0.719 115 6,12 10,24 22,57 NA 0/1 NA NA NA NA 12,21,34,48 T/TG PANCANCER NA FALSE COL11A2 chr6:33193883:33193885:T:TG indel 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 33268368 33268369 G C 41 61 0.672131147540984 MODIFIER RPS18 ENSG00000231500 C upstream_gene_variant Transcript ENST00000439602 protein_coding NA rs185988655 3707 1 SNV HGNC HGNC:10401 YES NM_022551.3 1 P1 CCDS4771.1 ENSP00000393241 P62269.182 UPI00000040B5 0.0020 0.0015 0.0029 0 0.005 0.001 0.005338 0.001015 0.008772 0.004716 0.002882 0.0001926 0.00773 0 0.008481 0.008118 0.0006206 0.008772 gnomADg_AMI 19 NA NA PASS SITE 28,23|17,24 NA NA 1 41 20,27 157,198 60,60 23 1.43 NA 7.48 NA FALSE 2.21 93 NA NA NA FALSE NA NA 118.23 19 33268368 HCC1395_HCC1395T 20 0.696 61 8,10 4,19 13,31 NA 0/1 NA NA NA NA 9,11,17,24 G/C PANCANCER NA FALSE RPS18 chr6:33268368:33268369:G:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 33277203 33277204 G A 43 93 0.462365591397849 MODIFIER WDR46 ENSG00000227057 A downstream_gene_variant Transcript ENST00000374617 protein_coding NA rs1336232136 1905 -1 SNV HGNC HGNC:13923 YES NM_005452.6 1 P1 CCDS4772.1 ENSP00000363746 O15213.182 UPI000045741F 1.314e-05 2.412e-05 0 0 0 0 0 0 1.47e-05 0 0 2.412e-05 gnomADg_AFR 19 NA NA PASS SITE 54,48|26,17 NA NA 1 93 20,20 147,148 60,60 30 1.56 NA 10.49 NA FALSE 4.61 93 NA NA NA FALSE NA NA 111.60 19 33277203 HCC1395_HCC1395T 50 0.476 93 14,15 18,14 32,29 NA 0/1 NA NA NA NA 27,23,26,17 G/A PANCANCER NA FALSE WDR46 chr6:33277203:33277204:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 33314561 33314562 G A 65 92 0.706521739130435 MODIFIER DAXX ENSG00000204209 A downstream_gene_variant Transcript ENST00000266000 protein_coding NA rs1061801 3997 -1 SNV HGNC HGNC:2681 1 P2 CCDS4776.1 ENSP00000266000 Q9UER7.214 A0A024RCS3.59 UPI0000128ED8 Q9UER7-1 1 0.1482 0.0401 0.1499 0.1071 0.1849 0.2975 0.1476 0.06413 0.1689 0.1507 0.246 0.098 0.1511 0.231 0.1849 0.1813 0.2787 0.2975 SAS 1 19 NA NA PASS SITE 40,37|31,34 NA NA 1 45 20,20 155,176 60,60 31 1.52 NA 9.63 NA FALSE 0.839 93 NA NA NA FALSE NA NA 170.46 19 33314561 HCC1395_HCC1395T 27 0.694 92 7,27 10,13 18,42 NA 0/1 NA NA NA NA 14,13,31,34 G/A PANCANCER TRUE FALSE DAXX chr6:33314561:33314562:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 33405647 33405648 C T 57 77 0.74025974025974 MODIFIER PHF1 ENSG00000112511 T upstream_gene_variant Transcript ENST00000427004 protein_coding NA rs9278048 4752 1 cds_end_NF SNV HGNC HGNC:8919 4 ENSP00000410494 A2AB22.127 UPI0000E5AD51 0.0138 0.0023 0.0375 0.004 0.0258 0.0102 0.02704 0.003774 0.02848 0.1161 0.001499 0.01482 0.03332 0.04022 0.02032 0.02272 0.004393 0.01206 0.03476 0.09937 0.002118 0.0154 0.07278 0.02992 0.03681 0.01614 0.1161 gnomADe_ASJ 19 NA NA PASS SITE 25,23|31,26 NA NA 1 20 34,20 173,163 60,60 30 1.36 NA 6.57 NA FALSE 1.68 93 NA NA NA FALSE NA NA 154.51 19 33405647 HCC1395_HCC1395T 20 0.707 77 9,17 7,21 16,40 NA 0/1 NA NA NA NA 10,10,31,26 C/T PANCANCER NA FALSE PHF1 chr6:33405647:33405648:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 33593339 33593340 G C 103 339 0.303834808259587 MODIFIER GGNBP1 ENSG00000204188 C downstream_gene_variant Transcript ENST00000374458 processed_transcript NA 4313 1 SNV HGNC HGNC:19427 1 19 NA NA PASS SITE 165,213|41,62 NA NA 1 93 20,20 162,160 60,60 31 1.97 NA 27.64 NA FALSE 6.00 93 NA NA NA FALSE NA NA 244.08 19 33593339 HCC1395_HCC1395T 236 0.295 339 65,25 80,31 157,65 NA 0/1 NA NA NA NA 105,131,41,62 G/C PANCANCER NA FALSE GGNBP1 chr6:33593339:33593340:G:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 34133501 34133502 G A 59 278 0.212230215827338 MODIFIER GRM4 ENSG00000124493 A intron_variant Transcript ENST00000374177 protein_coding 1/8 ENST00000374177.7:c.312+21578C>T NA -1 SNV HGNC HGNC:4596 2 CCDS59012.1 ENSP00000363292 Q14833.182 UPI000035E829 Q14833-5 19 NA NA PASS SITE 177,145|31,28 NA NA 1 93 20,20 162,142 60,60 23 1.86 NA 21.07 NA FALSE 6.00 80 NA NA NA FALSE NA NA 121.97 19 34133501 HCC1395_HCC1395T 219 0.201 278 61,12 75,24 146,36 NA 0/1 NA NA NA NA 121,98,31,28 G/A PANCANCER NA FALSE GRM4 chr6:34133501:34133502:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 34426089 34426090 G A 74 101 0.732673267326733 MODIFIER RPS10 ENSG00000124614 A upstream_gene_variant Transcript ENST00000344700 protein_coding NA rs78454682&COSV58243594 37 -1 SNV HGNC HGNC:10383 3 ENSP00000363169 F6U211.67 UPI0000458C01 1 0.0701 0.0159 0.0836 0.0536 0.1243 0.0951 0.09186 0.0373 0.1473 0.08272 0.129 0.04062 0.1293 0.09177 0.122 0.09178 0.1005 0.1473 gnomADg_AMI benign 0&1 1&1 19 NA NA PASS SITE 41,37|37,37 NA NA 1 41 20,20 150,161 60,60 33 1.51 NA 9.32 NA FALSE 1.02 93 NA NA NA FALSE NA NA 193.84 19 34426089 HCC1395_HCC1395T 27 0.746 101 6,26 8,16 15,46 NA 0/1 NA NA NA NA 13,14,37,37 G/A PANCANCER NA FALSE RPS10 chr6:34426089:34426090:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 34514881 34514882 G A 39 50 0.78 MODIFIER PACSIN1 ENSG00000124507 A intron_variant Transcript ENST00000244458 protein_coding 1/9 ENST00000244458.7:c.-63-11362G>A NA rs539393816 1 SNV HGNC HGNC:8570 YES NM_020804.5 1 P1 CCDS4793.1 ENSP00000244458 Q9BY11.169 Q5TZC3.146 UPI000000D983 0.0040 0.0061 0.0043 0 0.005 0.0041 0.007119 0.004417 0.001099 0.006351 0.003746 0 0.002731 0.003165 0.01091 0.004302 0.001658 0.01091 gnomADg_NFE 19 NA NA PASS SITE 21,13|23,16 NA NA 1 5 20,20 152,164 60,60 27 1.20 NA 4.47 NA FALSE 2.08 93 NA NA NA FALSE NA NA 108.86 19 34514881 HCC1395_HCC1395T 11 0.794 50 2,11 4,12 6,26 NA 0/1 NA NA NA NA 6,5,23,16 G/A PANCANCER NA FALSE PACSIN1 chr6:34514881:34514882:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 34792045 34792046 G A 52 70 0.742857142857143 MODIFIER BLTP3A ENSG00000065060 A upstream_gene_variant Transcript ENST00000192788 protein_coding NA rs539589206 38 1 SNV HGNC HGNC:21216 YES NM_017754.4 1 P1 CCDS43455.1 ENSP00000192788 Q6BDS2.140 UPI00001B654C 0.0026 0 0.0043 0 0.005 0.0051 0.008268 0.001943 0.002198 0.004495 0.007238 0 0.01771 0.01274 0.0127 0.006816 0.003724 0.01771 gnomADg_FIN 19 NA NA PASS SITE 29,20|33,19 NA NA 1 15 20,20 136,153 60,60 32 1.30 NA 5.72 NA FALSE 2.04 93 NA NA NA FALSE NA NA 129.11 19 34792045 HCC1395_HCC1395T 18 0.754 70 5,18 5,14 11,36 NA 0/1 NA NA NA NA 10,8,33,19 G/A PANCANCER NA FALSE BLTP3A chr6:34792045:34792046:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 35833696 35833697 G A 18 89 0.202247191011236 MODIFIER SRPK1 ENSG00000096063 A non_coding_transcript_exon_variant Transcript ENST00000346162 retained_intron 15/15 ENST00000346162.10:n.4100C>T NA 4100 rs1353108009 -1 SNV HGNC HGNC:11305 2 6.571e-06 0 0 0 0 0 0 0 1.47e-05 0 0 1.47e-05 gnomADg_NFE 19 NA NA PASS SITE 24,71|4,14 NA NA 1 41 38,39 202,241 60,60 21 1.34 NA 6.32 NA FALSE 4.61 46 NA NA NA FALSE NA NA 53.44 19 35833696 HCC1395_HCC1395T 71 0.225 89 25,5 34,12 61,17 NA 0/1 NA NA NA NA 19,52,4,14 G/A PANCANCER NA FALSE SRPK1 chr6:35833696:35833697:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 36326423 36326424 T C 76 115 0.660869565217391 MODIFIER BNIP5 ENSG00000189325 C intron_variant Transcript ENST00000437635 protein_coding 5/11 ENST00000437635.3:c.1036+87A>G NA rs763020 -1 SNV HGNC HGNC:33769 YES NM_001010903.5 1 P1 CCDS34439.1 ENSP00000418983 P0C671.93 UPI000022CB9B 0.0331 0.0053 0.0591 0.004 0.0954 0.0184 0.07735 0.02432 0.1042 0.05346 0.04207 0.003854 0.09715 0.05696 0.1226 0.05837 0.03644 0.1226 gnomADg_NFE 19 NA NA PASS SITE 31,33|43,33 NA NA 1 13 20,20 162,159 60,60 29 1.28 NA 5.12 NA FALSE 1.05 93 NA NA NA FALSE NA NA 193.17 19 36326423 HCC1395_HCC1395T 39 0.669 115 8,19 15,25 24,49 NA 0/1 NA NA NA NA 20,19,43,33 T/C PANCANCER NA FALSE BNIP5 chr6:36326423:36326424:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 36327087 36327088 A G 256 328 0.780487804878049 LOW BNIP5 ENSG00000189325 G synonymous_variant Transcript ENST00000437635 protein_coding 4/12 ENST00000437635.3:c.735T>C ENSP00000418983.1:p.A245= ENSP00000418983.1 p.A245= 916 735 245 A gcT/gcC rs41270098&COSV71325541 -1 SNV HGNC HGNC:33769 YES NM_001010903.5 1 P1 CCDS34439.1 ENSP00000418983 P0C671.93 UPI000022CB9B PANTHER:PTHR22435&Pfam:PF15661&AlphaFold_DB_import:AF-P0C671-F1 0.0331 0.0053 0.0591 0.004 0.0954 0.0184 0.07991 0.02215 0.04194 0.04755 0.003045 0.09869 0.1222 0.08717 0.03827 0.07748 0.02442 0.1042 0.05345 0.04263 0.003843 0.0971 0.05696 0.1228 0.0588 0.03641 0.1228 gnomADg_NFE 0&1 0&1 19 NA NA PASS SITE 93,82|144,112 NA NA 1 93 20,20 162,159 60,60 33 1.81 NA 18.96 NA FALSE 1.05 93 NA NA NA FALSE NA NA 731.74 19 36327087 HCC1395_HCC1395T 72 0.775 328 15,68 31,95 49,171 NA 0/1 NA NA NA NA 37,35,144,112 A/G PANCANCER NA FALSE BNIP5_p.A245= chr6:36327087:36327088:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 36328846 36328847 G A 66 91 0.725274725274725 MODIFIER BNIP5 ENSG00000189325 A intron_variant Transcript ENST00000437635 protein_coding 2/11 ENST00000437635.3:c.611-132C>T NA rs12192390 -1 SNV HGNC HGNC:33769 YES NM_001010903.5 1 P1 CCDS34439.1 ENSP00000418983 P0C671.93 UPI000022CB9B 0.0328 0.0053 0.0576 0.004 0.0944 0.0184 0.07731 0.02443 0.1044 0.05326 0.04207 0.003846 0.09728 0.05696 0.1224 0.05832 0.03635 0.1224 gnomADg_NFE 19 NA NA PASS SITE 18,37|23,43 NA NA 1 12 20,20 172,161 60,60 21 1.35 NA 6.32 NA FALSE 1.05 93 NA NA NA FALSE NA NA 180.78 19 36328846 HCC1395_HCC1395T 25 0.718 91 6,18 9,22 17,45 NA 0/1 NA NA NA NA 9,16,23,43 G/A PANCANCER NA FALSE BNIP5 chr6:36328846:36328847:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 36330487 36330488 A G 241 355 0.67887323943662 LOW BNIP5 ENSG00000189325 G synonymous_variant Transcript ENST00000437635 protein_coding 2/12 ENST00000437635.3:c.204T>C ENSP00000418983.1:p.A68= ENSP00000418983.1 p.A68= 385 204 68 A gcT/gcC rs149607586&COSV71325491 -1 SNV HGNC HGNC:33769 YES NM_001010903.5 1 P1 CCDS34439.1 ENSP00000418983 P0C671.93 UPI000022CB9B Low_complexity_(Seg):seg&PANTHER:PTHR22435&Pfam:PF15661&MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-P0C671-F1 0.0052 0.0015 0.0058 0.002 0.0089 0.0092 0.01029 0.002472 0.004308 0.00159 0.0004896 0.004627 0.01701 0.007178 0.00957 0.009346 0.002583 0 0.006154 0.002594 0.001351 0.003673 0 0.01632 0.005263 0.009313 0.01701 gnomADe_NFE 0&1 0&1 19 NA NA PASS SITE 151,136|132,109 NA NA 1 93 20,20 164,170 60,60 32 2.08 NA 35.67 NA FALSE 2.06 93 NA NA NA FALSE NA NA 685.93 19 36330487 HCC1395_HCC1395T 114 0.670 355 34,60 40,95 83,169 NA 0/1 NA NA NA NA 63,51,132,109 A/G PANCANCER NA FALSE BNIP5_p.A68= chr6:36330487:36330488:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 36400499 36400500 C T 188 272 0.691176470588235 LOW PXT1 ENSG00000179165 T synonymous_variant Transcript ENST00000454782 protein_coding 4/5 ENST00000454782.3:c.255G>A ENSP00000419944.1:p.Q85= ENSP00000419944.1 p.Q85= 704 255 85 Q caG/caA rs62403732&COSV71962595 -1 SNV HGNC HGNC:18312 YES NM_152990.4 1 P1 CCDS4820.2 ENSP00000419944 Q8NFP0.119 UPI0000EE4DF4 PDB-ENSP_mappings:7wjh.B&PANTHER:PTHR40381&Pfam:PF15214&AlphaFold_DB_import:AF-Q8NFP0-F1 0.0102 0.0023 0.0202 0.0079 0.0229 0.0031 0.0205 0.004245 0.01928 0.009425 0.003642 0.04042 0.02739 0.01874 0.004965 0.01873 0.004198 0.006579 0.01855 0.008934 0.006541 0.0384 0.006329 0.02727 0.01291 0.006416 0.04042 gnomADe_FIN 0&1 0&1 19 NA NA PASS SITE 96,98|97,91 NA NA 1 93 20,20 151,160 60,60 37 1.84 NA 20.17 NA FALSE 1.66 93 NA NA NA FALSE NA NA 500.21 19 36400499 HCC1395_HCC1395T 84 0.691 272 20,44 29,70 53,120 NA 0/1 NA NA NA NA 44,40,97,91 C/T PANCANCER NA FALSE PXT1_p.Q85= chr6:36400499:36400500:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 36443009 36443010 T C 70 88 0.795454545454545 MODIFIER KCTD20 ENSG00000112078 C upstream_gene_variant Transcript ENST00000265344 nonsense_mediated_decay NA rs561734799 27 1 SNV HGNC HGNC:21052 2 ENSP00000265344 H7BXH0.48 UPI0001B79380 0.0138 0.0189 0.0173 0.003 0.0258 0.0031 0.0257 0.0242 0.006623 0.02584 0.009265 0.006141 0.03743 0.006536 0.0291 0.01934 0.00541 0.03743 gnomADg_FIN 19 NA NA PASS SITE 35,33|32,38 NA NA 1 49 20,24 166,153 60,60 30 1.52 NA 9.63 NA FALSE 1.57 93 NA NA NA FALSE NA NA 205.40 19 36443009 HCC1395_HCC1395T 18 0.768 88 6,23 8,28 15,52 NA 0/1 NA NA NA NA 10,8,32,38 T/C PANCANCER NA FALSE KCTD20 chr6:36443009:36443010:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 36470072 36470073 G T 140 201 0.696517412935323 MODIFIER KCTD20 ENSG00000112078 T 5_prime_UTR_variant&NMD_transcript_variant Transcript ENST00000265344 nonsense_mediated_decay 2/7 ENST00000265344.8:c.-26G>T NA 97 rs41272162&COSV54804311 1 SNV HGNC HGNC:21052 2 ENSP00000265344 H7BXH0.48 UPI0001B79380 0.0100 0.0023 0.0202 0.0069 0.0229 0.0031 0.02078 0.004489 0.01965 0.00947 0.003597 0.04014 0.02739 0.01888 0.004705 0.01882 0.0042 0.006579 0.01977 0.009217 0.006346 0.03869 0.006329 0.02719 0.01291 0.005597 0.04014 gnomADe_FIN 0&1 0&1 19 NA NA PASS SITE 73,57|80,60 NA NA 1 93 20,20 159,158 60,60 41 1.67 NA 13.80 NA FALSE 1.66 93 NA NA NA FALSE NA NA 355.61 19 36470072 HCC1395_HCC1395T 61 0.680 201 18,31 21,55 40,86 NA 0/1 NA NA NA NA 33,28,80,60 G/T PANCANCER NA FALSE KCTD20 chr6:36470072:36470073:G:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 36490875 36490876 C T 317 447 0.70917225950783 MODIFIER STK38 ENSG00000112079 T downstream_gene_variant Transcript ENST00000229812 protein_coding NA rs62402192 3017 -1 SNV HGNC HGNC:17847 YES NM_007271.4 1 P1 CCDS4822.1 ENSP00000229812 Q15208.204 A0A024RD18.67 UPI0000047AC1 0.0138 0.0151 0.0231 0.0069 0.0229 0.0031 0.02391 0.02156 0.006579 0.0224 0.009217 0.006936 0.03856 0.006329 0.02718 0.01962 0.00559 0.03856 gnomADg_FIN 19 NA NA PASS SITE 146,128|180,137 NA NA 1 93 20,20 154,159 60,60 38 1.99 NA 28.85 NA FALSE 1.59 93 NA NA NA FALSE NA NA 859.31 19 36490875 HCC1395_HCC1395T 130 0.707 447 28,81 55,117 85,206 NA 0/1 NA NA NA NA 68,62,180,137 C/T PANCANCER NA FALSE STK38 chr6:36490875:36490876:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 36677811 36677812 A C 157 233 0.67381974248927 MODIFIER CDKN1A ENSG00000124762 C upstream_gene_variant Transcript ENST00000244741 protein_coding NA rs762624&CR095246&COSV55187169 903 1 SNV HGNC HGNC:1784 YES NM_000389.5 1 P1 CCDS4824.1 ENSP00000244741 P38936.238 A0A024RCX5.69 UPI0000048F7B 1 0.4467 0.5212 0.4121 0.5992 0.2376 0.4284 0.3746 0.4746 0.4986 0.3335 0.5925 0.2299 0.2699 0.338 0.388 0.3526 0.4606 0.2209 0.4343 0.3296 0.5979 0.2366 0.4082 0.266 0.3714 0.4115 0.5992 EAS 0&0&1 1&1&1 19 NA NA PASS SITE 96,72|75,83 NA NA 1 93 20,20 167,163 60,60 35 -2.182e-02 NA 16.35 NA FALSE 0.485 93 NA NA NA FALSE NA NA 425.27 19 36677811 HCC1395_HCC1395T 76 0.676 233 24,41 27,56 53,112 NA 0/1 NA NA NA NA 40,36,75,82 A/C PANCANCER TRUE FALSE CDKN1A chr6:36677811:36677812:A:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 36730592 36730593 G A 54 80 0.675 MODIFIER RAB44 ENSG00000255587 A intron_variant Transcript ENST00000612677 protein_coding 12/13 ENST00000612677.6:c.2899-81G>A NA rs147011832 1 SNV HGNC HGNC:21068 YES NM_001257357.2 5 P1 CCDS75442.1 ENSP00000481054 Q7Z6P3.128 UPI0002656658 0.0024 0 0.0029 0 0.007 0.0031 0.005817 0.001086 0 0.003732 0.00692 0.0001928 0.01214 0.006329 0.008557 0.005747 0.006835 0.01214 gnomADg_FIN 19 NA NA PASS SITE 33,27|29,25 NA NA 1 33 20,20 156,165 60,60 37 1.36 NA 6.58 NA FALSE 2.19 93 NA NA NA FALSE NA NA 140.08 19 36730592 HCC1395_HCC1395T 26 0.680 80 7,11 8,20 15,33 NA 0/1 NA NA NA NA 15,11,29,25 G/A PANCANCER NA FALSE RAB44 chr6:36730592:36730593:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 36871822 36871823 C G 95 132 0.71969696969697 MODIFIER C6orf89 ENSG00000198663 G upstream_gene_variant Transcript ENST00000359359 protein_coding NA rs12194408 48 1 SNV HGNC HGNC:21114 5 CCDS75444.1 ENSP00000352316 Q6UWU4.128 UPI000013F850 Q6UWU4-3 0.0098 0.0008 0.0159 0 0.0278 0.0092 0.0196 0.004708 0.01102 0.01583 0.0003855 0.01989 0.0291 0.02309 0.01344 0.01947 0.004464 0.06689 0.01938 0.01382 0 0.02018 0.03797 0.03003 0.01866 0.01346 0.06689 gnomADg_AMI 1 19 NA NA PASS SITE 40,40|37,58 NA NA 1 44 20,36 168,191 60,60 23 1.48 NA 8.73 NA FALSE 1.66 93 NA NA NA FALSE NA NA 303.34 19 36871822 HCC1395_HCC1395T 37 0.736 132 6,24 18,38 26,74 NA 0/1 NA NA NA NA 18,19,37,58 C/G PANCANCER NA FALSE C6orf89 chr6:36871822:36871823:C:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 37312940 37312941 C T 176 243 0.724279835390947 LOW TBC1D22B ENSG00000065491 T synonymous_variant Transcript ENST00000373491 protein_coding 9/13 ENST00000373491.3:c.1005C>T ENSP00000362590.3:p.D335= ENSP00000362590.3 p.D335= 1151 1005 335 D gaC/gaT rs41272218 1 SNV HGNC HGNC:21602 YES NM_017772.4 1 P1 CCDS4832.1 ENSP00000362590 Q9NU19.163 UPI00001C121F Gene3D:1.10.8.270&PDB-ENSP_mappings:6d0s.A&AlphaFold_DB_import:AF-Q9NU19-F1&Pfam:PF00566&PROSITE_profiles:PS50086&PANTHER:PTHR22957&SMART:SM00164&Superfamily:SSF47923 0.0007082 0.0002461 0.0001156 0 0 0.0004162 0.001373 0.0006521 3.266e-05 0.0008212 0.0004825 0 0 0 0 0.0001882 0.006329 0.001455 0.0009569 0 0.006329 gnomADg_MID 19 NA NA PASS SITE 61,95|77,99 NA NA 1 93 20,20 165,172 60,60 31 1.79 NA 18.06 NA FALSE 2.94 93 NA NA NA FALSE NA NA 527.86 19 37312940 HCC1395_HCC1395T 67 0.740 243 13,51 24,62 44,127 NA 0/1 NA NA NA NA 25,42,77,99 C/T PANCANCER NA FALSE TBC1D22B_p.D335= chr6:37312940:37312941:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 37333053 37333054 G A 96 121 0.793388429752066 MODIFIER TBC1D22B ENSG00000065491 A downstream_gene_variant Transcript ENST00000373491 protein_coding NA rs72852438 83 1 SNV HGNC HGNC:21602 YES NM_017772.4 1 P1 CCDS4832.1 ENSP00000362590 Q9NU19.163 UPI00001C121F 0.0256 0 0.0331 0.003 0.0666 0.0358 0.04715 0.01204 0.0636 0.051 0.1058 0.009811 0.04865 0.09494 0.06725 0.06609 0.03362 0.1058 gnomADg_ASJ 19 NA NA PASS SITE 9,59|14,82 NA NA 1 64 38,36 186,192 60,60 23 1.59 NA 11.44 NA FALSE 1.32 93 NA NA NA FALSE NA NA 319.71 19 37333053 HCC1395_HCC1395T 25 0.783 121 12,29 6,44 22,82 NA 0/1 NA NA NA NA 3,22,14,82 G/A PANCANCER NA FALSE TBC1D22B chr6:37333053:37333054:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 37631369 37631370 C T 63 83 0.759036144578313 MODIFIER MDGA1 ENSG00000112139 T downstream_gene_variant Transcript ENST00000373401 retained_intron NA rs59914728 2368 -1 SNV HGNC HGNC:19267 2 0.1272 0.2844 0.062 0.002 0.0855 0.1329 0.1158 0.2403 0.05482 0.09008 0.1074 0.009619 0.04359 0.2089 0.0654 0.1263 0.1221 0.2844 AFR 19 NA NA PASS SITE 25,25|26,37 NA NA 1 7 20,20 145,171 60,60 34 1.33 NA 6.02 NA FALSE 0.996 93 NA NA NA FALSE NA NA 177.44 19 37631369 HCC1395_HCC1395T 20 0.773 83 3,15 10,27 13,47 NA 0/1 NA NA NA NA 9,11,26,37 C/T PANCANCER NA FALSE MDGA1 chr6:37631369:37631370:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 37631592 37631593 G C 69 91 0.758241758241758 MODIFIER MDGA1 ENSG00000112139 C downstream_gene_variant Transcript ENST00000373401 retained_intron NA rs7776188 2145 -1 SNV HGNC HGNC:19267 2 0.0497 0.1324 0.0274 0.002 0.0239 0.0297 0.04794 0.1136 0.001096 0.03137 0.03691 0.007897 0.02801 0.0538 0.01999 0.04732 0.03422 0.1324 AFR 19 NA NA PASS SITE 28,28|34,35 NA NA 1 19 20,20 168,176 60,60 37 1.38 NA 6.92 NA FALSE 1.36 93 NA NA NA FALSE NA NA 218.64 19 37631592 HCC1395_HCC1395T 22 0.773 91 5,22 8,24 14,50 NA 0/1 NA NA NA NA 12,10,34,35 G/C PANCANCER NA FALSE MDGA1 chr6:37631592:37631593:G:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 37632186 37632187 T C 87 124 0.701612903225806 MODIFIER MDGA1 ENSG00000112139 C downstream_gene_variant Transcript ENST00000373401 retained_intron NA rs6926735 1551 -1 SNV HGNC HGNC:19267 2 0.2572 0.2216 0.1888 0.4415 0.1193 0.3057 0.1592 0.1995 0.2489 0.1523 0.07493 0.4201 0.1852 0.07911 0.1093 0.1354 0.261 0.4415 EAS 19 NA NA PASS SITE 37,47|41,46 NA NA 1 52 20,34 163,181 60,60 29 1.55 NA 10.23 NA FALSE 0.796 93 NA NA NA FALSE NA NA 275.71 19 37632186 HCC1395_HCC1395T 37 0.726 124 9,30 14,30 25,68 NA 0/1 NA NA NA NA 15,22,41,46 T/C PANCANCER NA FALSE MDGA1 chr6:37632186:37632187:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 37635040 37635041 C T 59 76 0.776315789473684 MODIFIER MDGA1 ENSG00000112139 T non_coding_transcript_exon_variant Transcript ENST00000373401 retained_intron 3/3 ENST00000373401.2:n.3817G>A NA 3817 rs45555536 -1 SNV HGNC HGNC:19267 2 0.0413 0.0847 0.0331 0.0238 0.0249 0.0235 0.04008 0.07511 0.001099 0.03363 0.0818 0.03137 0.02836 0.06329 0.0214 0.04589 0.03147 0.0847 AFR 19 NA NA PASS SITE 28,25|27,32 NA NA 1 35 34,20 181,180 60,60 28 1.47 NA 8.43 NA FALSE 1.42 77 NA NA NA FALSE NA NA 157.92 19 37635040 HCC1395_HCC1395T 17 0.724 76 6,10 9,26 15,41 NA 0/1 NA NA NA NA 8,9,27,32 C/T PANCANCER NA FALSE MDGA1 chr6:37635040:37635041:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 37654299 37654300 C T 140 442 0.316742081447964 LOW MDGA1 ENSG00000112139 T synonymous_variant Transcript ENST00000434837 protein_coding 6/17 ENST00000434837.8:c.957G>A ENSP00000402584.2:p.K319= ENSP00000402584.2 p.K319= 2029 957 319 K aaG/aaA -1 SNV HGNC HGNC:19267 YES NM_153487.4 1 P1 CCDS47417.1 ENSP00000402584 Q8NFP4.162 UPI0000071D28 Q8NFP4-1 PDB-ENSP_mappings:5xeq.B&PROSITE_profiles:PS50835&Gene3D:2.60.40.10&SMART:SM00409&Superfamily:SSF48726&Superfamily:SSF49265&AlphaFold_DB_import:AF-Q8NFP4-F1 19 NA NA PASS SITE 278,177|86,54 NA NA 1 93 20,20 158,158 60,60 31 2.01 NA 30.39 NA FALSE 6.00 93 NA NA NA FALSE NA NA 320.91 19 37654299 HCC1395_HCC1395T 302 0.304 442 104,39 97,47 206,90 NA 0/1 NA NA NA NA 186,116,86,54 C/T PANCANCER NA FALSE MDGA1_p.K319= chr6:37654299:37654300:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 37697712 37697713 G A 19 28 0.678571428571429 MODIFIER MDGA1 ENSG00000112139 A 5_prime_UTR_variant Transcript ENST00000434837 protein_coding 1/17 ENST00000434837.8:c.-901C>T NA 172 rs146513610 -1 SNV HGNC HGNC:19267 YES NM_153487.4 1 P1 CCDS47417.1 ENSP00000402584 Q8NFP4.162 UPI0000071D28 Q8NFP4-1 0.0122 0.0038 0.0173 0.001 0.0388 0.0041 0.0403 0.01156 0.06703 0.02216 0.02057 0.0001965 0.04707 0.006536 0.06762 0.02754 0.005189 0.06762 gnomADg_NFE 1 19 NA NA PASS SITE 16,19|10,9 NA NA 1 12 20,38 170,195 60,60 21 1.30 NA 5.72 NA FALSE 1.35 67 NA NA NA FALSE NA NA 62.05 19 37697712 HCC1395_HCC1395T 9 0.680 28 1,8 3,4 7,16 NA 0/1 NA NA NA NA 4,5,10,9 G/A PANCANCER NA FALSE MDGA1 chr6:37697712:37697713:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 38169008 38169009 T C 66 88 0.75 MODIFIER BTBD9 ENSG00000183826 C 3_prime_UTR_variant Transcript ENST00000314100 protein_coding 10/10 ENST00000314100.10:c.*5977A>G NA 7929 rs877527 -1 SNV HGNC HGNC:21228 1 CCDS43458.1 ENSP00000323408 Q96Q07.165 UPI000036739A Q96Q07-3 0.6272 0.8169 0.6052 0.4812 0.6183 0.546 0.6665 0.8068 0.6349 0.5959 0.6382 0.4744 0.5765 0.5949 0.6365 0.6531 0.5473 0.8169 AFR 19 NA NA PASS SITE 31,32|37,29 NA NA 1 22 20,20 169,164 60,60 32 1.48 NA 8.73 NA FALSE 0.181 87 NA NA NA FALSE NA NA 193.27 19 38169008 HCC1395_HCC1395T 22 0.750 88 7,12 8,32 15,47 NA 0/1 NA NA NA NA 10,12,37,29 T/C PANCANCER NA FALSE BTBD9 chr6:38169008:38169009:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 38676545 38676546 A C 10 483 0.020703933747412 MODIFIER GLO1 ENSG00000124767 C 3_prime_UTR_variant Transcript ENST00000373365 protein_coding 6/6 ENST00000373365.5:c.*750T>G NA 1396 -1 SNV HGNC HGNC:4323 YES NM_006708.3 1 P1 CCDS4837.1 ENSP00000362463 Q04760.218 X5DNM4.70 UPI0000169DF9 Q04760-1 19 NA NA PASS SITE 373,249|6,4 NA NA 1 93 20,20 163,168 60,60 28 1.98 NA 28.25 NA FALSE 6.00 32 NA NA NA FALSE NA NA 13.88 19 38676545 HCC1395_HCC1395T 473 0.021 483 117,1 189,5 321,6 NA 0/1 NA NA NA NA 286,187,6,4 A/C PANCANCER NA FALSE GLO1 chr6:38676545:38676546:A:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 39057383 39057384 C T 27 40 0.675 MODIFIER GLP1R ENSG00000112164 T intron_variant Transcript ENST00000373256 protein_coding 2/12 ENST00000373256.5:c.176-89C>T NA rs116391897 1 SNV HGNC HGNC:4324 YES NM_002062.5 1 P1 CCDS4839.1 ENSP00000362353 P43220.204 UPI0000061F20 0.0058 0 0.0072 0.005 0.0139 0.0051 0.00574 0.00186 0 0.00347 0.002017 0.005204 0.008577 0 0.008689 0.003346 0.004151 0.0139 EUR 19 NA NA PASS SITE 38,8|22,5 NA NA 1 43 37,37 185,192 60,60 28 1.44 NA 7.83 NA FALSE 2.21 93 NA NA NA FALSE NA NA 92.31 19 39057383 HCC1395_HCC1395T 13 0.650 40 8,13 5,11 13,25 NA 0/1 NA NA NA NA 13,0,22,5 C/T PANCANCER NA FALSE GLP1R chr6:39057383:39057384:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 39079281 39079282 G A 13 47 0.276595744680851 MODIFIER GLP1R ENSG00000112164 A intron_variant Transcript ENST00000373256 protein_coding 10/12 ENST00000373256.5:c.1043+81G>A NA 1 SNV HGNC HGNC:4324 YES NM_002062.5 1 P1 CCDS4839.1 ENSP00000362353 P43220.204 UPI0000061F20 19 NA NA PASS SITE 15,43|3,10 NA NA 1 56 36,38 162,173 60,60 29 1.30 NA 5.67 NA FALSE 6.00 24 NA NA NA FALSE NA NA 35.17 19 39079281 HCC1395_HCC1395T 34 0.289 47 5,2 7,1 26,10 NA 0/1 NA NA NA NA 10,24,3,10 G/A PANCANCER NA FALSE GLP1R chr6:39079281:39079282:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 39104905 39104906 A G 207 268 0.772388059701492 MODIFIER SAYSD1 ENSG00000112167 G 3_prime_UTR_variant Transcript ENST00000229903 protein_coding 2/2 ENST00000229903.5:c.*527T>C NA 1176 rs7696 -1 SNV HGNC HGNC:21025 YES NM_018322.3 1 P1 CCDS4840.1 ENSP00000229903 Q9NPB0.149 UPI0000039E7F Q9NPB0-1 0.3293 0.3525 0.3084 0.2897 0.3668 0.3149 0.3787 0.3453 0.3934 0.3338 0.4853 0.2849 0.3827 0.4809 0.4141 0.384 0.3113 0.4853 gnomADg_ASJ 19 NA NA PASS SITE 54,80|80,127 NA NA 1 84 20,20 174,178 60,60 30 1.71 NA 14.75 NA FALSE 0.413 93 NA NA NA FALSE NA NA 621.32 19 39104905 HCC1395_HCC1395T 61 0.772 268 11,44 25,83 44,152 NA 0/1 NA NA NA NA 20,41,80,127 A/G PANCANCER NA FALSE SAYSD1 chr6:39104905:39104906:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 41280496 41280497 G A 201 245 0.820408163265306 MODIFIER TREM1 ENSG00000124731 A intron_variant Transcript ENST00000244709 protein_coding 3/3 ENST00000244709.9:c.599+465C>T NA rs111673840 -1 SNV HGNC HGNC:17760 YES NM_018643.5 1 P2 CCDS4854.1 ENSP00000244709 Q9NP99.177 Q38L15.130 UPI0000047FA9 Q9NP99-1 0.0030 0.0015 0.0086 0 0.005 0.002 0.00588 0.001954 0 0.008511 0.001728 0 0.006688 0 0.008688 0.005263 0.001034 0.008688 gnomADg_NFE 19 NA NA PASS SITE 38,76|66,135 NA NA 1 93 20,20 164,174 60,60 27 1.71 NA 15.05 NA FALSE 2.18 93 NA NA NA FALSE NA NA 609.99 19 41280496 HCC1395_HCC1395T 44 0.800 245 15,42 16,88 35,143 NA 0/1 NA NA NA NA 12,32,66,135 G/A PANCANCER NA FALSE TREM1 chr6:41280496:41280497:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 41597079 41597080 C T 92 119 0.773109243697479 MODIFIER FOXP4 ENSG00000137166 T intron_variant Transcript ENST00000307972 protein_coding 14/16 ENST00000307972.10:c.1659-97C>T NA rs41273790 1 SNV HGNC HGNC:20842 YES NM_001012426.2 1 P4 CCDS34447.1 ENSP00000309823 Q8IVH2.172 UPI000007462D Q8IVH2-1 1 0.0002 0 0 0 0.001 0 0.005081 0.0014 0.01206 0.006153 0.01154 0.000193 0.0003764 0.009554 0.00813 0.004302 0 0.01206 gnomADg_AMI 19 NA NA PASS SITE 51,29|58,34 NA NA 1 73 20,20 165,154 60,60 26 1.59 NA 11.44 NA FALSE 2.31 93 NA NA NA FALSE NA NA 250.13 19 41597079 HCC1395_HCC1395T 27 0.747 119 9,23 11,36 20,61 NA 0/1 NA NA NA NA 19,8,58,34 C/T PANCANCER NA FALSE FOXP4 chr6:41597079:41597080:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 41601242 41601249 A AAAGGGG 99 134 0.738805970149254 MODIFIER FOXP4 ENSG00000137166 AAGGGG 3_prime_UTR_variant Transcript ENST00000307972 protein_coding 17/17 ENST00000307972.10:c.*2307_*2308insAGGGGA NA 4852-4853 rs145822036 1 insertion HGNC HGNC:20842 YES NM_001012426.2 1 P4 CCDS34447.1 ENSP00000309823 Q8IVH2.172 UPI000007462D Q8IVH2-1 1 1 0.0507 0.0522 0.0375 0.002 0.0994 0.0583 0.08218 0.05414 0.1104 0.0524 0.09741 0.002506 0.1557 0.1076 0.1005 0.07927 0.06698 0.1557 gnomADg_FIN 19 NA NA PASS SITE 43,53|40,59 NA NA 1 37 20,20 169,161 60,60 38 1.60 NA 11.74 NA FALSE 1.05 93 NA NA NA FALSE NA NA 418.45 19 41601242 HCC1395_HCC1395T 35 0.727 134 10,12 9,32 24,66 NA 0/1 NA NA NA NA 18,17,40,59 A/AAAGGGG PANCANCER NA FALSE FOXP4 chr6:41601242:41601249:A:AAAGGGG indel 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 41790098 41790099 C A 155 221 0.701357466063348 MODIFIER PRICKLE4 ENSG00000278224 A downstream_gene_variant Transcript ENST00000359201 protein_coding NA rs8393 2726 1 SNV HGNC HGNC:16805 1 A2 ENSP00000352128 Q2TBC4.142 UPI00006E2246 Q2TBC4-1 0.6056 0.646 0.6988 0.5407 0.5099 0.6503 0.5627 0.6415 0.4868 0.6418 0.5205 0.5326 0.5045 0.5255 0.5068 0.5499 0.6384 0.6988 AMR 19 NA NA PASS SITE 63,73|84,71 NA NA 1 93 36,25 170,174 60,60 30 1.77 NA 16.85 NA FALSE 0.262 93 NA NA NA FALSE NA NA 457.31 19 41790098 HCC1395_HCC1395T 66 0.698 221 14,28 21,57 53,123 NA 0/1 NA NA NA NA 35,31,84,71 C/A PANCANCER NA FALSE PRICKLE4 chr6:41790098:41790099:C:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 41792526 41792528 G GC 121 163 0.742331288343558 MODIFIER USP49 ENSG00000164663 C downstream_gene_variant Transcript ENST00000373010 protein_coding NA rs3833453 3971 -1 insertion HGNC HGNC:20078 5 ENSP00000362101 Q5T3E1.118 UPI000046FFF3 0.7700 0.6641 0.8314 0.8423 0.7654 0.7996 0.7526 0.6975 0.783 0.8041 0.7831 0.824 0.7422 0.6994 0.7658 0.7337 0.8054 0.8423 EAS 19 NA NA PASS SITE 58,34|85,36 NA NA 1 34 27,37 166,181 60,60 30 1.62 NA 11.67 NA FALSE 0.124 93 6,7 C NA TRUE NA 93 239.30 19 41792526 HCC1395_HCC1395T 42 0.754 163 8,28 17,58 31,94 NA 0/1 NA NA NA NA 26,16,85,36 G/GC PANCANCER NA FALSE USP49 chr6:41792526:41792528:G:GC indel 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 42077109 42077110 G C 127 168 0.755952380952381 MODERATE TAF8 ENSG00000137413 C missense_variant Transcript ENST00000372977 protein_coding 8/9 ENST00000372977.8:c.790G>C ENSP00000362068.3:p.G264R ENSP00000362068.3 p.G264R 808 790 264 G/R Gga/Cga rs189994370 1 SNV HGNC HGNC:17300 YES NM_138572.3 1 P4 CCDS43462.1 ENSP00000362068 Q7Z7C8.151 UPI00001A36D2 Q7Z7C8-1 1 tolerated(0.11) possibly_damaging(0.631) PDB-ENSP_mappings:5fur.L&PDB-ENSP_mappings:6mzc.K&PDB-ENSP_mappings:6mzl.K&PDB-ENSP_mappings:6mzm.K&PDB-ENSP_mappings:7edx.H&PDB-ENSP_mappings:7eg7.H&PDB-ENSP_mappings:7eg8.H&PDB-ENSP_mappings:7eg9.H&PDB-ENSP_mappings:7ega.H&PDB-ENSP_mappings:7egb.H&PDB-ENSP_mappings:7egc.H&PDB-ENSP_mappings:7egd.H&PDB-ENSP_mappings:7ege.H&PDB-ENSP_mappings:7egg.H&PDB-ENSP_mappings:7egh.H&PDB-ENSP_mappings:7egi.H&PDB-ENSP_mappings:7egj.H&PDB-ENSP_mappings:7ena.DH&PDB-ENSP_mappings:7enc.DH&PDB-ENSP_mappings:8gxq.DH&PDB-ENSP_mappings:8gxs.DH&AlphaFold_DB_import:AF-Q7Z7C8-F1&PANTHER:PTHR46469&MobiDB_lite:mobidb-lite 0.0006 0 0.0014 0 0.002 0 0.004211 0.0004526 0.001874 0.003597 0 0.007012 0.006585 0.005653 0.0003616 0.004981 0.000579 0 0.003665 0.00432 0 0.007724 0 0.008437 0.002871 0.000207 0.008437 gnomADg_NFE 19 NA NA PASS SITE 53,53|59,68 NA NA 1 86 20,20 151,156 60,60 32 1.64 NA 12.94 NA FALSE 2.07 93 NA NA NA FALSE NA NA 338.37 19 42077109 HCC1395_HCC1395T 41 0.755 168 8,28 15,47 26,82 NA 0/1 NA NA NA NA 18,23,59,68 G/C PANCANCER NA FALSE TAF8_p.G264R chr6:42077109:42077110:G:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 42083259 42083260 T C 73 99 0.737373737373737 MODIFIER TAF8 ENSG00000137413 C 3_prime_UTR_variant Transcript ENST00000372977 protein_coding 9/9 ENST00000372977.8:c.*5714T>C NA 6665 rs6904481 1 SNV HGNC HGNC:17300 YES NM_138572.3 1 P4 CCDS43462.1 ENSP00000362068 Q7Z7C8.151 UPI00001A36D2 Q7Z7C8-1 1 0.3506 0.0998 0.4741 0.4187 0.4881 0.3906 0.384 0.1467 0.4791 0.4761 0.5455 0.4116 0.5173 0.4177 0.4726 0.4047 0.4149 0.5455 gnomADg_ASJ 19 NA NA PASS SITE 27,43|27,46 NA NA 1 33 20,34 180,180 60,60 43 1.51 NA 9.33 NA FALSE 0.397 93 NA NA NA FALSE NA NA 229.03 19 42083259 HCC1395_HCC1395T 26 0.727 99 7,16 13,37 20,55 NA 0/1 NA NA NA NA 9,17,27,46 T/C PANCANCER NA FALSE TAF8 chr6:42083259:42083260:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 42107366 42107367 GGGTGGGGGTTCCAGCAGCAGGGGAGGT G 54 92 0.58695652173913 MODERATE C6orf132 ENSG00000188112 - inframe_deletion Transcript ENST00000341865 protein_coding 4/5 ENST00000341865.9:c.519_545del ENSP00000341368.4:p.L176_P184del ENSP00000341368.4 p.L176_P184del 695-721 519-545 173-182 PPPLLLEPPP/P ccACCTCCCCTGCTGCTGGAACCCCCACCc/ccc rs748748025 -1 deletion HGNC HGNC:21288 YES NM_001164446.3 5 P3 CCDS47428.1 ENSP00000341368 Q5T0Z8.115 UPI0001A5E4A3 Q5T0Z8-1 AlphaFold_DB_import:AF-Q5T0Z8-F1&Prints:PR01217&Prints:PR01217&PANTHER:PTHR35077&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg 0.07667 0.01447 0.05943 0.1393 0.0002094 0.1216 0.1165 0.1115 0.02324 0.06446 0.01441 0.1062 0.05659 0.1056 0.0008203 0.0909 0.09122 0.09813 0.07238 0.01229 0.1393 gnomADe_ASJ 19 NA NA PASS SITE 45,25|44,10 NA NA 1 32 20,39 165,184 60,60 31 1.41 NA 6.85 NA FALSE 1.11 93 NA NA NA FALSE NA NA 157.95 19 42107366 HCC1395_HCC1395T 38 0.666 92 2,17 10,30 24,47 NA 0/1 NA NA NA NA 23,15,44,10 GGGTGGGGGTTCCAGCAGCAGGGGAGGT/G PANCANCER NA FALSE C6orf132_p.L176_P184del chr6:42107366:42107367:GGGTGGGGGTTCCAGCAGCAGGGGAGGT:G indel 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 42592188 42592189 G A 96 152 0.631578947368421 MODERATE UBR2 ENSG00000024048 A missense_variant Transcript ENST00000372899 protein_coding 3/47 ENST00000372899.6:c.376G>A ENSP00000361990.1:p.E126K ENSP00000361990.1 p.E126K 667 376 126 E/K Gag/Aag rs62414610&COSV65770623 1 SNV HGNC HGNC:21289 1 P4 CCDS4870.1 ENSP00000361990 Q8IWV8.178 UPI0000074466 Q8IWV8-1 tolerated_low_confidence(0.08) benign(0.009) Gene3D:2.10.110.30&PDB-ENSP_mappings:3ny2.A&PDB-ENSP_mappings:3ny2.B&PDB-ENSP_mappings:3ny2.C&PDB-ENSP_mappings:3ny2.D&PDB-ENSP_mappings:3ny2.E&PDB-ENSP_mappings:3ny2.F&PDB-ENSP_mappings:3ny2.G&PDB-ENSP_mappings:3ny2.H&PDB-ENSP_mappings:3ny3.A&PDB-ENSP_mappings:5tda.A&PDB-ENSP_mappings:5tdb.A&PDB-ENSP_mappings:5tdd.A&PDB-ENSP_mappings:5um3.A&AlphaFold_DB_import:AF-Q8IWV8-F1&Pfam:PF02207&PROSITE_profiles:PS51157&PANTHER:PTHR21497&SMART:SM00396&CDD:cd19679 0.0194 0.0008 0.0144 0 0.0457 0.0409 0.0273 0.005426 0.01395 0.04089 0.0002926 0.02925 0.0352 0.02521 0.0344 0.02406 0.006312 0.002193 0.01694 0.04469 0.0003857 0.03183 0.04114 0.03528 0.02245 0.03797 0.0457 EUR 0&1 0&1 19 NA NA PASS SITE 62,65|48,48 NA NA 1 93 20,20 156,159 60,60 45 1.67 NA 13.85 NA FALSE 1.57 93 NA NA NA FALSE NA NA 255.33 19 42592188 HCC1395_HCC1395T 56 0.635 152 21,21 14,43 38,66 NA 0/1 NA NA NA NA 26,30,48,48 G/A PANCANCER NA FALSE UBR2_p.E126K chr6:42592188:42592189:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 42964993 42964994 C T 124 189 0.656084656084656 MODIFIER PEX6 ENSG00000124587 T intron_variant Transcript ENST00000244546 protein_coding 13/14 ENST00000244546.4:c.*203-64G>A NA rs41274888 -1 SNV HGNC HGNC:8859 1 ENSP00000244546 Q13608.193 UPI0000072806 Q13608-2 1 0.0160 0.0015 0.0159 0 0.0199 0.0481 0.01867 0.004656 0.01868 0.0182 0.03514 0.0005769 0.01959 0.01266 0.02572 0.0201 0.04655 0.0481 SAS likely_benign 1 19 NA NA PASS SITE 60,86|58,66 NA NA 2 93 20,33 164,180 60,60 28 1.74 NA 16.25 NA FALSE 1.72 93 NA NA NA FALSE NA NA 370.94 19 42964993 HCC1395_HCC1395T 65 0.660 189 18,32 20,50 49,96 NA 0/1 NA NA NA NA 26,39,58,66 C/T PANCANCER NA FALSE PEX6 chr6:42964993:42964994:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 43056549 43056550 T C 86 120 0.716666666666667 MODIFIER MRPL2 ENSG00000112651 C intron_variant Transcript ENST00000230413 protein_coding 2/5 ENST00000230413.9:c.266-104A>G NA rs143111037 -1 SNV HGNC HGNC:14056 2 CCDS75458.1 ENSP00000230413 C9IY40.90 UPI000015928D 0.0022 0 0 0 0.0089 0.002 0.004998 0.00116 0.002193 0.002554 0.0002884 0.0001923 0.01408 0 0.007409 0.003839 0.001659 0.01408 gnomADg_FIN 19 NA NA PASS SITE 12,56|19,67 NA NA 1 40 35,32 176,165 60,60 20 1.44 NA 7.83 NA FALSE 2.17 93 NA NA NA FALSE NA NA 243.53 19 43056549 HCC1395_HCC1395T 34 0.691 120 13,24 12,33 30,68 NA 0/1 NA NA NA NA 4,30,19,67 T/C PANCANCER NA FALSE MRPL2 chr6:43056549:43056550:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 43142265 43142266 C T 137 176 0.778409090909091 LOW PTK7 ENSG00000112655 T synonymous_variant&NMD_transcript_variant Transcript ENST00000230418 nonsense_mediated_decay 13/19 ENST00000230418.8:c.2013C>T ENSP00000230418.4:p.N671= ENSP00000230418.4 p.N671= 2160 2013 671 N aaC/aaT rs45453593&COSV57852143 1 SNV HGNC HGNC:9618 1 ENSP00000230418 Q13308.209 UPI000006FC42 Q13308-5 AlphaFold_DB_import:AF-Q13308-F1 0.0084 0 0.0029 0 0.0089 0.0317 0.007837 0.00117 0.003557 0.00129 0 0.01386 0.007248 0.008798 0.02081 0.006234 0.00123 0.002193 0.003336 0.001153 0.0001926 0.0144 0.006329 0.008187 0.004298 0.02463 0.0317 SAS benign 0&1 1&1 19 NA NA PASS SITE 51,56|59,78 NA NA 1 93 37,20 167,163 60,60 23 1.73 NA 15.61 NA FALSE 2.15 93 NA NA NA FALSE NA NA 395.04 19 43142265 HCC1395_HCC1395T 39 0.757 176 12,31 17,57 32,102 NA 0/1 NA NA NA NA 18,21,59,78 C/T PANCANCER NA FALSE PTK7_p.N671= chr6:43142265:43142266:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 43187096 43187097 G T 20 95 0.210526315789474 HIGH CUL9 ENSG00000112659 T splice_donor_variant Transcript ENST00000252050 protein_coding 5/40 ENST00000252050.9:c.1387+1G>T NA 1 SNV HGNC HGNC:15982 YES NM_015089.4 5 P2 CCDS4890.1 ENSP00000252050 Q8IWT3.183 UPI000006F22F Q8IWT3-1 19 NA NA PASS SITE 48,66|6,14 NA NA 1 60 20,27 158,179 60,60 42 1.39 NA 6.88 NA FALSE 6.00 53 NA NA NA FALSE NA NA 51.05 19 43187096 HCC1395_HCC1395T 75 0.247 95 20,9 25,5 48,15 NA 0/1 NA NA NA NA 32,43,6,14 G/T PANCANCER NA FALSE CUL9 chr6:43187096:43187097:G:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 43226475 43226476 A C 145 198 0.732323232323232 MODIFIER DNPH1 ENSG00000112667 C intron_variant Transcript ENST00000230431 protein_coding 1/3 ENST00000230431.11:c.197-80T>G NA rs41274938 -1 SNV HGNC HGNC:21218 YES NM_006443.3 1 P1 CCDS4891.1 ENSP00000230431 O43598.166 UPI0000072046 O43598-1 0.0060 0 0.0014 0 0.007 0.0225 0.006435 0.001327 0.002198 0.005304 0.004037 0.0001925 0.01395 0.006329 0.008292 0.00478 0.02114 0.0225 SAS 19 NA NA PASS SITE 57,63|71,74 NA NA 1 93 20,20 164,159 60,60 35 1.69 NA 14.05 NA FALSE 2.15 93 NA NA NA FALSE NA NA 381.50 19 43226475 HCC1395_HCC1395T 53 0.721 198 12,36 19,51 35,92 NA 0/1 NA NA NA NA 28,25,71,74 A/C PANCANCER NA FALSE DNPH1 chr6:43226475:43226476:A:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 43283595 43283596 A T 57 230 0.247826086956522 MODERATE TTBK1 ENSG00000146216 T missense_variant Transcript ENST00000259750 protein_coding 14/15 ENST00000259750.9:c.2855A>T ENSP00000259750.4:p.E952V ENSP00000259750.4 p.E952V 3137 2855 952 E/V gAg/gTg 1 SNV HGNC HGNC:19140 YES NM_032538.3 1 P3 CCDS34455.1 ENSP00000259750 Q5TCY1.151 UPI000041512B Q5TCY1-1 deleterious_low_confidence(0) probably_damaging(0.952) AlphaFold_DB_import:AF-Q5TCY1-F1 19 NA NA PASS SITE 124,150|26,31 NA NA 1 93 20,20 173,179 60,60 30 1.89 NA 22.88 NA FALSE 6.00 56 NA NA NA FALSE NA NA 140.27 19 43283595 HCC1395_HCC1395T 173 0.252 230 28,9 82,29 127,42 NA 0/1 NA NA NA NA 77,96,26,31 A/T PANCANCER NA FALSE TTBK1_p.E952V chr6:43283595:43283596:A:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 43287642 43287643 G T 91 132 0.689393939393939 MODIFIER TTBK1 ENSG00000146216 T 3_prime_UTR_variant Transcript ENST00000259750 protein_coding 15/15 ENST00000259750.9:c.*2266G>T NA 6514 rs111981370 1 SNV HGNC HGNC:19140 YES NM_032538.3 1 P3 CCDS34455.1 ENSP00000259750 Q5TCY1.151 UPI000041512B Q5TCY1-1 0.0465 0.003 0.0922 0.002 0.0855 0.0787 0.08021 0.01859 0.1107 0.1019 0.05882 0.002121 0.124 0.03481 0.1134 0.06574 0.07936 0.124 gnomADg_FIN 19 NA NA PASS SITE 45,52|40,51 NA NA 1 76 20,20 168,158 60,60 33 1.61 NA 11.95 NA FALSE 1.05 93 NA NA NA FALSE NA NA 233.54 19 43287642 HCC1395_HCC1395T 41 0.674 132 10,25 15,29 27,57 NA 0/1 NA NA NA NA 20,21,40,51 G/T PANCANCER NA FALSE TTBK1 chr6:43287642:43287643:G:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 43298896 43298897 G T 89 135 0.659259259259259 MODIFIER SLC22A7 ENSG00000137204 T intron_variant Transcript ENST00000372574 protein_coding 1/8 ENST00000372574.7:c.393+145G>T NA rs70953677 1 SNV HGNC HGNC:10971 1 ENSP00000361655 Q9Y694.178 UPI0000470143 Q9Y694-3 0.0080 0 0.0029 0 0.0149 0.0235 0.01694 0.004175 0.01864 0.008708 0.02016 0.0003848 0.02668 0.006329 0.02534 0.01769 0.02835 0.02835 gnomADg_SAS 1 19 NA NA PASS SITE 45,58|36,53 NA NA 1 93 32,33 177,177 60,60 19 1.65 NA 13.15 NA FALSE 1.72 93 NA NA NA FALSE NA NA 263.38 19 43298896 HCC1395_HCC1395T 46 0.664 135 10,26 21,38 35,70 NA 0/1 NA NA NA NA 20,26,36,53 G/T PANCANCER NA FALSE SLC22A7 chr6:43298896:43298897:G:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 43340178 43340179 C G 67 158 0.424050632911392 MODERATE ZNF318 ENSG00000171467 G missense_variant Transcript ENST00000361428 protein_coding 10/10 ENST00000361428.3:c.3820G>C ENSP00000354964.2:p.G1274R ENSP00000354964.2 p.G1274R 4102 3820 1274 G/R Ggg/Cgg COSV58938631 -1 SNV HGNC HGNC:13578 YES NM_014345.3 1 P1 CCDS4895.2 ENSP00000354964 Q5VUA4.156 UPI000049E044 Q5VUA4-1 deleterious(0) probably_damaging(1) AlphaFold_DB_import:AF-Q5VUA4-F1&PANTHER:PTHR15577&MobiDB_lite:mobidb-lite 1 1 19 NA NA PASS SITE 69,77|32,35 NA NA 1 93 20,26 183,174 60,60 30 1.65 NA 12.94 NA FALSE 6.00 93 NA NA NA FALSE NA NA 180.96 19 43340178 HCC1395_HCC1395T 91 0.426 158 18,23 44,24 68,50 NA 0/1 NA NA NA NA 43,48,32,35 C/G PANCANCER NA FALSE ZNF318_p.G1274R chr6:43340178:43340179:C:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 43573453 43573454 C T 133 174 0.764367816091954 MODIFIER XPO5 ENSG00000124571 T intron_variant Transcript ENST00000265351 protein_coding 2/31 ENST00000265351.12:c.227+27G>A NA rs45574641 -1 SNV HGNC HGNC:17675 YES NM_020750.3 1 P1 CCDS47430.1 ENSP00000265351 Q9HAV4.175 UPI000006CC97 0.0003372 0.0001292 0.0001161 0 0 0 0.0006728 0.0003309 0 0.0003681 0.0001207 0.002193 6.556e-05 0 0 0 0 0.0006909 0.000478 0 0.002193 gnomADg_AMI 19 NA NA PASS SITE 49,32|86,47 NA NA 1 50 20,20 146,161 60,60 33 1.46 NA 8.13 NA FALSE 3.29 93 NA NA NA FALSE NA NA 384.72 19 43573453 HCC1395_HCC1395T 41 0.771 174 11,34 16,57 27,93 NA 0/1 NA NA NA NA 25,16,86,47 C/T PANCANCER NA FALSE XPO5 chr6:43573453:43573454:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 43587457 43587458 G A 101 341 0.296187683284457 MODERATE POLH ENSG00000170734 A missense_variant Transcript ENST00000372226 protein_coding 4/11 ENST00000372226.1:c.458G>A ENSP00000361300.1:p.G153D ENSP00000361300.1 p.G153D 606 458 153 G/D gGc/gAc rs367709714&COSV64781338 1 SNV HGNC HGNC:9181 1 CCDS78147.1 ENSP00000361300 Q9Y253.186 UPI000006CEF7 Q9Y253-2 1 tolerated(0.42) benign(0.013) PROSITE_profiles:PS50173&CDD:cd01702&PANTHER:PTHR45873&Gene3D:3.30.70.270&Pfam:PF00817&PIRSF:PIRSF036603&Superfamily:SSF56672&AlphaFold_DB_import:AF-Q9Y253-F1 2.784e-05 0 2.891e-05 0 0 4.619e-05 4.395e-05 0 0 2.629e-05 0 0 0 0 0 0 0 5.88e-05 0 0 5.88e-05 gnomADg_NFE uncertain_significance 0&1 1&1 19 NA NA PASS SITE 170,180|47,54 NA NA 1 93 20,20 160,162 60,60 39 1.86 NA 21.33 NA FALSE 6.00 93 NA NA NA FALSE NA NA 222.46 19 43587457 HCC1395_HCC1395T 240 0.283 341 69,24 86,37 163,64 NA 0/1 NA NA NA NA 119,121,47,54 G/A PANCANCER NA FALSE POLH_p.G153D chr6:43587457:43587458:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 44151761 44151762 G A 43 64 0.671875 MODIFIER TMEM63B ENSG00000137216 A intron_variant Transcript ENST00000259746 protein_coding 18/23 ENST00000259746.13:c.1674-85G>A NA rs186614587 1 SNV HGNC HGNC:17735 2 P1 CCDS34461.1 ENSP00000259746 Q5T3F8.134 UPI000020DDEE Q5T3F8-1 0.0008 0 0.0029 0.001 0 0.001 0.002694 0.001062 0 0.002683 0.004325 0.0001923 0.001317 0.009494 0.004131 0.003343 0.0008271 0.009494 gnomADg_MID 19 NA NA PASS SITE 43,8|38,5 NA NA 1 48 36,34 176,201 60,60 25 1.44 NA 7.82 NA FALSE 2.61 93 NA NA NA FALSE NA NA 129.86 19 44151761 HCC1395_HCC1395T 21 0.678 64 4,16 13,19 18,39 NA 0/1 NA NA NA NA 18,3,38,5 G/A PANCANCER NA FALSE TMEM63B chr6:44151761:44151762:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 44152773 44152774 C G 6 20 0.3 MODIFIER TMEM63B ENSG00000137216 G intron_variant Transcript ENST00000259746 protein_coding 20/23 ENST00000259746.13:c.1942+75C>G NA 1 SNV HGNC HGNC:17735 2 P1 CCDS34461.1 ENSP00000259746 Q5T3F8.134 UPI000020DDEE Q5T3F8-1 19 NA NA PASS SITE 2,21|0,6 NA NA 1 25 40,39 195,220 60,60 31 0.951 NA 2.36 NA FALSE 6.00 57 NA NA NA FALSE NA NA 19.38 19 44152773 HCC1395_HCC1395T 14 0.333 20 4,2 8,4 13,6 NA 0/1 NA NA NA NA 1,13,0,6 C/G PANCANCER NA FALSE TMEM63B chr6:44152773:44152774:C:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 44181247 44181248 TC T 97 136 0.713235294117647 LOW CAPN11 ENSG00000137225 - splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000398776 protein_coding 18/22 ENST00000398776.2:c.1870-3del NA 1 deletion HGNC HGNC:1478 YES NM_007058.4 1 P1 CCDS47436.1 ENSP00000381758 Q9UMQ6.185 UPI00000383D5 1 19 NA NA PASS SITE 50,35|52,45 NA NA 2 74 20,20 147,145 60,60 32 1.48 NA 8.73 NA FALSE 6.00 93 2,1 C NA TRUE NA 93 388.56 19 44181247 HCC1395_HCC1395T 39 0.702 136 10,28 13,22 24,58 NA 0|1 0|1 44181247_TC_T NA 44181247 22,17,52,45 TC|T PANCANCER NA FALSE CAPN11 chr6:44181247:44181248:TC:T indel 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 44181251 44181252 G T 98 138 0.710144927536232 HIGH CAPN11 ENSG00000137225 T splice_acceptor_variant Transcript ENST00000398776 protein_coding 18/22 ENST00000398776.2:c.1870-1G>T NA 1 SNV HGNC HGNC:1478 YES NM_007058.4 1 P1 CCDS47436.1 ENSP00000381758 Q9UMQ6.185 UPI00000383D5 19 NA NA PASS SITE 50,36|53,45 NA NA 2 89 20,20 147,145 60,60 32 1.49 NA 8.72 NA FALSE 6.00 93 NA NA NA FALSE NA NA 391.59 19 44181251 HCC1395_HCC1395T 40 0.706 138 10,27 12,25 24,59 NA 0|1 0|1 44181247_TC_T NA 44181247 22,18,53,45 G|T PANCANCER NA FALSE CAPN11 chr6:44181251:44181252:G:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 44230061 44230062 G A 85 388 0.219072164948454 MODIFIER SLC29A1 ENSG00000112759 A intron_variant Transcript ENST00000371708 protein_coding 4/11 ENST00000371708.1:c.454+15G>A NA 1 SNV HGNC HGNC:11003 1 P1 CCDS4908.1 ENSP00000360773 Q99808.197 UPI0000001BCC Q99808-1 19 NA NA PASS SITE 182,254|38,47 NA NA 1 93 20,20 157,146 60,60 37 1.94 NA 25.84 NA FALSE 6.00 69 NA NA NA FALSE NA NA 178.61 19 44230061 HCC1395_HCC1395T 303 0.210 388 76,13 111,34 202,53 NA 0/1 NA NA NA NA 126,177,38,47 G/A PANCANCER NA FALSE SLC29A1 chr6:44230061:44230062:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 44828922 44828923 C T 74 129 0.573643410852713 MODIFIER SUPT3H ENSG00000196284 T downstream_gene_variant Transcript ENST00000371458 protein_coding NA rs752921065 845 -1 SNV HGNC HGNC:11466 5 ENSP00000360513 Q5VWT9.115 UPI00004589A9 4.6e-05 4.826e-05 0 0 0 0 0 0 7.351e-05 0 0 7.351e-05 gnomADg_NFE 19 NA NA PASS SITE 62,57|36,38 NA NA 1 93 20,20 175,195 60,60 30 1.61 NA 11.74 NA FALSE 4.61 93 NA NA NA FALSE NA NA 201.40 19 44828922 HCC1395_HCC1395T 55 0.589 129 15,18 16,30 35,50 NA 0/1 NA NA NA NA 30,25,36,38 C/T PANCANCER NA FALSE SUPT3H chr6:44828922:44828923:C:T SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 44953376 44953377 G C 162 225 0.72 LOW SUPT3H ENSG00000196284 C synonymous_variant Transcript ENST00000371458 protein_coding 3/5 ENST00000371458.1:c.84C>G ENSP00000360513.1:p.T28= ENSP00000360513.1 p.T28= 441 84 28 T acC/acG rs374520794&COSV60937284 -1 SNV HGNC HGNC:11466 5 ENSP00000360513 Q5VWT9.115 UPI00004589A9 AlphaFold_DB_import:AF-Q5VWT9-F1&PANTHER:PTHR11380 3.181e-05 0 0 0 0 0 7.033e-05 0 0 4.601e-05 2.415e-05 0 0 0 0 0 0 8.82e-05 0 0 8.82e-05 gnomADg_NFE 0&1 0&1 19 NA NA PASS SITE 51,58|77,85 NA NA 1 72 20,20 168,162 60,60 34 1.48 NA 8.43 NA FALSE 4.61 93 NA NA NA FALSE NA NA 419.20 19 44953376 HCC1395_HCC1395T 63 0.714 225 19,27 19,65 41,103 NA 0/1 NA NA NA NA 29,34,77,85 G/C PANCANCER NA FALSE SUPT3H_p.T28= chr6:44953376:44953377:G:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 46144635 46144636 T C 253 312 0.810897435897436 MODIFIER ENPP4 ENSG00000001561 C 3_prime_UTR_variant Transcript ENST00000321037 protein_coding 4/4 ENST00000321037.5:c.*995T>C NA 2591 rs1048076 1 SNV HGNC HGNC:3359 YES NM_014936.5 1 P1 CCDS34468.1 ENSP00000318066 Q9Y6X5.147 UPI0000048E43 0.4467 0.1921 0.4467 0.4544 0.5348 0.6922 0.4429 0.2357 0.5998 0.46 0.6019 0.433 0.4955 0.6741 0.5289 0.4909 0.6707 0.6922 SAS 19 NA NA PASS SITE 91,68|149,104 NA NA 2 93 20,20 179,164 60,60 27 1.86 NA 21.37 NA FALSE 0.349 93 NA NA NA FALSE NA NA 693.51 19 46144635 HCC1395_HCC1395T 59 0.803 312 9,56 27,99 39,161 NA 0/1 NA NA NA NA 30,29,149,104 T/C PANCANCER NA FALSE ENPP4 chr6:46144635:46144636:T:C SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 46144687 46144688 T A 257 317 0.810725552050473 MODIFIER ENPP4 ENSG00000001561 A 3_prime_UTR_variant Transcript ENST00000321037 protein_coding 4/4 ENST00000321037.5:c.*1047T>A NA 2643 rs1048079 1 SNV HGNC HGNC:3359 YES NM_014936.5 1 P1 CCDS34468.1 ENSP00000318066 Q9Y6X5.147 UPI0000048E43 0.2664 0.1793 0.3285 0.1677 0.3628 0.3425 0.31 0.2013 0.3432 0.3325 0.3623 0.1498 0.3446 0.4272 0.3705 0.3522 0.3471 0.4272 gnomADg_MID 19 NA NA PASS SITE 86,89|129,128 NA NA 2 93 20,20 185,162 60,60 45 1.91 NA 24.38 NA FALSE 0.500 93 NA NA NA FALSE NA NA 720.06 19 46144687 HCC1395_HCC1395T 60 0.805 317 9,53 23,81 42,175 NA 0/1 NA NA NA NA 28,32,129,128 T/A PANCANCER NA FALSE ENPP4 chr6:46144687:46144688:T:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 46160532 46160533 A G 124 168 0.738095238095238 MODIFIER ENPP5 ENSG00000112796 G 3_prime_UTR_variant Transcript ENST00000230565 protein_coding 4/4 ENST00000230565.3:c.*794T>C NA 2427 rs14781 -1 SNV HGNC HGNC:13717 1 P1 CCDS4915.1 ENSP00000230565 Q9UJA9.155 UPI0000072511 0.4461 0.1891 0.4467 0.4494 0.5348 0.6984 0.4421 0.2321 0.5998 0.4599 0.6023 0.4286 0.4964 0.6772 0.5291 0.4923 0.6748 0.6984 SAS 19 NA NA PASS SITE 50,58|56,68 NA NA 1 71 20,20 169,170 60,60 39 1.66 NA 13.24 NA FALSE 0.350 93 NA NA NA FALSE NA NA 344.29 19 46160532 HCC1395_HCC1395T 44 0.748 168 7,29 18,50 27,82 NA 0/1 NA NA NA NA 20,24,56,68 A/G PANCANCER NA FALSE ENPP5 chr6:46160532:46160533:A:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 46221166 46221167 C G 27 97 0.278350515463918 MODIFIER RCAN2 ENSG00000172348 G 3_prime_UTR_variant Transcript ENST00000306764 protein_coding 5/5 ENST00000306764.11:c.*1975G>C NA 2812 -1 SNV HGNC HGNC:3041 1 CCDS59023.1 ENSP00000305223 Q14206.166 UPI00001AEE48 Q14206-2 19 NA NA PASS SITE 45,64|11,16 NA NA 1 93 40,40 207,215 60,60 24 1.55 NA 10.23 NA FALSE 6.00 71 NA NA NA FALSE NA NA 86.49 19 46221166 HCC1395_HCC1395T 70 0.279 97 18,6 45,14 68,26 NA 0/1 NA NA NA NA 28,42,11,16 C/G PANCANCER NA FALSE RCAN2 chr6:46221166:46221167:C:G SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 46221774 46221775 G A 142 209 0.679425837320574 MODIFIER RCAN2 ENSG00000172348 A 3_prime_UTR_variant Transcript ENST00000306764 protein_coding 5/5 ENST00000306764.11:c.*1367C>T NA 2204 rs1057102 -1 SNV HGNC HGNC:3041 1 CCDS59023.1 ENSP00000305223 Q14206.166 UPI00001AEE48 Q14206-2 0.0004 0 0 0 0.002 0 0.004168 0.0009175 0 0.000983 0 0 0.004437 0 0.007762 0.002392 0.0002074 0.007762 gnomADg_NFE 19 NA NA PASS SITE 30,73|41,101 NA NA 1 63 34,35 184,183 60,60 24 1.48 NA 8.43 NA FALSE 2.36 93 NA NA NA FALSE NA NA 441.64 19 46221774 HCC1395_HCC1395T 67 0.671 209 21,42 21,58 55,113 NA 0/1 NA NA NA NA 20,47,41,101 G/A PANCANCER NA FALSE RCAN2 chr6:46221774:46221775:G:A SNV 7:0 chr6:10724710:46596080:7:0:1 NA NA 0.96 +chr6 46662452 46662453 C G 46 112 0.410714285714286 MODERATE SLC25A27 ENSG00000153291 G missense_variant Transcript ENST00000371347 protein_coding 4/9 ENST00000371347.10:c.460C>G ENSP00000360398.3:p.Q154E ENSP00000360398.3 p.Q154E 678 460 154 Q/E Cag/Gag 1 SNV HGNC HGNC:21065 YES NM_004277.5 1 P1 CCDS43470.1 ENSP00000360398 O95847.168 UPI0000038A00 O95847-1 deleterious(0) probably_damaging(0.913) PROSITE_profiles:PS50920&PANTHER:PTHR45618&Pfam:PF00153&Gene3D:1.50.40.10&Superfamily:SSF103506&AlphaFold_DB_import:AF-O95847-F1 19 NA NA PASS SITE 58,54|25,21 NA NA 1 93 20,20 163,164 60,60 33 1.52 NA 9.63 NA FALSE 6.00 93 NA NA NA FALSE NA NA 121.25 19 46662452 HCC1395_HCC1395T 66 0.432 112 11,12 28,16 41,31 NA 0/1 NA NA NA NA 35,31,25,21 C/G PANCANCER NA FALSE SLC25A27_p.Q154E chr6:46662452:46662453:C:G SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 47000272 47000273 C T 41 120 0.341666666666667 MODERATE ADGRF1 ENSG00000153292 T missense_variant Transcript ENST00000283297 protein_coding 9/9 ENST00000283297.5:c.2092G>A ENSP00000283297.5:p.G698R ENSP00000283297.5 p.G698R 2092 2092 698 G/R Gga/Aga rs1460768834 -1 SNV HGNC HGNC:18990 1 ENSP00000283297 A0A0C4DH10.47 UPI000007411B tolerated(0.07) benign(0.007) AlphaFold_DB_import:AF-A0A0C4DH10-F1&PANTHER:PTHR45813 19 NA NA PASS SITE 62,88|13,28 NA NA 1 93 20,34 169,195 60,60 31 1.71 NA 14.70 NA FALSE 6.00 65 NA NA NA FALSE NA NA 112.37 19 47000272 HCC1395_HCC1395T 79 0.387 120 11,8 35,19 53,33 NA 0/1 NA NA NA NA 35,44,13,28 C/T PANCANCER NA FALSE ADGRF1_p.G698R chr6:47000272:47000273:C:T SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 47900781 47900782 C T 42 132 0.318181818181818 MODIFIER PTCHD4 ENSG00000244694 T intron_variant Transcript ENST00000339488 protein_coding 4/4 ENST00000339488.9:c.899-20845G>A NA rs9395327 -1 SNV HGNC HGNC:21345 YES NM_001384253.1 2 P1 CCDS93929.1 ENSP00000341914 Q6ZW05.115 UPI0005410A54 Q6ZW05-3 0.6685 0.5393 0.7853 0.747 0.667 0.681 0.6588 0.5693 0.6758 0.7505 0.6658 0.7826 0.7214 0.6741 0.6701 0.673 0.6882 0.7853 AMR 19 NA NA PASS SITE 103,88|28,14 NA NA 1 93 20,29 178,188 60,60 31 1.83 NA 19.86 NA FALSE 0.177 61 NA NA NA FALSE NA NA 107.27 19 47900781 HCC1395_HCC1395T 90 0.337 132 26,9 33,21 62,31 NA 0/1 NA NA NA NA 50,40,28,14 C/T PANCANCER NA FALSE PTCHD4 chr6:47900781:47900782:C:T SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 49430402 49430403 C T 130 294 0.442176870748299 MODIFIER MMUT ENSG00000146085 T 3_prime_UTR_variant Transcript ENST00000274813 protein_coding 13/13 ENST00000274813.4:c.*1326G>A NA 3769 rs9381784 -1 SNV HGNC HGNC:7526 YES NM_000255.4 1 P1 CCDS4924.1 ENSP00000274813 P22033.223 A0A024RD82.60 UPI000013DA28 1 0.3293 0.0227 0.5591 0.5417 0.3946 0.2945 0.3034 0.07021 0.3451 0.5123 0.431 0.5394 0.3909 0.4204 0.3569 0.3519 0.3174 0.5591 AMR benign 1 19 NA NA PASS SITE 175,147|72,58 NA NA 1 93 20,20 161,153 60,60 36 2.03 NA 31.26 NA FALSE 0.516 93 NA NA NA FALSE NA NA 313.93 19 49430402 HCC1395_HCC1395T 164 0.435 294 42,26 55,49 104,80 NA 0/1 NA NA NA NA 90,74,72,58 C/T PANCANCER NA FALSE MMUT chr6:49430402:49430403:C:T SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 49713544 49713545 G T 39 73 0.534246575342466 MODIFIER CRISP2 ENSG00000124490 T upstream_gene_variant Transcript ENST00000339139 protein_coding NA rs699957 1 -1 SNV HGNC HGNC:12024 YES NM_003296.4 1 P1 CCDS4928.1 ENSP00000339155 P16562.179 A0A024RD74.66 UPI000013728C P16562-1 0.2853 0.2126 0.1945 0.4365 0.2555 0.3231 0.255 0.2107 0.1123 0.2048 0.1898 0.4667 0.2934 0.1752 0.2757 0.2402 0.2791 0.4667 gnomADg_EAS 19 NA NA PASS SITE 39,49|19,20 NA NA 1 56 20,20 163,156 60,60 23 1.57 NA 10.83 NA FALSE 0.573 93 NA NA NA FALSE NA NA 104.43 19 49713544 HCC1395_HCC1395T 34 0.531 73 11,10 10,15 22,25 NA 0/1 NA NA NA NA 14,20,19,20 G/T PANCANCER NA FALSE CRISP2 chr6:49713544:49713545:G:T SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 52498817 52498818 G A 23 47 0.48936170212766 MODIFIER TRAM2 ENSG00000065308 A 3_prime_UTR_variant Transcript ENST00000182527 protein_coding 11/11 ENST00000182527.4:c.*4380C>T NA 5638 rs62407914 -1 SNV HGNC HGNC:16855 YES NM_012288.4 1 P1 CCDS34477.1 ENSP00000182527 Q15035.160 A0A024RD84.59 UPI00000012BF 0.0483 0.0113 0.0893 0.002 0.1223 0.0409 0.09641 0.03231 0.1645 0.08124 0.1043 0.001349 0.1481 0.04114 0.1403 0.08812 0.05355 0.1645 gnomADg_AMI 19 NA NA PASS SITE 27,25|12,11 NA NA 1 5 20,20 166,171 60,60 35 1.27 NA 5.12 NA FALSE 0.975 51 NA NA NA FALSE NA NA 62.06 19 52498817 HCC1395_HCC1395T 24 0.515 47 5,4 10,10 15,16 NA 0/1 NA NA NA NA 13,11,12,11 G/A PANCANCER NA FALSE TRAM2 chr6:52498817:52498818:G:A SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 52978459 52978460 G A 84 190 0.442105263157895 MODIFIER GSTA4 ENSG00000170899 A downstream_gene_variant Transcript ENST00000370959 protein_coding NA 5 -1 SNV HGNC HGNC:4629 5 P1 CCDS4948.1 ENSP00000359998 O15217.203 A0A024RD58.51 UPI00001119FD O15217-1 19 NA NA PASS SITE 84,101|37,47 NA NA 1 93 20,20 157,178 60,60 35 1.77 NA 17.46 NA FALSE 6.00 91 NA NA NA FALSE NA NA 224.21 19 52978459 HCC1395_HCC1395T 106 0.456 190 26,16 39,38 74,62 NA 0/1 NA NA NA NA 45,61,37,47 G/A PANCANCER NA FALSE GSTA4 chr6:52978459:52978460:G:A SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 53268210 53268211 G A 42 102 0.411764705882353 MODIFIER ELOVL5 ENSG00000012660 A 3_prime_UTR_variant Transcript ENST00000304434 protein_coding 8/8 ENST00000304434.11:c.*917C>T NA 1959 rs1048706 -1 SNV HGNC HGNC:21308 YES NM_021814.5 1 P1 CCDS4951.1 ENSP00000306640 Q9NYP7.172 A0A024RD35.62 UPI0000051C67 Q9NYP7-1 1 0.0817 0.1513 0.0865 0 0.1292 0.0194 0.1179 0.1558 0.09211 0.08706 0.07934 0.0001929 0.1087 0.1234 0.1211 0.1089 0.02869 0.1558 gnomADg_AFR 19 NA NA PASS SITE 21,93|7,35 NA NA 1 88 38,38 179,210 60,60 34 1.69 NA 13.80 NA FALSE 0.914 93 NA NA NA FALSE NA NA 140.52 19 53268210 HCC1395_HCC1395T 60 0.435 102 18,17 30,21 51,39 NA 0/1 NA NA NA NA 11,49,7,35 G/A PANCANCER NA FALSE ELOVL5 chr6:53268210:53268211:G:A SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 53268436 53268437 T G 98 186 0.526881720430108 MODIFIER ELOVL5 ENSG00000012660 G 3_prime_UTR_variant Transcript ENST00000304434 protein_coding 8/8 ENST00000304434.11:c.*691A>C NA 1733 rs41273874 -1 SNV HGNC HGNC:21308 YES NM_021814.5 1 P1 CCDS4951.1 ENSP00000306640 Q9NYP7.172 A0A024RD35.62 UPI0000051C67 Q9NYP7-1 1 0.0180 0.003 0.0317 0 0.0606 0.0031 0.03361 0.008982 0.01206 0.03391 0.0245 0.0001924 0.06969 0.02215 0.04838 0.03161 0.004967 0.06969 gnomADg_FIN 19 NA NA PASS SITE 97,56|67,31 NA NA 1 93 26,20 175,163 60,60 29 1.72 NA 15.30 NA FALSE 1.39 93 NA NA NA FALSE NA NA 272.54 19 53268436 HCC1395_HCC1395T 88 0.521 186 22,21 41,47 65,71 NA 0/1 NA NA NA NA 58,30,67,31 T/G PANCANCER NA FALSE ELOVL5 chr6:53268436:53268437:T:G SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 53348681 53348682 C T 131 239 0.548117154811716 MODIFIER ELOVL5 ENSG00000012660 T intron_variant Transcript ENST00000304434 protein_coding 1/7 ENST00000304434.11:c.-9+136G>A NA rs113274699 -1 SNV HGNC HGNC:21308 YES NM_021814.5 1 P1 CCDS4951.1 ENSP00000306640 Q9NYP7.172 A0A024RD35.62 UPI0000051C67 Q9NYP7-1 1 0.1024 0.2277 0.0807 0 0.1362 0.0194 0.1358 0.2139 0.09211 0.09157 0.07378 0.0003867 0.1276 0.1234 0.1219 0.1187 0.02899 0.2277 AFR 19 NA NA PASS SITE 154,91|73,58 NA NA 1 93 20,20 164,163 60,60 33 1.97 NA 27.64 NA FALSE 0.851 93 NA NA NA FALSE NA NA 322.79 19 53348681 HCC1395_HCC1395T 108 0.513 239 28,37 45,41 76,80 NA 0/1 NA NA NA NA 71,37,73,58 C/T PANCANCER NA FALSE ELOVL5 chr6:53348681:53348682:C:T SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 55327603 55327604 C T 63 126 0.5 MODIFIER GFRAL ENSG00000187871 T intron_variant Transcript ENST00000340465 protein_coding 1/8 ENST00000340465.2:c.22+27C>T NA 1 SNV HGNC HGNC:32789 YES NM_207410.2 1 P1 CCDS4957.1 ENSP00000343636 Q6UXV0.126 UPI000023780D 19 NA NA PASS SITE 37,83|24,39 NA NA 1 93 20,20 173,154 60,60 24 1.61 NA 12.04 NA FALSE 6.00 93 NA NA NA FALSE NA NA 156.37 19 55327603 HCC1395_HCC1395T 63 0.471 126 13,16 28,24 46,41 NA 0/1 NA NA NA NA 17,46,24,39 C/T PANCANCER NA FALSE GFRAL chr6:55327603:55327604:C:T SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 55351465 55351466 G C 53 119 0.445378151260504 MODERATE GFRAL ENSG00000187871 C missense_variant Transcript ENST00000340465 protein_coding 5/9 ENST00000340465.2:c.583G>C ENSP00000343636.2:p.D195H ENSP00000343636.2 p.D195H 669 583 195 D/H Gat/Cat rs1224725337&COSV61236571 1 SNV HGNC HGNC:32789 YES NM_207410.2 1 P1 CCDS4957.1 ENSP00000343636 Q6UXV0.126 UPI000023780D deleterious(0) probably_damaging(1) PDB-ENSP_mappings:5vz4.B&PDB-ENSP_mappings:6q2j.C&PDB-ENSP_mappings:6q2j.D&PDB-ENSP_mappings:6wmw.B&AlphaFold_DB_import:AF-Q6UXV0-F1&Pfam:PF02351&PANTHER:PTHR10269&SMART:SM00907&Superfamily:SSF110035 3.983e-06 0 0 0 0 0 0 0 3.266e-05 3.266e-05 gnomADe_SAS 0&1 0&1 19 NA NA PASS SITE 63,77|21,32 NA NA 1 93 20,20 161,175 60,60 25 1.71 NA 15.05 NA FALSE 6.00 93 NA NA NA FALSE NA NA 155.05 19 55351465 HCC1395_HCC1395T 66 0.476 119 15,11 25,26 42,38 NA 0/1 NA NA NA NA 31,35,21,32 G/C PANCANCER NA FALSE GFRAL_p.D195H chr6:55351465:55351466:G:C SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 57109382 57109383 G C 105 206 0.509708737864078 MODIFIER ZNF451 ENSG00000112200 C intron_variant Transcript ENST00000357489 protein_coding 3/13 ENST00000357489.7:c.186+10241G>C NA 1 SNV HGNC HGNC:21091 1 A2 CCDS4960.1 ENSP00000350083 Q9Y4E5.189 UPI000004A56F Q9Y4E5-2 19 NA NA PASS SITE 122,72|72,33 NA NA 1 93 20,20 169,170 60,60 26 1.83 NA 19.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 306.36 19 57109382 HCC1395_HCC1395T 101 0.510 206 28,26 34,46 74,77 NA 0/1 NA NA NA NA 65,36,72,33 G/C PANCANCER NA FALSE ZNF451 chr6:57109382:57109383:G:C SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 57924378 57924379 C G 23 41 0.560975609756098 MODIFIER GUSBP4 ENSG00000239650 G intron_variant&non_coding_transcript_variant Transcript ENST00000423899 transcribed_unprocessed_pseudogene 4/4 ENST00000423899.1:n.536+39G>C NA -1 SNV HGNC HGNC:18220 YES 19 NA NA PASS SITE 44,26|16,7 NA NA 1 93 20,20 161,167 40,58 41 1.57 NA 10.83 NA FALSE 6.00 93 NA NA NA FALSE NA NA 61.10 19 57924378 HCC1395_HCC1395T 18 0.581 41 5,7 4,9 12,17 NA 0/1 NA NA NA NA 9,9,16,7 C/G PANCANCER NA FALSE GUSBP4 chr6:57924378:57924379:C:G SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 63572351 63572352 T A 79 129 0.612403100775194 MODIFIER ENSG00000285976 A upstream_gene_variant Transcript ENST00000370651 protein_coding NA 121 1 SNV YES 1 P1 ENSP00000359685 A0A3F2YNX1.12 UPI000268B497 19 NA NA PASS SITE 146,112|42,37 NA NA 1 93 20,24 162,161 60,60 23 2.17 NA 43.64 NA FALSE 6.00 93 NA NA NA FALSE NA NA 228.75 19 63572351 HCC1395_HCC1395T 50 0.620 129 11,28 23,26 37,61 NA 0/1 NA NA NA NA 28,22,42,37 T/A PANCANCER NA FALSE chr6:63572351:63572352:T:A SNV 2:2 chr6:46658616:64912570:2:2:1 FALSE NA 0.96 +chr6 70190344 70190345 G C 16 51 0.313725490196078 MODERATE COL19A1 ENSG00000082293 C missense_variant Transcript ENST00000620364 protein_coding 48/51 ENST00000620364.5:c.3057G>C ENSP00000480474.1:p.K1019N ENSP00000480474.1 p.K1019N 3174 3057 1019 K/N aaG/aaC COSV59591570 1 SNV HGNC HGNC:2196 YES NM_001858.6 1 P1 CCDS4970.1 ENSP00000480474 Q14993.190 UPI000004F1E3 deleterious(0.02) possibly_damaging(0.899) AlphaFold_DB_import:AF-Q14993-F1 1 1 19 NA NA PASS SITE 52,22|14,2 NA NA 1 93 37,39 198,204 60,60 31 1.53 NA 9.63 NA FALSE 6.00 93 NA NA NA FALSE NA NA 55.77 19 70190344 HCC1395_HCC1395T 35 0.381 51 5,8 19,8 27,16 NA 0/1 NA NA NA NA 26,9,14,2 G/C PANCANCER NA FALSE COL19A1_p.K1019N chr6:70190344:70190345:G:C SNV 3:1 chr6:69790559:73129733:3:1:1 NA NA 0.96 +chr6 73363141 73363142 CTTGATTCACGTGAATCGATTGGACCCTAACG C 62 357 0.173669467787115 HIGH KHDC3L ENSG00000203908 - frameshift_variant Transcript ENST00000370367 protein_coding 2/3 ENST00000370367.4:c.217_247del ENSP00000359392.3:p.L73Afs*20 ENSP00000359392.3 p.L73Afs*20 289-319 217-247 73-83 LIHVNRLDPNG/X TTGATTCACGTGAATCGATTGGACCCTAACGgc/gc 1 deletion HGNC HGNC:33699 YES NM_001017361.3 1 P1 CCDS34484.1 ENSP00000359392 Q587J8.119 UPI00001D8131 1 CDD:cd12795&PANTHER:PTHR19447&Pfam:PF16005&Gene3D:3.30.1370.10&Superfamily:SSF54791&AlphaFold_DB_import:AF-Q587J8-F1 19 NA NA PASS SITE 407,280|41,21 NA NA 2 93 20,27 160,170 60,60 38 2.39 NA 73.66 NA FALSE 6.00 93 NA NA NA FALSE NA NA 231.39 19 73363141 HCC1395_HCC1395T 295 0.191 357 45,15 87,27 185,43 NA 0|1 0|1 73363141_CTTGATTCACGTGAATCGATTGGACCCTAACG_C NA 73363141 179,116,41,21 CTTGATTCACGTGAATCGATTGGACCCTAACG|C PANCANCER NA FALSE KHDC3L_p.L73Afs*20 chr6:73363141:73363142:CTTGATTCACGTGAATCGATTGGACCCTAACG:C indel 1:1 chr6:73196096:73756654:1:1:1 NA NA 0.96 +chr6 73363176 73363177 AG A 66 364 0.181318681318681 HIGH KHDC3L ENSG00000203908 - frameshift_variant Transcript ENST00000370367 protein_coding 2/3 ENST00000370367.4:c.253del ENSP00000359392.3:p.A85Lfs*18 ENSP00000359392.3 p.A85Lfs*18 324 252 84 E/X gaG/ga 1 deletion HGNC HGNC:33699 YES NM_001017361.3 1 P1 CCDS34484.1 ENSP00000359392 Q587J8.119 UPI00001D8131 1 CDD:cd12795&PANTHER:PTHR19447&Pfam:PF16005&Gene3D:3.30.1370.10&Superfamily:SSF54791&AlphaFold_DB_import:AF-Q587J8-F1 1 19 NA NA PASS SITE 399,292|45,21 NA NA 2 93 20,34 160,169 60,60 41 2.40 NA 74.30 NA FALSE 6.00 93 2,1 G NA TRUE NA 93 241.28 19 73363176 HCC1395_HCC1395T 298 0.199 364 65,16 102,28 192,47 NA 0|1 0|1 73363141_CTTGATTCACGTGAATCGATTGGACCCTAACG_C NA 73363141 176,122,45,21 AG|A PANCANCER NA FALSE KHDC3L_p.A85Lfs*18 chr6:73363176:73363177:AG:A indel 1:1 chr6:73196096:73756654:1:1:1 NA NA 0.96 +chr6 79699851 79699852 G C 40 117 0.341880341880342 MODIFIER SH3BGRL2 ENSG00000198478 C 3_prime_UTR_variant Transcript ENST00000369838 protein_coding 4/4 ENST00000369838.6:c.*342G>C NA 799 1 SNV HGNC HGNC:15567 YES NM_031469.4 1 P1 CCDS4991.1 ENSP00000358853 Q9UJC5.164 UPI0000049FF7 19 NA NA PASS SITE 110,91|18,22 NA NA 1 93 20,36 176,185 60,60 24 1.96 NA 27.04 NA FALSE 6.00 93 NA NA NA FALSE NA NA 112.87 19 79699851 HCC1395_HCC1395T 77 0.348 117 20,10 35,20 59,31 NA 0/1 NA NA NA NA 42,35,18,22 G/C PANCANCER NA FALSE SH3BGRL2 chr6:79699851:79699852:G:C SNV 2:1 chr6:73783709:84738385:2:1:1 TRUE NA 0.96 +chr6 82363828 82363829 C A 53 78 0.67948717948718 MODIFIER TPBG ENSG00000146242 A 5_prime_UTR_variant Transcript ENST00000369750 protein_coding 1/2 ENST00000369750.4:c.-420C>A NA 12 1 SNV HGNC HGNC:12004 YES NM_001376922.1 1 P1 CCDS4995.1 ENSP00000358765 Q13641.188 UPI000004CAD5 19 NA NA PASS SITE 38,71|19,34 NA NA 1 93 31,20 170,174 60,60 33 1.81 NA 18.66 NA FALSE 6.00 88 NA NA NA FALSE NA NA 155.58 19 82363828 HCC1395_HCC1395T 25 0.645 78 11,12 10,25 21,39 NA 0/1 NA NA NA NA 8,17,19,34 C/A PANCANCER NA FALSE TPBG chr6:82363828:82363829:C:A SNV 2:1 chr6:73783709:84738385:2:1:1 TRUE NA 0.96 +chr6 83157374 83157375 G A 15 35 0.428571428571429 MODIFIER DOP1A ENSG00000083097 A intron_variant Transcript ENST00000237163 protein_coding 35/39 ENST00000237163.9:c.6714+56G>A NA 1 SNV HGNC HGNC:21194 5 P4 CCDS64467.1 ENSP00000237163 Q5TA12.129 UPI0001EFAC80 19 NA NA PASS SITE 5,43|4,11 NA NA 1 77 38,20 193,185 60,60 17 1.41 NA 7.53 NA FALSE 6.00 63 NA NA NA FALSE NA NA 39.77 19 83157374 HCC1395_HCC1395T 20 0.387 35 2,4 15,6 18,11 NA 0/1 NA NA NA NA 2,18,4,11 G/A PANCANCER NA FALSE DOP1A chr6:83157374:83157375:G:A SNV 2:1 chr6:73783709:84738385:2:1:1 TRUE NA 0.96 +chr6 83523696 83523697 G A 50 166 0.301204819277108 LOW PRSS35 ENSG00000146250 A synonymous_variant Transcript ENST00000369700 protein_coding 2/2 ENST00000369700.4:c.255G>A ENSP00000358714.3:p.E85= ENSP00000358714.3 p.E85= 436 255 85 E gaG/gaA 1 SNV HGNC HGNC:21387 YES NM_153362.3 1 P1 CCDS4999.1 ENSP00000358714 Q8N3Z0.148 UPI000006D2C7 AlphaFold_DB_import:AF-Q8N3Z0-F1&PANTHER:PTHR15462 19 NA NA PASS SITE 113,142|24,26 NA NA 1 93 20,20 158,171 60,60 27 1.97 NA 27.99 NA FALSE 6.00 88 NA NA NA FALSE NA NA 121.67 19 83523696 HCC1395_HCC1395T 116 0.302 166 35,12 42,20 80,34 NA 0/1 NA NA NA NA 47,69,24,26 G/A PANCANCER NA FALSE PRSS35_p.E85= chr6:83523696:83523697:G:A SNV 2:1 chr6:73783709:84738385:2:1:1 TRUE NA 0.96 +chr6 97140093 97140095 TT AA 2 5 0.4 MODIFIER MMS22L ENSG00000146263 AA downstream_gene_variant Transcript ENST00000275053 protein_coding NA 2067 -1 substitution HGNC HGNC:21475 2 P1 CCDS5039.1 ENSP00000275053 Q6ZRQ5.135 UPI00003673C9 19 NA NA PASS SITE 17,14|1,1 NA NA 1 82 36,20 234,147 60,60 14 1.47 NA 8.13 NA FALSE 6.00 20 NA NA NA FALSE NA NA 5.84 19 97140093 HCC1395_HCC1395T 3 0.329 5 1,1 2,0 3,1 NA 0/1 NA NA NA NA 1,2,1,1 TT/AA PANCANCER NA FALSE MMS22L chr6:97140093:97140095:TT:AA indel 1:0 chr6:90271934:97229242:1:0:1 NA NA 0.96 +chr6 109255552 109255553 A G 4 22 0.181818181818182 MODIFIER CCDC162P ENSG00000203799 G intron_variant&non_coding_transcript_variant Transcript ENST00000368966 transcribed_unitary_pseudogene 17/45 ENST00000368966.10:n.2456+60A>G NA 1 SNV HGNC HGNC:21565 YES 19 NA NA PASS SITE 2,33|1,3 NA NA 1 51 39,28 209,190 60,60 13 1.23 NA 4.82 NA FALSE 6.00 20 NA NA NA FALSE NA NA 8.96 19 109255552 HCC1395_HCC1395T 18 0.181 22 10,2 6,1 17,3 NA 0/1 NA NA NA NA 1,17,1,3 A/G PANCANCER NA FALSE CCDC162P chr6:109255552:109255553:A:G SNV 3:0 chr6:98836656:114055566:3:0:1 NA NA 0.96 +chr6 109451608 109451609 G T 138 140 0.985714285714286 MODERATE MICAL1 ENSG00000135596 T missense_variant Transcript ENST00000358577 protein_coding 7/24 ENST00000358577.7:c.925C>A ENSP00000351385.3:p.L309M ENSP00000351385.3 p.L309M 992 925 309 L/M Ctg/Atg COSV100668480&COSV62196726 -1 SNV HGNC HGNC:20619 1 CCDS55047.1 ENSP00000351385 Q8TDZ2.192 UPI0000252328 Q8TDZ2-2 1 deleterious(0) Gene3D:3.50.50.60&Superfamily:SSF47576&Superfamily:SSF51905&AlphaFold_DB_import:AF-Q8TDZ2-F1 1&1 1&1 19 NA NA PASS SITE 81,44|92,46 NA NA 1 93 20,20 170,167 60,60 26 1.95 NA 25.89 NA FALSE 6.00 93 NA NA NA FALSE NA NA 417.01 19 109451608 HCC1395_HCC1395T 2 0.980 140 1,41 0,52 1,95 NA 0/1 NA NA NA NA 1,1,92,46 G/T PANCANCER NA FALSE MICAL1_p.L309M chr6:109451608:109451609:G:T SNV 3:0 chr6:98836656:114055566:3:0:1 NA NA 0.96 +chr6 116516500 116516501 C A 62 374 0.165775401069519 MODIFIER TRAPPC3L ENSG00000173626 A upstream_gene_variant Transcript ENST00000356128 protein_coding NA 4157 -1 SNV HGNC HGNC:21090 2 ENSP00000348445 Q5T215.121 UPI0000161893 Q5T215-2 19 NA NA PASS SITE 255,251|36,28 NA NA 1 93 20,20 168,182 60,60 30 2.11 NA 38.94 NA FALSE 6.00 76 NA NA NA FALSE NA NA 150.85 19 116516500 HCC1395_HCC1395T 312 0.175 374 72,14 130,28 220,46 NA 0/1 NA NA NA NA 162,150,34,28 C/A PANCANCER NA FALSE TRAPPC3L chr6:116516500:116516501:C:A SNV 4:0 chr6:114057806:123218464:4:0:1 NA NA 0.96 +chr6 117709850 117709851 C G 5 18 0.277777777777778 MODIFIER NUS1 ENSG00000153989 G 3_prime_UTR_variant Transcript ENST00000368494 protein_coding 5/5 ENST00000368494.4:c.*2835C>G NA 3919 1 SNV HGNC HGNC:21042 YES NM_138459.5 1 P1 CCDS5118.1 ENSP00000357480 Q96E22.163 UPI000006FECA 1 19 NA NA PASS SITE 21,5|2,3 NA NA 1 34 38,39 224,230 60,60 44 1.08 NA 3.31 NA FALSE 6.00 38 NA NA NA FALSE NA NA 13.95 19 117709850 HCC1395_HCC1395T 13 0.293 18 4,1 7,3 11,4 NA 0/1 NA NA NA NA 11,2,2,3 C/G PANCANCER NA FALSE NUS1 chr6:117709850:117709851:C:G SNV 4:0 chr6:114057806:123218464:4:0:1 NA NA 0.96 +chr6 118491774 118491775 G A 57 107 0.532710280373832 MODERATE CEP85L ENSG00000111860 A missense_variant Transcript ENST00000360290 protein_coding 6/6 ENST00000360290.7:c.1043C>T ENSP00000353434.3:p.S348F ENSP00000353434.3 p.S348F 1393 1043 348 S/F tCt/tTt rs960323800&COSV63829549 -1 SNV HGNC HGNC:21638 1 ENSP00000353434 Q5SZL2.129 UPI0000457494 Q5SZL2-3 1 deleterious(0) possibly_damaging(0.63) AlphaFold_DB_import:AF-Q5SZL2-F1&PANTHER:PTHR31075 0&1 0&1 19 NA NA PASS SITE 56,61|33,24 NA NA 1 93 20,20 168,160 60,60 39 1.66 NA 13.54 NA FALSE 6.00 75 NA NA NA FALSE NA NA 150.70 19 118491774 HCC1395_HCC1395T 50 0.554 107 8,10 21,26 31,39 NA 0/1 NA NA NA NA 24,26,33,24 G/A PANCANCER NA FALSE CEP85L_p.S348F chr6:118491774:118491775:G:A SNV 4:0 chr6:114057806:123218464:4:0:1 NA NA 0.96 +chr6 122781240 122781241 C G 119 310 0.383870967741935 MODERATE FABP7 ENSG00000164434 G missense_variant Transcript ENST00000356535 protein_coding 3/3 ENST00000356535.4:c.394C>G ENSP00000348931.4:p.P132A ENSP00000348931.4 p.P132A 430 394 132 P/A Ccg/Gcg 1 SNV HGNC HGNC:3562 1 CCDS83121.1 ENSP00000348931 O15540.185 UPI00000735DA O15540-2 deleterious_low_confidence(0.02) Low_complexity_(Seg):seg&AlphaFold_DB_import:AF-O15540-F1 19 NA NA PASS SITE 125,188|46,73 NA NA 1 93 20,20 157,160 60,60 37 1.94 NA 25.58 NA FALSE 6.00 93 NA NA NA FALSE NA NA 286.63 19 122781240 HCC1395_HCC1395T 191 0.373 310 42,27 77,41 125,74 NA 0/1 NA NA NA NA 76,115,46,73 C/G PANCANCER NA FALSE FABP7_p.P132A chr6:122781240:122781241:C:G SNV 4:0 chr6:114057806:123218464:4:0:1 NA NA 0.96 +chr6 127475148 127475149 C T 4 7 0.571428571428571 MODIFIER SOGA3 ENSG00000214338 T intron_variant Transcript ENST00000465909 protein_coding 6/6 ENST00000465909.3:c.2724+154G>A NA rs1474525289 -1 SNV HGNC HGNC:21494 5 A2 ENSP00000435559 E9PJP2.69 UPI0001F78873 6.57e-06 2.412e-05 0 0 0 0 0 0 0 0 0 2.412e-05 gnomADg_AFR 19 NA NA PASS SITE 14,0|4,0 NA NA 1 34 40,37 272,213 60,60 31 1.09 NA 3.31 NA FALSE 6.00 44 NA NA NA FALSE NA NA 13.96 19 127475148 HCC1395_HCC1395T 3 0.556 7 1,2 2,2 3,4 NA 0/1 NA NA NA NA 3,0,4,0 C/T PANCANCER NA FALSE SOGA3 chr6:127475148:127475149:C:T SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 127969860 127969861 G C 205 205 1 MODIFIER PTPRK ENSG00000152894 C downstream_gene_variant Transcript ENST00000368207 protein_coding NA 253 -1 SNV HGNC HGNC:9674 5 ENSP00000357190 E9PGC5.90 UPI0001F7888C 1 19 NA NA PASS SITE 93,59|125,80 NA NA 1 93 20,20 158,161 60,60 35 1.98 NA 28.25 NA FALSE 6.00 93 NA NA NA FALSE NA NA 597.12 19 127969860 HCC1395_HCC1395T 0 0.993 205 0,54 0,72 0,129 NA 0/1 NA NA NA NA 0,0,125,80 G/C PANCANCER NA FALSE PTPRK chr6:127969860:127969861:G:C SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 132391535 132391537 G GT 49 49 1 MODIFIER MOXD1 ENSG00000079931 T intron_variant Transcript ENST00000367963 protein_coding 1/11 ENST00000367963.8:c.264+9627_264+9628insA NA rs938525577 -1 insertion HGNC HGNC:21063 YES NM_015529.4 1 P1 CCDS5152.2 ENSP00000356940 Q6UVY6.155 UPI000003F04F Q6UVY6-1 2.638e-05 7.274e-05 0 0 0 0 0 0 1.473e-05 0 0 7.274e-05 gnomADg_AFR 19 NA NA PASS SITE 64,9|45,4 NA NA 2 93 39,40 200,227 60,60 18 1.84 NA 19.99 NA FALSE 4.31 93 8,9 T NA TRUE NA 93 132.26 19 132391535 HCC1395_HCC1395T 0 0.980 49 0,20 0,25 0,48 NA 0/1 NA NA NA NA 0,0,45,4 G/GT PANCANCER NA FALSE MOXD1 chr6:132391535:132391537:G:GT indel 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 132470717 132470718 C G 4 19 0.210526315789474 MODIFIER STX7 ENSG00000079950 G intron_variant Transcript ENST00000367937 protein_coding 5/9 ENST00000367937.4:c.388-91G>C NA -1 SNV HGNC HGNC:11442 5 CCDS87441.1 ENSP00000356914 O15400.196 UPI000046FF43 O15400-2 19 NA NA PASS SITE 4,28|1,3 NA NA 1 47 39,28 193,175 60,60 22 1.20 NA 4.52 NA FALSE 6.00 26 NA NA NA FALSE NA NA 9.07 19 132470717 HCC1395_HCC1395T 15 0.211 19 2,2 4,0 14,3 NA 0/1 NA NA NA NA 2,13,1,3 C/G PANCANCER NA FALSE STX7 chr6:132470717:132470718:C:G SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 138307050 138307051 C G 7 7 1 MODIFIER ARFGEF3 ENSG00000112379 G intron_variant Transcript ENST00000251691 protein_coding 22/33 ENST00000251691.5:c.3829-203C>G NA 1 SNV HGNC HGNC:21213 YES NM_020340.5 1 P1 CCDS5189.2 ENSP00000251691 Q5TH69.134 UPI000150AF4A 19 NA NA PASS SITE 8,0|7,0 NA NA 1 39 38,41 203,253 60,60 41 0.954 NA 2.41 NA FALSE 6.00 89 NA NA NA FALSE NA NA 30.45 19 138307050 HCC1395_HCC1395T 0 0.893 7 0,5 0,2 0,7 NA 0/1 NA NA NA NA 0,0,7,0 C/G PANCANCER NA FALSE ARFGEF3 chr6:138307050:138307051:C:G SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 142760564 142760565 T C 47 160 0.29375 LOW HIVEP2 ENSG00000010818 C synonymous_variant Transcript ENST00000012134 protein_coding 8/9 ENST00000012134.7:c.5724A>G ENSP00000012134.2:p.G1908= ENSP00000012134.2 p.G1908= 6500 5724 1908 G ggA/ggG -1 SNV HGNC HGNC:4921 5 P1 CCDS43510.1 ENSP00000012134 P31629.193 UPI00004708DD 1 AlphaFold_DB_import:AF-P31629-F1&PANTHER:PTHR45944&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg 19 NA NA PASS SITE 105,142|23,24 NA NA 1 93 20,20 161,147 60,60 36 1.94 NA 25.88 NA FALSE 6.00 79 NA NA NA FALSE NA NA 114.16 19 142760564 HCC1395_HCC1395T 113 0.274 160 20,15 44,10 81,30 NA 0/1 NA NA NA NA 48,65,23,24 T/C PANCANCER NA FALSE HIVEP2_p.G1908= chr6:142760564:142760565:T:C SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 144499195 144499196 C A 46 46 1 MODIFIER UTRN ENSG00000152818 A intron_variant Transcript ENST00000367545 protein_coding 33/74 ENST00000367545.8:c.4594-62C>A NA 1 SNV HGNC HGNC:12635 YES NM_007124.3 5 P1 CCDS34547.1 ENSP00000356515 P46939.217 UPI00003673F1 P46939-1 19 NA NA PASS SITE 25,9|34,12 NA NA 1 93 20,30 167,188 60,60 28 1.41 NA 7.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 146.18 19 144499195 HCC1395_HCC1395T 0 0.974 46 0,14 0,21 0,36 NA 0/1 NA NA NA NA 0,0,34,12 C/A PANCANCER NA FALSE UTRN chr6:144499195:144499196:C:A SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 150841324 150841325 A G 59 208 0.283653846153846 MODIFIER PLEKHG1 ENSG00000120278 G 3_prime_UTR_variant Transcript ENST00000358517 protein_coding 16/16 ENST00000358517.6:c.*428A>G NA 4797 1 SNV HGNC HGNC:20884 5 P1 CCDS34552.1 ENSP00000351318 Q9ULL1.149 Q5JYA6.157 UPI000015FC80 19 NA NA PASS SITE 173,155|28,31 NA NA 1 93 20,20 173,159 60,60 24 2.10 NA 37.62 NA FALSE 6.00 85 NA NA NA FALSE NA NA 148.04 19 150841324 HCC1395_HCC1395T 149 0.279 208 38,14 64,26 113,43 NA 0/1 NA NA NA NA 80,69,28,31 A/G PANCANCER NA FALSE PLEKHG1 chr6:150841324:150841325:A:G SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 152325134 152325135 C T 16 36 0.444444444444444 MODERATE SYNE1 ENSG00000131018 T missense_variant Transcript ENST00000367255 protein_coding 81/146 ENST00000367255.10:c.15607G>A ENSP00000356224.5:p.E5203K ENSP00000356224.5 p.E5203K 16172 15607 5203 E/K Gag/Aag COSV54898439 -1 SNV HGNC HGNC:17089 YES NM_182961.4 1 P1 CCDS5236.2 ENSP00000356224 Q8NF91.201 UPI000204AF58 Q8NF91-1 1 benign(0.429) Gene3D:1.20.58.60&SMART:SM00150&Superfamily:SSF46966&Superfamily:SSF46966&CDD:cd00176 1 1 19 NA NA PASS SITE 46,19|13,3 NA NA 1 92 20,34 162,143 60,60 22 1.50 NA 9.03 NA FALSE 6.00 70 NA NA NA FALSE NA NA 46.21 19 152325134 HCC1395_HCC1395T 20 0.454 36 7,5 8,8 16,13 NA 0/1 NA NA NA NA 16,4,13,3 C/T PANCANCER NA FALSE SYNE1_p.E5203K chr6:152325134:152325135:C:T SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 152326289 152326290 G A 109 109 1 LOW SYNE1 ENSG00000131018 A splice_region_variant&intron_variant Transcript ENST00000367255 protein_coding 79/145 ENST00000367255.10:c.15293+7C>T NA -1 SNV HGNC HGNC:17089 YES NM_182961.4 1 P1 CCDS5236.2 ENSP00000356224 Q8NF91.201 UPI000204AF58 Q8NF91-1 1 19 NA NA PASS SITE 78,68|57,52 NA NA 1 93 20,20 169,158 60,60 37 1.99 NA 28.87 NA FALSE 6.00 93 NA NA NA FALSE NA NA 318.83 19 152326289 HCC1395_HCC1395T 0 0.987 109 0,28 0,38 0,72 NA 0/1 NA NA NA NA 0,0,57,52 G/A PANCANCER NA FALSE SYNE1 chr6:152326289:152326290:G:A SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 155244748 155244749 G C 37 183 0.202185792349727 MODERATE TIAM2 ENSG00000146426 C missense_variant Transcript ENST00000275246 protein_coding 4/13 ENST00000275246.11:c.283G>C ENSP00000275246.7:p.D95H ENSP00000275246.7 p.D95H 794 283 95 D/H Gac/Cac 1 SNV HGNC HGNC:11806 1 CCDS34559.1 ENSP00000275246 Q8IVF5.158 UPI000013EEEC Q8IVF5-3 deleterious_low_confidence(0) probably_damaging(0.967) PROSITE_profiles:PS50010&CDD:cd00160&PANTHER:PTHR46001&Pfam:PF00621&Gene3D:1.20.900.10&SMART:SM00325&Superfamily:SSF48065&AlphaFold_DB_import:AF-Q8IVF5-F1 19 NA NA PASS SITE 130,166|14,23 NA NA 1 93 20,20 159,159 60,60 43 2.00 NA 29.70 NA FALSE 6.00 92 NA NA NA FALSE NA NA 82.94 19 155244748 HCC1395_HCC1395T 146 0.203 183 42,8 45,14 97,24 NA 0/1 NA NA NA NA 65,81,14,23 G/C PANCANCER NA FALSE TIAM2_p.D95H chr6:155244748:155244749:G:C SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 157133136 157133137 G C 97 97 1 MODERATE ARID1B ENSG00000049618 C missense_variant Transcript ENST00000319584 protein_coding 5/12 ENST00000319584.11:c.704G>C ENSP00000313006.7:p.G235A ENSP00000313006.7 p.G235A 704 704 235 G/A gGa/gCa COSV51684508 1 cds_start_NF SNV HGNC HGNC:18040 2 ENSP00000313006 H0Y2R3.67 UPI000014064F 1 deleterious_low_confidence(0) possibly_damaging(0.683) AlphaFold_DB_import:AF-H0Y2R3-F1&PANTHER:PTHR12656&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite 1 1 19 NA NA PASS SITE 32,54|43,54 NA NA 1 93 20,20 154,154 60,60 27 1.77 NA 17.46 NA FALSE 6.00 93 NA NA NA FALSE NA NA 283.63 19 157133136 HCC1395_HCC1395T 0 0.984 97 0,25 0,33 0,61 NA 0/1 NA NA NA NA 0,0,43,54 G/C PANCANCER TRUE TRUE ARID1B_p.G235A chr6:157133136:157133137:G:C SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 158077821 158077822 C G 35 35 1 MODIFIER SYNJ2 ENSG00000078269 G intron_variant Transcript ENST00000355585 protein_coding 17/26 ENST00000355585.9:c.2450-343C>G NA 1 SNV HGNC HGNC:11504 YES NM_003898.4 1 P2 CCDS5254.1 ENSP00000347792 O15056.209 UPI000006E2F8 O15056-1 19 NA NA PASS SITE 17,14|15,20 NA NA 1 93 20,36 166,181 60,60 23 1.31 NA 5.72 NA FALSE 6.00 93 NA NA NA FALSE NA NA 121.21 19 158077821 HCC1395_HCC1395T 0 0.966 35 0,10 0,13 0,27 NA 0/1 NA NA NA NA 0,0,15,20 C/G PANCANCER NA FALSE SYNJ2 chr6:158077821:158077822:C:G SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 160711032 160711033 GGTGTCTTGTGAAA G 37 37 1 MODIFIER PLG ENSG00000122194 - intron_variant Transcript ENST00000297289 protein_coding 1/10 ENST00000297289.9:c.49+8681_49+8693del NA 1 deletion HGNC HGNC:9071 5 ENSP00000516619 1 1 19 NA NA PASS SITE 20,1|33,4 NA NA 1 93 40,40 220,195 60,59 22 1.33 NA 6.00 NA FALSE 6.00 93 NA NA NA FALSE NA NA 165.82 19 160711032 HCC1395_HCC1395T 0 0.972 37 0,15 0,18 0,33 NA 0/1 NA NA NA NA 0,0,33,4 GGTGTCTTGTGAAA/G PANCANCER NA FALSE PLG chr6:160711032:160711033:GGTGTCTTGTGAAA:G indel 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 165293227 165293228 T G 60 60 1 MODIFIER C6orf118 ENSG00000112539 G intron_variant Transcript ENST00000230301 protein_coding 6/8 ENST00000230301.9:c.1120+186A>C NA COSV100025158 -1 SNV HGNC HGNC:21233 YES NM_144980.4 1 P1 CCDS5288.1 ENSP00000230301 Q5T5N4.115 UPI0000367401 1 1 19 NA NA PASS SITE 22,14|42,18 NA NA 1 93 20,20 151,166 60,60 26 1.37 NA 6.62 NA FALSE 6.00 93 NA NA NA FALSE NA NA 192.97 19 165293227 HCC1395_HCC1395T 0 0.978 60 0,20 0,22 0,43 NA 0/1 NA NA NA NA 0,0,42,18 T/G PANCANCER NA FALSE C6orf118 chr6:165293227:165293228:T:G SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 166306502 166306503 G A 17 91 0.186813186813187 MODIFIER PRR18 ENSG00000176381 A 3_prime_UTR_variant Transcript ENST00000322583 protein_coding 1/1 ENST00000322583.5:c.*753C>T NA 1891 -1 SNV HGNC HGNC:28574 YES NM_175922.4 P1 CCDS5291.1 ENSP00000319590 Q8N4B5.103 UPI0000140E82 19 NA NA PASS SITE 67,101|8,9 NA NA 1 93 20,20 170,187 60,60 36 1.85 NA 20.42 NA FALSE 6.00 44 NA NA NA FALSE NA NA 39.91 19 166306502 HCC1395_HCC1395T 74 0.200 91 20,4 26,8 51,12 NA 0/1 NA NA NA NA 30,44,8,9 G/A PANCANCER NA FALSE PRR18 chr6:166306502:166306503:G:A SNV 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 166369816 166369817 ACAGAATTATACAACACCATCTCCT A 17 37 0.459459459459459 MODIFIER MPC1 ENSG00000060762 - intron_variant Transcript ENST00000360961 protein_coding 2/4 ENST00000360961.11:c.75+378_75+401del NA -1 deletion HGNC HGNC:21606 YES NM_016098.4 5 P2 CCDS5293.1 ENSP00000354223 Q9Y5U8.156 UPI000004F9EF 1 19 NA NA PASS SITE 49,14|12,5 NA NA 1 81 38,39 191,155 60,60 27 1.52 NA 9.56 NA FALSE 6.00 93 NA NA NA FALSE NA NA 67.56 19 166369816 HCC1395_HCC1395T 20 0.419 37 4,6 8,6 17,12 NA 0/1 NA NA NA NA 17,3,12,5 ACAGAATTATACAACACCATCTCCT/A PANCANCER NA FALSE MPC1 chr6:166369816:166369817:ACAGAATTATACAACACCATCTCCT:A indel 3:0 chr6:123218539:166410857:3:0:1 NA NA 0.96 +chr6 167041641 167041642 C T 217 343 0.63265306122449 MODIFIER CEP43 ENSG00000213066 T 3_prime_UTR_variant Transcript ENST00000349556 protein_coding 12/12 ENST00000349556.5:c.*1663C>T NA 3042 1 SNV HGNC HGNC:17012 1 P3 CCDS5297.1 ENSP00000230248 O95684.168 UPI000013C927 O95684-2 1 19 NA NA PASS SITE 242,195|120,97 NA NA 1 93 20,20 166,179 60,60 28 2.33 NA 62.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 586.68 19 167041641 HCC1395_HCC1395T 126 0.629 343 25,48 57,99 89,152 NA 0/1 NA NA NA NA 68,58,120,97 C/T PANCANCER NA FALSE CEP43 chr6:167041641:167041642:C:T SNV 2:1 chr6:166413948:170583760:2:1:1 TRUE NA 0.96 +chr6 167208829 167208830 G C 19 67 0.283582089552239 MODIFIER ENSG00000216966 C non_coding_transcript_exon_variant Transcript ENST00000404577 processed_pseudogene 1/1 ENST00000404577.1:n.69C>G NA 69 -1 SNV YES 19 NA NA PASS SITE 51,66|9,10 NA NA 1 93 20,20 166,157 57,48 25 1.40 NA 14.44 NA FALSE 6.00 93 NA NA NA FALSE NA NA 45.74 19 167208829 HCC1395_HCC1395T 48 0.277 67 14,5 10,6 33,12 NA 0/1 NA NA NA NA 21,27,9,10 G/C PANCANCER NA FALSE chr6:167208829:167208830:G:C SNV 2:1 chr6:166413948:170583760:2:1:1 TRUE NA 0.96 +chr6 168038430 168038431 C A 25 48 0.520833333333333 MODIFIER KIF25 ENSG00000125337 A intron_variant Transcript ENST00000443060 protein_coding 5/9 ENST00000443060.6:c.318-123C>A NA 1 SNV HGNC HGNC:6390 5 P1 CCDS5305.1 ENSP00000388878 Q9UIL4.172 UPI000012DDAB Q9UIL4-1 19 NA NA PASS SITE 45,12|21,4 NA NA 1 84 37,37 192,223 60,60 29 1.46 NA 8.13 NA FALSE 6.00 81 NA NA NA FALSE NA NA 77.79 19 168038430 HCC1395_HCC1395T 23 0.533 48 6,8 8,12 19,22 NA 0/1 NA NA NA NA 19,4,21,4 C/A PANCANCER NA FALSE KIF25 chr6:168038430:168038431:C:A SNV 2:1 chr6:166413948:170583760:2:1:1 TRUE NA 0.96 +chr6 168066830 168066831 C T 21 73 0.287671232876712 MODERATE FRMD1 ENSG00000153303 T missense_variant&splice_region_variant Transcript ENST00000283309 protein_coding 4/11 ENST00000283309.11:c.386G>A ENSP00000283309.6:p.G129E ENSP00000283309.6 p.G129E 504 386 129 G/E gGa/gAa rs776892866&COSV51960435 -1 SNV HGNC HGNC:21240 YES NM_024919.6 1 CCDS5306.1 ENSP00000283309 Q8N878.153 UPI000013F36A Q8N878-1 tolerated(0.09) probably_damaging(0.951) AlphaFold_DB_import:AF-Q8N878-F1&PROSITE_profiles:PS50057&PANTHER:PTHR13429&SMART:SM00295&Superfamily:SSF54236&CDD:cd17197 0&1 0&1 19 NA NA PASS SITE 55,64|8,13 NA NA 1 93 20,20 175,165 60,60 35 1.66 NA 13.54 NA FALSE 6.00 54 NA NA NA FALSE NA NA 43.83 19 168066830 HCC1395_HCC1395T 52 0.300 73 13,4 17,8 34,14 NA 0/1 NA NA NA NA 21,31,8,13 C/T PANCANCER NA FALSE FRMD1_p.G129E chr6:168066830:168066831:C:T SNV 2:1 chr6:166413948:170583760:2:1:1 TRUE NA 0.96 +chr7 2393711 2393712 C T 34 34 1 MODIFIER NGRNP3 ENSG00000271163 T downstream_gene_variant Transcript ENST00000603368 processed_pseudogene NA 136 -1 SNV HGNC HGNC:56572 YES 20 NA NA PASS SITE 18,7|19,15 NA NA 1 93 39,35 208,182 60,60 21 1.40 NA 6.92 NA FALSE 6.00 93 NA NA NA FALSE NA NA 106.92 20 2393711 HCC1395_HCC1395T 0 0.965 34 0,14 0,11 0,26 NA 0/1 NA NA NA NA 0,0,19,15 C/T PANCANCER NA FALSE NGRNP3 chr7:2393711:2393712:C:T SNV 4:0 chr7:498640:10933735:4:0:1 NA NA 0.96 +chr7 2512831 2512832 A C 61 61 1 MODIFIER LFNG ENSG00000106003 C intron_variant Transcript ENST00000402506 protein_coding 1/8 ENST00000402506.5:c.47+130A>C NA 1 SNV HGNC HGNC:6560 2 CCDS55081.1 ENSP00000385764 Q8NES3.171 UPI000173A1FB Q8NES3-4 1 20 NA NA PASS SITE 23,42|15,46 NA NA 1 93 20,35 160,164 60,60 23 1.68 NA 13.53 NA FALSE 6.00 93 NA NA NA FALSE NA NA 209.47 20 2512831 HCC1395_HCC1395T 0 0.980 61 0,20 0,22 0,48 NA 0/1 NA NA NA NA 0,0,15,46 A/C PANCANCER NA FALSE LFNG chr7:2512831:2512832:A:C SNV 4:0 chr7:498640:10933735:4:0:1 NA NA 0.96 +chr7 2712473 2712474 G T 85 208 0.408653846153846 LOW AMZ1 ENSG00000174945 T synonymous_variant Transcript ENST00000312371 protein_coding 7/7 ENST00000312371.8:c.1092G>T ENSP00000308149.4:p.V364= ENSP00000308149.4 p.V364= 1460 1092 364 V gtG/gtT 1 SNV HGNC HGNC:22231 1 P1 CCDS34589.1 ENSP00000308149 Q400G9.127 A4D202.116 UPI00001C1E77 Q400G9-1 AlphaFold_DB_import:AF-Q400G9-F1&PANTHER:PTHR32205&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite 20 NA NA PASS SITE 169,174|45,40 NA NA 1 93 20,20 162,173 60,60 28 2.17 NA 43.95 NA FALSE 6.00 93 NA NA NA FALSE NA NA 229.14 20 2712473 HCC1395_HCC1395T 123 0.416 208 40,21 38,37 86,61 NA 0/1 NA NA NA NA 61,62,45,40 G/T PANCANCER NA FALSE AMZ1_p.V364= chr7:2712473:2712474:G:T SNV 4:0 chr7:498640:10933735:4:0:1 NA NA 0.96 +chr7 4145951 4145952 G A 141 235 0.6 MODIFIER SDK1 ENSG00000146555 A intron_variant Transcript ENST00000389531 protein_coding 29/43 ENST00000389531.7:c.4423+35G>A NA rs1259928505 1 SNV HGNC HGNC:19307 5 A2 ENSP00000374182 F8W6X9.70 UPI000173A21C 5.053e-06 0 0 0 0 0 0 0 4.578e-05 4.578e-05 gnomADe_SAS 20 NA NA PASS SITE 107,171|52,89 NA NA 1 93 20,20 164,156 60,60 33 2.10 NA 37.28 NA FALSE 6.00 93 NA NA NA FALSE NA NA 370.43 20 4145951 HCC1395_HCC1395T 94 0.613 235 30,37 23,39 59,94 NA 0/1 NA NA NA NA 38,56,52,89 G/A PANCANCER NA FALSE SDK1 chr7:4145951:4145952:G:A SNV 4:0 chr7:498640:10933735:4:0:1 NA NA 0.96 +chr7 4909705 4909706 G C 51 52 0.980769230769231 MODIFIER MMD2 ENSG00000136297 C intron_variant Transcript ENST00000401401 protein_coding 6/6 ENST00000401401.8:c.537+176C>G NA -1 SNV HGNC HGNC:30133 YES NM_198403.4 1 P1 CCDS47530.1 ENSP00000384141 Q8IY49.148 UPI000020EA2D Q8IY49-2 20 NA NA PASS SITE 25,8|39,12 NA NA 1 93 38,34 186,195 60,60 18 1.43 NA 7.83 NA FALSE 6.00 93 NA NA NA FALSE NA NA 171.49 20 4909705 HCC1395_HCC1395T 1 0.975 52 0,20 0,19 1,41 NA 0/1 NA NA NA NA 1,0,39,12 G/C PANCANCER NA FALSE MMD2 chr7:4909705:4909706:G:C SNV 4:0 chr7:498640:10933735:4:0:1 NA NA 0.96 +chr7 5307049 5307050 C G 157 159 0.987421383647799 MODIFIER SLC29A4 ENSG00000164638 G downstream_gene_variant Transcript ENST00000297195 protein_coding NA 2989 1 SNV HGNC HGNC:23097 1 P1 CCDS5340.1 ENSP00000297195 Q7RTT9.146 UPI0000051F6F Q7RTT9-1 20 NA NA PASS SITE 49,47|79,80 NA NA 1 93 20,20 152,150 60,60 39 -1.382e+00 NA 12.54 NA FALSE 6.00 93 NA NA NA FALSE NA NA 421.85 20 5307049 HCC1395_HCC1395T 2 0.980 159 0,31 1,61 1,96 NA 0/1 NA NA NA NA 0,2,78,79 C/G PANCANCER NA FALSE SLC29A4 chr7:5307049:5307050:C:G SNV 4:0 chr7:498640:10933735:4:0:1 NA NA 0.96 +chr7 12234179 12234180 T G 4 20 0.2 MODIFIER TMEM106B ENSG00000106460 G 3_prime_UTR_variant Transcript ENST00000396667 protein_coding 9/9 ENST00000396667.7:c.*2204T>G NA 3351 1 SNV HGNC HGNC:22407 1 P1 CCDS5358.1 ENSP00000379901 Q9NUM4.147 A0A024R9Z1.49 UPI000003ED3C 1 20 NA NA PASS SITE 12,36|2,2 NA NA 1 86 36,20 191,103 60,60 52 1.41 NA 7.53 NA FALSE 6.00 33 NA NA NA FALSE NA NA 6.61 20 12234179 HCC1395_HCC1395T 16 0.176 20 5,2 7,0 13,2 NA 0/1 NA NA NA NA 4,12,2,2 T/G PANCANCER NA FALSE TMEM106B chr7:12234179:12234180:T:G SNV 2:0 chr7:10982603:23684745:2:0:1 TRUE NA 0.96 +chr7 27130624 27130625 C T 132 411 0.321167883211679 MODIFIER HOXA3 ENSG00000105997 T intron_variant Transcript ENST00000317201 protein_coding 1/4 ENST00000317201.7:c.-389-3554G>A NA COSV57829417 -1 SNV HGNC HGNC:5104 5 P1 CCDS5404.1 ENSP00000324884 O43365.191 A0A024RA33.61 UPI000012CF22 1 1 20 NA NA PASS SITE 370,242|83,49 NA NA 1 93 20,20 161,176 60,60 29 2.36 NA 66.77 NA FALSE 6.00 93 NA NA NA FALSE NA NA 324.82 20 27130624 HCC1395_HCC1395T 279 0.333 411 69,34 115,59 192,95 NA 0/1 NA NA NA NA 176,103,83,49 C/T PANCANCER NA FALSE HOXA3 chr7:27130624:27130625:C:T SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 28823878 28823879 G T 215 344 0.625 MODIFIER CREB5 ENSG00000146592 T 3_prime_UTR_variant Transcript ENST00000357727 protein_coding 11/11 ENST00000357727.7:c.*4599G>T NA 6523 1 SNV HGNC HGNC:16844 YES NM_182898.4 1 A1 CCDS5417.1 ENSP00000350359 Q02930.192 UPI0000457534 Q02930-1 20 NA NA PASS SITE 211,213|103,112 NA NA 1 93 20,20 155,152 60,60 34 2.30 NA 59.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 557.09 20 28823878 HCC1395_HCC1395T 129 0.622 344 35,48 42,78 84,139 NA 0/1 NA NA NA NA 57,72,103,112 G/T PANCANCER NA FALSE CREB5 chr7:28823878:28823879:G:T SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 29947395 29947396 T C 35 125 0.28 MODIFIER SCRN1 ENSG00000136193 C intron_variant Transcript ENST00000242059 protein_coding 3/7 ENST00000242059.10:c.342-3216A>G NA -1 SNV HGNC HGNC:22192 YES NM_014766.5 1 P1 CCDS5422.1 ENSP00000242059 Q12765.167 A0A090N7T9.42 UPI000019B3D5 Q12765-1 20 NA NA PASS SITE 66,103|13,22 NA NA 1 93 20,20 161,154 60,60 38 1.75 NA 16.55 NA FALSE 6.00 93 NA NA NA FALSE NA NA 82.08 20 29947395 HCC1395_HCC1395T 90 0.298 125 25,10 26,10 55,23 NA 0/1 NA NA NA NA 40,50,13,22 T/C PANCANCER NA FALSE SCRN1 chr7:29947395:29947396:T:C SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 30667184 30667185 T C 60 206 0.29126213592233 MODIFIER CRHR2 ENSG00000106113 C intron_variant Transcript ENST00000341843 protein_coding 5/13 ENST00000341843.8:c.273+44A>G NA -1 SNV HGNC HGNC:2358 5 CCDS56477.1 ENSP00000344304 Q13324.180 UPI000002A721 Q13324-3 20 NA NA PASS SITE 161,124|39,21 NA NA 1 93 20,20 152,160 60,60 37 1.96 NA 26.79 NA FALSE 6.00 93 NA NA NA FALSE NA NA 147.27 20 30667184 HCC1395_HCC1395T 146 0.306 206 33,13 56,25 92,40 NA 0/1 NA NA NA NA 80,66,39,21 T/C PANCANCER NA FALSE CRHR2 chr7:30667184:30667185:T:C SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 30689299 30689300 G A 14 64 0.21875 LOW CRHR2 ENSG00000106113 A splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000341843 protein_coding 1/13 ENST00000341843.8:c.-260-15C>T NA rs1249108139 -1 SNV HGNC HGNC:2358 5 CCDS56477.1 ENSP00000344304 Q13324.180 UPI000002A721 Q13324-3 20 NA NA PASS SITE 66,54|6,8 NA NA 1 93 20,20 150,160 60,60 32 1.67 NA 13.54 NA FALSE 6.00 47 NA NA NA FALSE NA NA 29.60 20 30689299 HCC1395_HCC1395T 50 0.238 64 15,3 14,4 31,9 NA 0/1 NA NA NA NA 27,23,6,8 G/A PANCANCER NA FALSE CRHR2 chr7:30689299:30689300:G:A SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 30883201 30883202 C G 20 63 0.317460317460317 MODIFIER MINDY4 ENSG00000106125 G intron_variant Transcript ENST00000265299 protein_coding 17/17 ENST00000265299.6:c.2225+208C>G NA 1 SNV HGNC HGNC:21916 YES NM_032222.3 1 P1 CCDS43565.1 ENSP00000265299 Q4G0A6.114 UPI0000D60E7B 20 NA NA PASS SITE 34,52|9,11 NA NA 1 81 20,20 176,160 60,60 27 1.46 NA 8.12 NA FALSE 6.00 40 NA NA NA FALSE NA NA 42.31 20 30883201 HCC1395_HCC1395T 43 0.293 63 9,2 16,9 28,11 NA 0/1 NA NA NA NA 16,27,9,11 C/G PANCANCER NA FALSE MINDY4 chr7:30883201:30883202:C:G SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 33605419 33605420 C G 162 411 0.394160583941606 MODIFIER BBS9 ENSG00000122507 G 3_prime_UTR_variant Transcript ENST00000242067 protein_coding 23/23 ENST00000242067.11:c.*193C>G NA 3346 1 SNV HGNC HGNC:30000 YES NM_198428.3 1 P3 CCDS43566.1 ENSP00000242067 Q3SYG4.142 A0A090N8P4.51 UPI000020ED57 Q3SYG4-1 1 20 NA NA PASS SITE 260,209|90,72 NA NA 1 93 20,20 164,163 60,60 35 2.16 NA 42.39 NA FALSE 6.00 93 NA NA NA FALSE NA NA 415.15 20 33605419 HCC1395_HCC1395T 249 0.400 411 58,39 95,61 159,106 NA 0/1 NA NA NA NA 143,106,90,72 C/G PANCANCER NA FALSE BBS9 chr7:33605419:33605420:C:G SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 35668735 35668736 G C 3 14 0.214285714285714 MODIFIER HERPUD2 ENSG00000122557 C intron_variant Transcript ENST00000311350 protein_coding 4/8 ENST00000311350.8:c.340-1147C>G NA -1 SNV HGNC HGNC:21915 YES NM_022373.5 1 P1 CCDS5446.1 ENSP00000310729 Q9BSE4.153 A0A024RA77.61 UPI000013F159 20 NA NA PASS SITE 0,21|0,3 NA NA 1 31 40,42 206,215 60,60 30 1.04 NA 3.01 NA FALSE 6.00 52 NA NA NA FALSE NA NA 9.36 20 35668735 HCC1395_HCC1395T 11 0.250 14 2,1 5,2 11,3 NA 0/1 NA NA NA NA 0,11,0,3 G/C PANCANCER NA FALSE HERPUD2 chr7:35668735:35668736:G:C SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 36690236 36690237 C G 33 81 0.407407407407407 MODIFIER AOAH ENSG00000136250 G intron_variant&NMD_transcript_variant Transcript ENST00000414637 nonsense_mediated_decay 1/2 ENST00000414637.1:c.128-56G>C NA -1 SNV HGNC HGNC:548 5 ENSP00000416472 F8WCP9.47 UPI0000E0A9CC 20 NA NA PASS SITE 32,63|13,20 NA NA 1 93 20,20 167,149 60,60 33 1.52 NA 9.59 NA FALSE 6.00 91 NA NA NA FALSE NA NA 83.84 20 36690236 HCC1395_HCC1395T 48 0.396 81 7,10 13,6 34,22 NA 0/1 NA NA NA NA 16,32,13,20 C/G PANCANCER NA FALSE AOAH chr7:36690236:36690237:C:G SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 39339739 39339740 G C 44 102 0.431372549019608 MODERATE POU6F2 ENSG00000106536 C missense_variant Transcript ENST00000403058 protein_coding 6/11 ENST00000403058.6:c.609G>C ENSP00000384004.1:p.Q203H ENSP00000384004.1 p.Q203H 752 609 203 Q/H caG/caC 1 SNV HGNC HGNC:21694 5 A2 ENSP00000384004 P78424.192 UPI0000480E81 P78424-1 1 tolerated(0.61) unknown(0) Low_complexity_(Seg):seg&MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-P78424-F1 20 NA NA PASS SITE 30,95|11,33 NA NA 1 93 37,34 178,162 60,60 21 1.75 NA 16.46 NA FALSE 6.00 93 NA NA NA FALSE NA NA 122.84 20 39339739 HCC1395_HCC1395T 58 0.410 102 20,15 24,16 49,34 NA 0/1 NA NA NA NA 12,46,11,33 G/C PANCANCER NA FALSE POU6F2_p.Q203H chr7:39339739:39339740:G:C SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 42237065 42237066 G A 114 188 0.606382978723404 MODIFIER GLI3 ENSG00000106571 A 5_prime_UTR_variant Transcript ENST00000395925 protein_coding 1/15 ENST00000395925.8:c.-137C>T NA 145 -1 SNV HGNC HGNC:4319 YES NM_000168.6 5 P1 CCDS5465.1 ENSP00000379258 P10071.225 UPI000020EE4C 1 20 NA NA PASS SITE 96,170|44,70 NA NA 1 93 20,20 145,135 60,60 27 2.10 NA 36.73 NA FALSE 6.00 93 NA NA NA FALSE NA NA 289.98 20 42237065 HCC1395_HCC1395T 74 0.587 188 28,29 17,32 49,70 NA 0/1 NA NA NA NA 25,49,44,70 G/A PANCANCER NA FALSE GLI3 chr7:42237065:42237066:G:A SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 44020406 44020407 GAAGACACCTGTTGCC G 11 22 0.5 MODIFIER ENSG00000290872 - upstream_gene_variant Transcript ENST00000326391 lncRNA NA 1237 -1 deletion YES 1 20 NA NA PASS SITE 21,20|5,6 NA NA 1 36 20,20 155,180 60,57 37 1.26 NA 5.12 NA FALSE 6.00 93 NA NA NA FALSE NA NA 44.84 20 44020406 HCC1395_HCC1395T 11 0.537 22 3,1 3,3 6,7 NA 0/1 NA NA NA NA 6,5,5,6 GAAGACACCTGTTGCC/G PANCANCER NA FALSE chr7:44020406:44020407:GAAGACACCTGTTGCC:G indel 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 44044659 44044660 G C 244 432 0.564814814814815 MODIFIER DBNL ENSG00000136279 C upstream_gene_variant Transcript ENST00000411855 nonsense_mediated_decay NA 61 1 SNV HGNC HGNC:2696 2 ENSP00000390397 F8WBB2.57 UPI000198CD54 20 NA NA PASS SITE 352,314|127,117 NA NA 1 93 20,20 157,159 60,60 28 2.50 NA 93.37 NA FALSE 6.00 93 NA NA NA FALSE NA NA 662.96 20 44044659 HCC1395_HCC1395T 188 0.568 432 50,78 66,79 127,167 NA 0/1 NA NA NA NA 96,92,127,117 G/C PANCANCER NA FALSE DBNL chr7:44044659:44044660:G:C SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 44254518 44254519 A G 54 129 0.418604651162791 MODIFIER CAMK2B ENSG00000058404 G intron_variant Transcript ENST00000258682 protein_coding 5/19 ENST00000258682.10:c.341+24T>C NA -1 SNV HGNC HGNC:1461 1 A1 CCDS43573.1 ENSP00000258682 Q13554.220 UPI0000164A3F Q13554-8 1 20 NA NA PASS SITE 113,91|26,28 NA NA 1 93 20,20 164,166 60,60 34 1.96 NA 26.79 NA FALSE 6.00 93 NA NA NA FALSE NA NA 128.66 20 44254518 HCC1395_HCC1395T 75 0.402 129 19,15 32,17 51,34 NA 0/1 NA NA NA NA 44,31,26,28 A/G PANCANCER NA FALSE CAMK2B chr7:44254518:44254519:A:G SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 44878100 44878101 G A 219 725 0.302068965517241 MODIFIER PURB ENSG00000146676 A 3_prime_UTR_variant Transcript ENST00000395699 protein_coding 1/1 ENST00000395699.5:c.*6310C>T NA 7431 -1 SNV HGNC HGNC:9702 YES NM_033224.5 P1 CCDS5499.1 ENSP00000379051 Q96QR8.172 UPI000006F6CE 20 NA NA PASS SITE 433,527|93,126 NA NA 1 93 20,20 164,162 60,60 35 2.49 NA 92.50 NA FALSE 6.00 93 NA NA NA FALSE NA NA 539.12 20 44878100 HCC1395_HCC1395T 506 0.297 725 132,47 189,87 352,148 NA 0/1 NA NA NA NA 220,286,93,126 G/A PANCANCER NA FALSE PURB chr7:44878100:44878101:G:A SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 47833095 47833096 G A 12 62 0.193548387096774 MODERATE PKD1L1 ENSG00000158683 A missense_variant Transcript ENST00000289672 protein_coding 41/57 ENST00000289672.7:c.6332C>T ENSP00000289672.2:p.T2111I ENSP00000289672.2 p.T2111I 6358 6332 2111 T/I aCt/aTt rs1435246712 -1 SNV HGNC HGNC:18053 YES NM_138295.5 1 P4 CCDS34633.1 ENSP00000289672 Q8TDX9.168 UPI0000130FA9 Q8TDX9-1 1 tolerated(0.08) benign(0.01) PANTHER:PTHR10877 4.076e-06 0 2.942e-05 0 0 0 0 0 0 2.942e-05 gnomADe_AMR 20 NA NA PASS SITE 57,22|10,2 NA NA 1 79 33,36 176,191 60,60 30 1.40 NA 7.22 NA FALSE 6.00 45 NA NA NA FALSE NA NA 31.74 20 47833095 HCC1395_HCC1395T 50 0.220 62 17,3 19,7 38,10 NA 0/1 NA NA NA NA 37,13,10,2 G/A PANCANCER NA FALSE PKD1L1_p.T2111I chr7:47833095:47833096:G:A SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 48295642 48295643 C T 11 19 0.578947368421053 MODIFIER ABCA13 ENSG00000179869 T intron_variant Transcript ENST00000435803 protein_coding 20/61 ENST00000435803.6:c.8956-58C>T NA 1 SNV HGNC HGNC:14638 YES NM_152701.5 1 P1 CCDS47584.1 ENSP00000411096 A0A0A0MT16.56 UPI00043788D8 20 NA NA PASS SITE 20,2|10,1 NA NA 1 36 39,35 174,198 60,60 17 1.11 NA 3.61 NA FALSE 6.00 40 NA NA NA FALSE NA NA 33.00 20 48295642 HCC1395_HCC1395T 8 0.546 19 1,2 7,7 8,10 NA 0/1 NA NA NA NA 8,0,10,1 C/T PANCANCER NA FALSE ABCA13 chr7:48295642:48295643:C:T SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 55399981 55399982 T G 40 131 0.305343511450382 LOW LANCL2 ENSG00000132434 G synonymous_variant Transcript ENST00000254770 protein_coding 4/9 ENST00000254770.3:c.555T>G ENSP00000254770.2:p.V185= ENSP00000254770.2 p.V185= 1244 555 185 V gtT/gtG 1 SNV HGNC HGNC:6509 YES NM_018697.4 1 P1 CCDS5517.1 ENSP00000254770 Q9NS86.167 UPI000006F7D0 PDB-ENSP_mappings:6wq1.A&PDB-ENSP_mappings:6wq1.B&PDB-ENSP_mappings:6wq1.C&PDB-ENSP_mappings:6wq1.D&CDD:cd04794&PANTHER:PTHR12736&Gene3D:1.50.10.10&Pfam:PF05147&SMART:SM01260&Superfamily:SSF158745&AlphaFold_DB_import:AF-Q9NS86-F1 20 NA NA PASS SITE 119,54|29,11 NA NA 1 93 20,20 164,164 60,60 29 1.79 NA 17.76 NA FALSE 6.00 67 NA NA NA FALSE NA NA 103.18 20 55399981 HCC1395_HCC1395T 91 0.303 131 22,7 46,21 68,29 NA 0/1 NA NA NA NA 65,26,29,11 T/G PANCANCER NA FALSE LANCL2_p.V185= chr7:55399981:55399982:T:G SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 55887460 55887461 T A 69 206 0.33495145631068 MODIFIER ZNF713 ENSG00000178665 A upstream_gene_variant Transcript ENST00000411863 nonsense_mediated_decay NA 77 1 SNV HGNC HGNC:22043 5 ENSP00000416974 F8WD84.57 UPI0000D4D6E9 1 20 NA NA PASS SITE 146,220|29,40 NA NA 1 93 20,20 162,162 60,60 34 2.20 NA 46.91 NA FALSE 6.00 93 NA NA NA FALSE NA NA 162.79 20 55887460 HCC1395_HCC1395T 137 0.322 206 42,27 47,16 100,47 NA 0/1 NA NA NA NA 50,87,29,40 T/A PANCANCER NA FALSE ZNF713 chr7:55887460:55887461:T:A SNV 2:1 chr7:26183674:57472903:2:1:1 TRUE NA 0.96 +chr7 73469636 73469637 G C 59 165 0.357575757575758 HIGH BAZ1B ENSG00000009954 C stop_gained Transcript ENST00000339594 protein_coding 9/20 ENST00000339594.9:c.2747C>G ENSP00000342434.4:p.S916* ENSP00000342434.4 p.S916* 3107 2747 916 S/* tCa/tGa COSV59995276 -1 SNV HGNC HGNC:961 YES NM_032408.4 1 P1 CCDS5549.1 ENSP00000342434 Q9UIG0.209 UPI0000126731 Q9UIG0-1 1 AlphaFold_DB_import:AF-Q9UIG0-F1&Pfam:PF15613&PANTHER:PTHR46802 1 1 20 NA NA PASS SITE 83,152|20,39 NA NA 1 93 20,37 175,183 60,60 22 1.95 NA 26.19 NA FALSE 6.00 93 NA NA NA FALSE NA NA 167.36 20 73469636 HCC1395_HCC1395T 106 0.372 165 30,14 44,26 78,46 NA 0/1 NA NA NA NA 35,71,20,39 G/C PANCANCER NA FALSE BAZ1B_p.S916* chr7:73469636:73469637:G:C SNV 2:1 chr7:66399848:75052639:2:1:1 TRUE NA 0.96 +chr7 73865621 73865622 G C 23 67 0.343283582089552 LOW TMEM270 ENSG00000175877 C synonymous_variant Transcript ENST00000320531 protein_coding 3/3 ENST00000320531.3:c.546G>C ENSP00000316775.2:p.L182= ENSP00000316775.2 p.L182= 582 546 182 L ctG/ctC COSV57638442 1 SNV HGNC HGNC:23018 YES NM_182504.4 1 P1 CCDS43597.1 ENSP00000316775 Q6UE05.116 UPI00001408E5 Q6UE05-1 1 AlphaFold_DB_import:AF-Q6UE05-F1&Pfam:PF15164&PANTHER:PTHR37369&Low_complexity_(Seg):seg 1 1 20 NA NA PASS SITE 72,53|15,8 NA NA 1 93 20,20 146,146 60,60 33 1.73 NA 15.35 NA FALSE 6.00 68 NA NA NA FALSE NA NA 57.84 20 73865621 HCC1395_HCC1395T 44 0.354 67 9,4 21,11 30,16 NA 0/1 NA NA NA NA 25,19,15,8 G/C PANCANCER NA FALSE TMEM270_p.L182= chr7:73865621:73865622:G:C SNV 2:1 chr7:66399848:75052639:2:1:1 TRUE NA 0.96 +chr7 74189610 74189611 G C 15 29 0.517241379310345 MODIFIER EIF4H ENSG00000106682 C intron_variant Transcript ENST00000265753 protein_coding 2/6 ENST00000265753.13:c.248-63G>C NA 1 SNV HGNC HGNC:12741 YES NM_022170.2 2 CCDS5564.1 ENSP00000265753 Q15056.210 UPI000012D373 Q15056-1 1 20 NA NA PASS SITE 25,0|15,0 NA NA 1 35 39,40 231,226 60,60 18 1.11 NA 3.31 NA FALSE 6.00 87 NA NA NA FALSE NA NA 56.50 20 74189610 HCC1395_HCC1395T 14 0.516 29 4,9 10,6 14,15 NA 0/1 NA NA NA NA 14,0,15,0 G/C PANCANCER NA FALSE EIF4H chr7:74189610:74189611:G:C SNV 2:1 chr7:66399848:75052639:2:1:1 TRUE NA 0.96 +chr7 74601327 74601328 G T 53 150 0.353333333333333 MODIFIER GTF2IRD1 ENSG00000006704 T intron_variant Transcript ENST00000265755 protein_coding 26/26 ENST00000265755.7:c.2811+147G>T NA 1 SNV HGNC HGNC:4661 1 CCDS5571.1 ENSP00000265755 Q9UHL9.198 UPI000012AE30 Q9UHL9-1 1 20 NA NA PASS SITE 125,111|28,25 NA NA 1 93 20,20 166,160 60,60 33 2.03 NA 30.91 NA FALSE 6.00 93 NA NA NA FALSE NA NA 128.48 20 74601327 HCC1395_HCC1395T 97 0.359 150 29,15 36,21 67,37 NA 0/1 NA NA NA NA 56,41,28,25 G/T PANCANCER NA FALSE GTF2IRD1 chr7:74601327:74601328:G:T SNV 2:1 chr7:66399848:75052639:2:1:1 TRUE NA 0.96 +chr7 75535086 75535087 G C 207 648 0.319444444444444 MODIFIER HIP1 ENSG00000127946 C 3_prime_UTR_variant Transcript ENST00000336926 protein_coding 31/31 ENST00000336926.11:c.*3086C>G NA 6221 COSV61187475 -1 SNV HGNC HGNC:4913 YES NM_005338.7 1 P1 CCDS34669.1 ENSP00000336747 O00291.214 UPI000013D65F O00291-1 1 1 1 20 NA NA PASS SITE 325,399|89,118 NA NA 1 93 20,20 170,170 60,60 36 2.30 NA 59.29 NA FALSE 6.00 93 NA NA NA FALSE NA NA 543.98 20 75535086 HCC1395_HCC1395T 441 0.318 648 108,53 191,87 315,146 NA 0/1 NA NA NA NA 201,240,89,118 G/C PANCANCER NA FALSE HIP1 chr7:75535086:75535087:G:C SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 77600799 77600800 C T 16 43 0.372093023255814 MODERATE PTPN12 ENSG00000127947 T missense_variant Transcript ENST00000248594 protein_coding 8/18 ENST00000248594.11:c.688C>T ENSP00000248594.6:p.H230Y ENSP00000248594.6 p.H230Y 940 688 230 H/Y Cat/Tat COSV50378393 1 SNV HGNC HGNC:9645 YES NM_002835.4 1 P1 CCDS5592.1 ENSP00000248594 Q05209.206 UPI000013CC4C Q05209-1 1 deleterious(0) probably_damaging(0.999) PDB-ENSP_mappings:5hde.A&PDB-ENSP_mappings:5j8r.A&PDB-ENSP_mappings:5j8r.B&PDB-ENSP_mappings:5j8r.C&PDB-ENSP_mappings:5j8r.D&CDD:cd14604&PIRSF:PIRSF000932&Gene3D:3.90.190.10&Pfam:PF00102&SMART:SM00404&SMART:SM00194&Superfamily:SSF52799&PROSITE_profiles:PS50056&PROSITE_profiles:PS50055&PANTHER:PTHR45983&PROSITE_patterns:PS00383&Prints:PR00700&AlphaFold_DB_import:AF-Q05209-F1 1 1 20 NA NA PASS SITE 5,48|0,16 NA NA 1 91 41,34 191,205 60,60 27 1.39 NA 6.92 NA FALSE 6.00 60 NA NA NA FALSE NA NA 48.76 20 77600799 HCC1395_HCC1395T 27 0.386 43 10,5 15,11 26,16 NA 0/1 NA NA NA NA 2,25,0,16 C/T PANCANCER NA FALSE PTPN12_p.H230Y chr7:77600799:77600800:C:T SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 82908983 82908984 C G 163 381 0.427821522309711 MODERATE PCLO ENSG00000186472 G missense_variant Transcript ENST00000333891 protein_coding 8/25 ENST00000333891.14:c.13331G>C ENSP00000334319.8:p.W4444S ENSP00000334319.8 p.W4444S 13623 13331 4444 W/S tGg/tCg -1 SNV HGNC HGNC:13406 YES NM_033026.6 2 P1 CCDS47630.1 ENSP00000334319 Q9Y6V0.201 UPI0001573469 Q9Y6V0-5 1 PANTHER:PTHR14113 20 NA NA PASS SITE 186,201|78,85 NA NA 1 93 20,20 164,162 60,60 30 2.07 NA 34.92 NA FALSE 6.00 93 NA NA NA FALSE NA NA 411.95 20 82908983 HCC1395_HCC1395T 218 0.424 381 45,44 90,59 147,108 NA 0/1 NA NA NA NA 104,114,78,85 C/G PANCANCER NA FALSE PCLO_p.W4444S chr7:82908983:82908984:C:G SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 82916603 82916604 C A 90 475 0.189473684210526 MODERATE PCLO ENSG00000186472 A missense_variant Transcript ENST00000333891 protein_coding 7/25 ENST00000333891.14:c.11383G>T ENSP00000334319.8:p.D3795Y ENSP00000334319.8 p.D3795Y 11675 11383 3795 D/Y Gat/Tat -1 SNV HGNC HGNC:13406 YES NM_033026.6 2 P1 CCDS47630.1 ENSP00000334319 Q9Y6V0.201 UPI0001573469 Q9Y6V0-5 1 Coiled-coils_(Ncoils):Coil&PANTHER:PTHR14113 20 NA NA PASS SITE 293,317|45,45 NA NA 1 93 20,20 171,171 60,60 33 2.22 NA 48.11 NA FALSE 6.00 74 NA NA NA FALSE NA NA 211.82 20 82916603 HCC1395_HCC1395T 385 0.198 475 97,19 164,43 273,67 NA 0/1 NA NA NA NA 179,206,45,45 C/A PANCANCER NA FALSE PCLO_p.D3795Y chr7:82916603:82916604:C:A SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 86644321 86644322 G T 98 119 0.823529411764706 MODIFIER GRM3 ENSG00000198822 T 5_prime_UTR_variant Transcript ENST00000361669 protein_coding 1/6 ENST00000361669.7:c.-692G>T NA 413 1 SNV HGNC HGNC:4595 YES NM_000840.3 1 P1 CCDS5600.1 ENSP00000355316 Q14832.189 A4D1D0.138 UPI0000153EFC Q14832-1 1 20 NA NA PASS SITE 37,36|49,49 NA NA 1 93 20,20 177,172 60,60 24 1.60 NA 11.44 NA FALSE 6.00 93 NA NA NA FALSE NA NA 287.34 20 86644321 HCC1395_HCC1395T 21 0.818 119 5,32 8,33 15,71 NA 0/1 NA NA NA NA 10,11,49,49 G/T PANCANCER TRUE FALSE GRM3 chr7:86644321:86644322:G:T SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 92077867 92077868 G C 25 58 0.431034482758621 MODERATE AKAP9 ENSG00000127914 C missense_variant Transcript ENST00000356239 protein_coding 30/50 ENST00000356239.8:c.6937G>C ENSP00000348573.3:p.D2313H ENSP00000348573.3 p.D2313H 7175 6937 2313 D/H Gat/Cat COSV62361271 1 SNV HGNC HGNC:379 YES NM_005751.5 1 P4 CCDS5622.1 ENSP00000348573 Q99996.210 UPI000002A38D Q99996-2 1 deleterious_low_confidence(0) probably_damaging(0.999) Coiled-coils_(Ncoils):Coil&PANTHER:PTHR44981 1 1 20 NA NA PASS SITE 7,53|2,23 NA NA 1 93 39,39 199,212 60,60 17 1.41 NA 7.22 NA FALSE 6.00 93 NA NA NA FALSE NA NA 86.32 20 92077867 HCC1395_HCC1395T 33 0.439 58 7,9 21,13 31,24 NA 0/1 NA NA NA NA 2,31,2,23 G/C PANCANCER NA FALSE AKAP9_p.D2313H chr7:92077867:92077868:G:C SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 94427866 94427867 CCACCCAGAGTGGAGCAGTGGTAGGTCAAGATGTCCA C 4 345 0.0115942028985507 HIGH COL1A2 ENSG00000164692 - splice_donor_variant&splice_donor_5th_base_variant&coding_sequence_variant&intron_variant Transcript ENST00000297268 protein_coding 49/52 49/51 ENST00000297268.11:c.3508_3526+17del NA 3645-? 3508-? 1170-? 1 deletion HGNC HGNC:2198 YES NM_000089.4 1 P1 CCDS34682.1 ENSP00000297268 P08123.240 A0A0S2Z3H5.37 UPI00003B0CFC 1 20 NA NA PASS SITE 198,278|2,2 NA NA 1 93 20,20 170,192 60,60 37 1.95 NA 26.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 11.28 20 94427866 HCC1395_HCC1395T 341 0.014 345 59,0 79,2 218,2 NA 0/1 NA NA NA NA 141,200,2,2 CCACCCAGAGTGGAGCAGTGGTAGGTCAAGATGTCCA/C PANCANCER NA FALSE COL1A2 chr7:94427866:94427867:CCACCCAGAGTGGAGCAGTGGTAGGTCAAGATGTCCA:C indel 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 97006044 97006045 G C 72 179 0.402234636871508 MODIFIER DLX6-AS1 ENSG00000231764 C intron_variant&non_coding_transcript_variant Transcript ENST00000430027 lncRNA 1/2 ENST00000430027.3:n.141+7881C>G NA -1 SNV HGNC HGNC:37151 YES 2 20 NA NA PASS SITE 88,114|31,41 NA NA 1 93 20,20 154,159 60,60 36 1.82 NA 19.23 NA FALSE 6.00 93 NA NA NA FALSE NA NA 179.82 20 97006044 HCC1395_HCC1395T 107 0.407 179 17,20 29,11 69,47 NA 0/1 NA NA NA NA 45,62,31,41 G/C PANCANCER NA FALSE DLX6-AS1 chr7:97006044:97006045:G:C SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 98953141 98953142 G C 60 195 0.307692307692308 MODIFIER TRRAP ENSG00000196367 C intron_variant Transcript ENST00000355540 protein_coding 37/70 ENST00000355540.7:c.5389-26G>C NA 1 SNV HGNC HGNC:12347 1 CCDS5659.1 ENSP00000347733 Q9Y4A5.211 UPI0000070329 Q9Y4A5-2 1 20 NA NA PASS SITE 144,73|40,20 NA NA 1 93 20,23 167,171 60,60 31 1.78 NA 17.71 NA FALSE 6.00 93 NA NA NA FALSE NA NA 163.99 20 98953141 HCC1395_HCC1395T 135 0.325 195 41,18 54,26 97,46 NA 0/1 NA NA NA NA 90,45,40,20 G/C PANCANCER TRUE FALSE TRRAP chr7:98953141:98953142:G:C SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 100127573 100127574 G C 102 258 0.395348837209302 MODIFIER CNPY4 ENSG00000166997 C downstream_gene_variant Transcript ENST00000262932 protein_coding NA COSV53542251 2065 1 SNV HGNC HGNC:28631 YES NM_152755.2 1 P1 CCDS34701.1 ENSP00000262932 Q8N129.135 UPI000003B115 1 1 20 NA NA PASS SITE 135,156|41,61 NA NA 1 93 20,36 161,172 60,60 38 1.99 NA 28.89 NA FALSE 6.00 93 NA NA NA FALSE NA NA 294.38 20 100127573 HCC1395_HCC1395T 156 0.417 258 52,35 37,28 109,78 NA 0/1 NA NA NA NA 67,89,41,61 G/C PANCANCER NA FALSE CNPY4 chr7:100127573:100127574:G:C SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 100188780 100188781 C T 208 552 0.376811594202899 MODIFIER STAG3 ENSG00000066923 T intron_variant Transcript ENST00000317296 protein_coding 6/33 ENST00000317296.9:c.511-32C>T NA 1 SNV HGNC HGNC:11356 1 P3 CCDS34703.1 ENSP00000319318 Q9UJ98.165 UPI000020F6E0 Q9UJ98-1 1 20 NA NA PASS SITE 306,269|116,92 NA NA 1 93 20,20 161,168 60,60 29 2.22 NA 49.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 537.91 20 100188780 HCC1395_HCC1395T 344 0.384 552 74,52 147,91 238,148 NA 0/1 NA NA NA NA 186,158,116,92 C/T PANCANCER NA FALSE STAG3 chr7:100188780:100188781:C:T SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 100466864 100466865 GGGACACGGGGACATTAAAGCTGCATA G 99 534 0.185393258426966 MODIFIER TSC22D4 ENSG00000166925 - 3_prime_UTR_variant Transcript ENST00000300181 protein_coding 5/5 ENST00000300181.7:c.*69_*94del NA 1947-1972 -1 deletion HGNC HGNC:21696 YES NM_030935.5 1 P1 CCDS5695.1 ENSP00000300181 Q9Y3Q8.187 UPI0000001C0B Q9Y3Q8-1 20 NA NA PASS SITE 432,398|52,47 NA NA 1 93 20,39 153,182 60,60 38 2.39 NA 72.78 NA FALSE 6.00 93 NA NA NA FALSE NA NA 372.41 20 100466864 HCC1395_HCC1395T 435 0.203 534 86,29 117,27 273,68 NA 0/1 NA NA NA NA 231,204,52,47 GGGACACGGGGACATTAAAGCTGCATA/G PANCANCER NA FALSE TSC22D4 chr7:100466864:100466865:GGGACACGGGGACATTAAAGCTGCATA:G indel 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 100478224 100478225 G C 58 155 0.374193548387097 MODIFIER TSC22D4 ENSG00000166925 C 5_prime_UTR_variant Transcript ENST00000300181 protein_coding 2/5 ENST00000300181.7:c.-186C>G NA 505 -1 SNV HGNC HGNC:21696 YES NM_030935.5 1 P1 CCDS5695.1 ENSP00000300181 Q9Y3Q8.187 UPI0000001C0B Q9Y3Q8-1 20 NA NA PASS SITE 88,108|28,30 NA NA 1 93 20,20 148,154 60,60 39 1.79 NA 18.01 NA FALSE 6.00 88 NA NA NA FALSE NA NA 134.93 20 100478224 HCC1395_HCC1395T 97 0.364 155 27,21 29,10 62,35 NA 0/1 NA NA NA NA 45,52,28,30 G/C PANCANCER NA FALSE TSC22D4 chr7:100478224:100478225:G:C SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 100479150 100479151 T A 59 276 0.213768115942029 MODIFIER NYAP1 ENSG00000166924 A upstream_gene_variant Transcript ENST00000300179 protein_coding NA 4777 1 SNV HGNC HGNC:22009 YES NM_173564.4 2 P1 CCDS5696.1 ENSP00000300179 Q6ZVC0.121 UPI00001C0A2E Q6ZVC0-1 20 NA NA PASS SITE 201,203|31,28 NA NA 1 93 20,20 157,160 60,60 30 2.08 NA 35.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 128.75 20 100479150 HCC1395_HCC1395T 217 0.213 276 54,21 77,17 143,38 NA 0/1 NA NA NA NA 110,107,31,28 T/A PANCANCER NA FALSE NYAP1 chr7:100479150:100479151:T:A SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 100648916 100648917 C T 34 98 0.346938775510204 MODIFIER ACTL6B ENSG00000077080 T intron_variant Transcript ENST00000160382 protein_coding 5/13 ENST00000160382.10:c.468-93G>A NA rs1441300992 -1 SNV HGNC HGNC:160 YES NM_016188.5 1 P1 CCDS5702.1 ENSP00000160382 O94805.177 UPI0000126725 1 20 NA NA PASS SITE 43,69|13,21 NA NA 1 93 20,20 168,172 60,60 39 1.51 NA 9.32 NA FALSE 6.00 89 NA NA NA FALSE NA NA 88.96 20 100648916 HCC1395_HCC1395T 64 0.371 98 16,12 21,9 43,25 NA 0/1 NA NA NA NA 23,41,13,21 C/T PANCANCER NA FALSE ACTL6B chr7:100648916:100648917:C:T SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 101215248 101215249 T A 21 105 0.2 MODIFIER PLOD3 ENSG00000106397 A intron_variant Transcript ENST00000223127 protein_coding 5/18 ENST00000223127.8:c.616-96A>T NA -1 SNV HGNC HGNC:9083 YES NM_001084.5 1 P1 CCDS5715.1 ENSP00000223127 O60568.197 UPI0000046664 1 20 NA NA PASS SITE 23,103|3,18 NA NA 1 93 37,36 188,197 60,60 15 1.57 NA 10.83 NA FALSE 6.00 93 NA NA NA FALSE NA NA 58.53 20 101215248 HCC1395_HCC1395T 84 0.228 105 24,8 34,9 70,20 NA 0/1 NA NA NA NA 17,67,3,18 T/A PANCANCER NA FALSE PLOD3 chr7:101215248:101215249:T:A SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 101314919 101314920 C G 13 53 0.245283018867925 MODIFIER IFT22 ENSG00000128581 G 3_prime_UTR_variant Transcript ENST00000315322 protein_coding 5/5 ENST00000315322.10:c.*215G>C NA 876 -1 SNV HGNC HGNC:21895 YES NM_022777.4 1 P1 CCDS5719.1 ENSP00000320359 Q9H7X7.148 A0A024QYV3.56 UPI000006DC5A Q9H7X7-1 20 NA NA PASS SITE 39,29|6,7 NA NA 1 56 20,20 185,192 60,60 28 1.30 NA 5.67 NA FALSE 6.00 27 NA NA NA FALSE NA NA 30.68 20 101314919 HCC1395_HCC1395T 40 0.250 53 12,1 14,7 29,9 NA 0/1 NA NA NA NA 23,17,6,7 C/G PANCANCER NA FALSE IFT22 chr7:101314919:101314920:C:G SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 101817586 101817587 C T 175 427 0.409836065573771 MODIFIER CUX1 ENSG00000257923 T upstream_gene_variant Transcript ENST00000292535 protein_coding NA rs1480118483 40 1 SNV HGNC HGNC:2557 YES NM_181552.4 1 A2 CCDS5721.1 ENSP00000292535 P39880.203 UPI0000246CDF P39880-1 1 20 NA NA PASS SITE 347,156|120,55 NA NA 1 93 20,20 166,169 60,60 26 2.26 NA 53.27 NA FALSE 6.00 93 NA NA NA FALSE NA NA 446.47 20 101817586 HCC1395_HCC1395T 252 0.397 427 76,51 105,69 185,122 NA 0/1 NA NA NA NA 177,75,120,55 C/T PANCANCER TRUE FALSE CUX1 chr7:101817586:101817587:C:T SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 102317256 102317257 A G 186 993 0.187311178247734 MODERATE SH2B2 ENSG00000160999 G missense_variant Transcript ENST00000444095 protein_coding 7/9 ENST00000444095.3:c.1256A>G ENSP00000401883.3:p.H419R ENSP00000401883.3 p.H419R 1512 1256 419 H/R cAc/cGc rs1418380985 1 SNV HGNC HGNC:17381 YES NM_001359228.2 2 P1 CCDS78264.2 ENSP00000401883 O14492.181 C9JK89.82 UPI000022D3DD O14492-1 deleterious(0) Gene3D:3.30.505.10&AlphaFold_DB_import:AF-O14492-F1&Pfam:PF00017&Prints:PR00401&PROSITE_profiles:PS50001&PANTHER:PTHR10872&SMART:SM00252&Superfamily:SSF55550&CDD:cd10411 20 NA NA PASS SITE 595,721|78,108 NA NA 1 93 20,20 158,159 60,60 34 2.53 NA 98.49 NA FALSE 6.00 93 NA NA NA FALSE NA NA 428.08 20 102317256 HCC1395_HCC1395T 807 0.194 993 233,60 249,57 536,128 NA 0/1 NA NA NA NA 351,456,78,108 A/G PANCANCER NA FALSE SH2B2_p.H419R chr7:102317256:102317257:A:G SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 108106624 108106625 GTCAAACACACTCTTTTTTTTTT G 12 31 0.387096774193548 MODIFIER LAMB4 ENSG00000091128 - intron_variant Transcript ENST00000205386 protein_coding 6/33 ENST00000205386.8:c.592-74_592-53del NA -1 deletion HGNC HGNC:6491 1 P1 CCDS34732.1 ENSP00000205386 A4D0S4.123 UPI0000198CD5 A4D0S4-1 20 NA NA PASS SITE 8,28|1,11 NA NA 1 37 34,39 213,224 60,60 39 1.13 NA 3.49 NA FALSE 6.00 93 NA NA NA FALSE NA NA 45.66 20 108106624 HCC1395_HCC1395T 19 0.402 31 3,3 5,1 17,11 NA 0/1 NA NA NA NA 3,16,1,11 GTCAAACACACTCTTTTTTTTTT/G PANCANCER NA FALSE LAMB4 chr7:108106624:108106625:GTCAAACACACTCTTTTTTTTTT:G indel 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 108573741 108573742 A T 11 652 0.0168711656441718 MODIFIER DNAJB9 ENSG00000128590 T 3_prime_UTR_variant Transcript ENST00000249356 protein_coding 3/3 ENST00000249356.4:c.*388A>T NA 1300 1 SNV HGNC HGNC:6968 YES NM_012328.3 1 P1 CCDS5752.1 ENSP00000249356 Q9UBS3.180 Q6FIF1.147 UPI000000D769 20 NA NA PASS SITE 497,411|7,4 NA NA 1 93 20,36 172,199 60,60 32 2.28 NA 56.23 NA FALSE 6.00 28 NA NA NA FALSE NA NA 17.26 20 108573741 HCC1395_HCC1395T 641 0.021 652 160,2 286,7 466,9 NA 0/1 NA NA NA NA 355,286,7,4 A/T PANCANCER NA FALSE DNAJB9 chr7:108573741:108573742:A:T SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 112342711 112342712 G C 77 177 0.435028248587571 MODERATE ZNF277 ENSG00000198839 C missense_variant Transcript ENST00000361822 protein_coding 12/12 ENST00000361822.8:c.1335G>C ENSP00000354501.3:p.L445F ENSP00000354501.3 p.L445F 1357 1335 445 L/F ttG/ttC COSV62466600 1 SNV HGNC HGNC:13070 YES NM_021994.3 1 P1 CCDS5755.2 ENSP00000354501 Q9NRM2.165 UPI00000437E2 deleterious(0) probably_damaging(0.998) AlphaFold_DB_import:AF-Q9NRM2-F1&PANTHER:PTHR13267 1 1 20 NA NA PASS SITE 74,117|29,48 NA NA 1 93 20,20 181,182 60,60 31 1.81 NA 18.92 NA FALSE 6.00 93 NA NA NA FALSE NA NA 215.90 20 112342711 HCC1395_HCC1395T 100 0.453 177 21,17 37,38 70,58 NA 0/1 NA NA NA NA 33,67,29,48 G/C PANCANCER NA FALSE ZNF277_p.L445F chr7:112342711:112342712:G:C SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 112821985 112821986 G T 32 215 0.148837209302326 MODERATE BMT2 ENSG00000164603 T missense_variant Transcript ENST00000297145 protein_coding 5/5 ENST00000297145.9:c.977C>A ENSP00000297145.4:p.T326K ENSP00000297145.4 p.T326K 1102 977 326 T/K aCa/aAa -1 SNV HGNC HGNC:26475 YES NM_152556.3 1 P1 CCDS43634.1 ENSP00000297145 Q1RMZ1.120 UPI000020F946 tolerated(0.07) benign(0.057) Gene3D:3.40.50.150&AlphaFold_DB_import:AF-Q1RMZ1-F1&HAMAP:MF_03044&PANTHER:PTHR21008 20 NA NA PASS SITE 141,113|17,15 NA NA 1 93 20,20 166,180 60,60 30 1.74 NA 16.25 NA FALSE 6.00 52 NA NA NA FALSE NA NA 72.35 20 112821985 HCC1395_HCC1395T 183 0.160 215 55,6 70,17 130,24 NA 0/1 NA NA NA NA 107,76,17,15 G/T PANCANCER NA FALSE BMT2_p.T326K chr7:112821985:112821986:G:T SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 115014479 115014480 C G 96 322 0.298136645962733 MODIFIER MDFIC ENSG00000135272 G intron_variant Transcript ENST00000393486 protein_coding 4/4 ENST00000393486.6:c.494-1209C>G NA 1 SNV HGNC HGNC:28870 YES NM_001166345.3 1 P1 CCDS55155.1 ENSP00000377126 Q9P1T7.143 UPI000006E384 Q9P1T7-2 1 20 NA NA PASS SITE 180,170|53,43 NA NA 1 93 20,20 155,158 60,60 38 1.90 NA 23.43 NA FALSE 6.00 93 NA NA NA FALSE NA NA 211.75 20 115014479 HCC1395_HCC1395T 226 0.289 322 36,24 97,32 139,56 NA 0/1 NA NA NA NA 120,106,53,43 C/G PANCANCER NA FALSE MDFIC chr7:115014479:115014480:C:G SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 120956238 120956239 CTCTTTTTCATTTGAAACA C 15 70 0.214285714285714 MODIFIER ING3 ENSG00000071243 - intron_variant Transcript ENST00000315870 protein_coding 4/11 ENST00000315870.10:c.267+619_267+636del NA 1 deletion HGNC HGNC:14587 YES NM_019071.3 1 P1 CCDS5778.1 ENSP00000320566 Q9NXR8.184 UPI00000373B3 Q9NXR8-1 4 20 NA NA PASS SITE 71,29|11,4 NA NA 1 93 39,40 245,256 60,60 21 1.67 NA 13.04 NA FALSE 6.00 93 NA NA NA FALSE NA NA 51.26 20 120956238 HCC1395_HCC1395T 55 0.227 70 10,3 28,11 54,15 NA 0/1 NA NA NA NA 40,15,11,4 CTCTTTTTCATTTGAAACA/C PANCANCER NA FALSE ING3 chr7:120956238:120956239:CTCTTTTTCATTTGAAACA:C indel 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 122304134 122304135 C T 12 573 0.0209424083769634 MODIFIER FEZF1 ENSG00000128610 T downstream_gene_variant Transcript ENST00000418046 protein_coding NA 197 -1 cds_end_NF SNV HGNC HGNC:22788 2 ENSP00000406919 C9J0C5.66 UPI000198CFDE 1 20 NA NA PASS SITE 425,446|5,7 NA NA 1 93 20,20 165,182 60,60 17 2.35 NA 64.97 NA FALSE 6.00 5 NA NA NA FALSE NA NA 17.08 20 122304134 HCC1395_HCC1395T 561 0.023 573 152,6 204,2 383,8 NA 0/1 NA NA NA NA 275,286,5,7 C/T PANCANCER NA FALSE FEZF1 chr7:122304134:122304135:C:T SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 123570897 123570898 A T 29 227 0.127753303964758 MODIFIER ASB15 ENSG00000146809 T intron_variant Transcript ENST00000451558 protein_coding 1/13 ENST00000451558.5:c.-443+3809A>T NA 1 SNV HGNC HGNC:19767 5 P1 CCDS34742.1 ENSP00000397655 Q8WXK1.160 A0A384NYV2.16 UPI000022D0FF 20 NA NA PASS SITE 191,100|19,10 NA NA 1 93 20,20 162,166 60,60 36 1.82 NA 19.47 NA FALSE 6.00 70 NA NA NA FALSE NA NA 59.44 20 123570897 HCC1395_HCC1395T 198 0.129 227 48,7 87,12 140,20 NA 0/1 NA NA NA NA 129,69,19,10 A/T PANCANCER NA FALSE ASB15 chr7:123570897:123570898:A:T SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 128815876 128815877 C G 30 180 0.166666666666667 MODERATE CCDC136 ENSG00000128596 G missense_variant Transcript ENST00000297788 protein_coding 16/18 ENST00000297788.9:c.3308C>G ENSP00000297788.4:p.S1103C ENSP00000297788.4 p.S1103C 3752 3308 1103 S/C tCt/tGt COSV52798737 1 SNV HGNC HGNC:22225 YES NM_022742.5 1 A2 CCDS47704.1 ENSP00000297788 Q96JN2.136 UPI0000E445DE Q96JN2-1 deleterious_low_confidence(0) possibly_damaging(0.453) Low_complexity_(Seg):seg&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-Q96JN2-F1 1 1 20 NA NA PASS SITE 148,134|16,14 NA NA 1 93 20,33 169,194 60,60 37 1.96 NA 26.74 NA FALSE 6.00 40 NA NA NA FALSE NA NA 77.24 20 128815876 HCC1395_HCC1395T 150 0.182 180 46,4 56,18 107,23 NA 0/1 NA NA NA NA 82,68,16,14 C/G PANCANCER NA FALSE CCDC136_p.S1103C chr7:128815876:128815877:C:G SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 128856685 128856686 G A 7 460 0.0152173913043478 MODIFIER FLNC ENSG00000128591 A intron_variant Transcript ENST00000325888 protein_coding 44/47 ENST00000325888.13:c.7384+35G>A NA rs1343619081 1 SNV HGNC HGNC:3756 YES NM_001458.5 1 P3 CCDS43644.1 ENSP00000327145 Q14315.227 UPI000006DE6D Q14315-1 1 4.027e-06 0 0 0 0 0 8.899e-06 0 0 8.899e-06 gnomADe_NFE 20 NA NA PASS SITE 359,407|4,3 NA NA 1 93 20,20 165,200 60,60 11 2.32 NA 61.01 NA FALSE 6.00 23 NA NA NA FALSE NA NA 9.13 20 128856685 HCC1395_HCC1395T 453 0.019 460 99,2 182,3 311,5 NA 0/1 NA NA NA NA 209,244,4,3 G/A PANCANCER NA FALSE FLNC chr7:128856685:128856686:G:A SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 129389571 129389572 G C 13 45 0.288888888888889 MODIFIER AHCYL2 ENSG00000158467 C intron_variant Transcript ENST00000325006 protein_coding 3/16 ENST00000325006.8:c.620-63G>C NA COSV61488701 1 SNV HGNC HGNC:22204 YES NM_015328.4 1 CCDS5812.1 ENSP00000315931 Q96HN2.168 UPI00001354E4 Q96HN2-1 1 1 20 NA NA PASS SITE 51,14|10,3 NA NA 1 91 37,38 190,190 60,60 42 1.46 NA 8.43 NA FALSE 6.00 57 NA NA NA FALSE NA NA 39.27 20 129389571 HCC1395_HCC1395T 32 0.324 45 8,7 16,3 24,11 NA 0/1 NA NA NA NA 23,9,10,3 G/C PANCANCER NA FALSE AHCYL2 chr7:129389571:129389572:G:C SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 130686475 130686476 G A 498 632 0.787974683544304 MODIFIER TSGA13 ENSG00000213265 A 5_prime_UTR_variant Transcript ENST00000356588 protein_coding 1/8 ENST00000356588.8:c.-364C>T NA 71 -1 SNV HGNC HGNC:12369 YES NM_052933.4 1 P1 CCDS5824.1 ENSP00000348996 Q96PP4.130 A0A024R769.44 UPI0000073CFB 20 NA NA PASS SITE 216,240|244,255 NA NA 1 93 20,20 164,168 60,60 35 0.909 NA 62.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 1433.00 20 130686475 HCC1395_HCC1395T 134 0.794 632 20,111 63,214 90,348 NA 0/1 NA NA NA NA 68,66,243,255 G/A PANCANCER NA FALSE TSGA13 chr7:130686475:130686476:G:A SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 131504508 131504509 G A 57 223 0.255605381165919 HIGH PODXL ENSG00000128567 A stop_gained&splice_region_variant Transcript ENST00000322985 protein_coding 8/8 ENST00000322985.9:c.1384C>T ENSP00000319782.9:p.Q462* ENSP00000319782.9 p.Q462* 1634 1384 462 Q/* Cag/Tag COSV59869758 -1 SNV HGNC HGNC:9171 1 A2 CCDS47714.1 ENSP00000319782 O00592.166 UPI00001B94DE O00592-2 1 AlphaFold_DB_import:AF-O00592-F1&Pfam:PF06365&PIRSF:PIRSF038143&PANTHER:PTHR12067 1 1 20 NA NA PASS SITE 120,170|21,36 NA NA 1 93 20,20 152,142 60,60 30 1.91 NA 23.78 NA FALSE 6.00 93 NA NA NA FALSE NA NA 128.58 20 131504508 HCC1395_HCC1395T 166 0.255 223 58,18 44,17 110,37 NA 0/1 NA NA NA NA 65,101,21,36 G/A PANCANCER NA FALSE PODXL_p.Q462* chr7:131504508:131504509:G:A SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 137577331 137577332 G A 90 111 0.810810810810811 MODIFIER DGKI ENSG00000157680 A intron_variant Transcript ENST00000288490 protein_coding 16/33 ENST00000288490.9:c.1699-47C>T NA -1 SNV HGNC HGNC:2855 5 CCDS5845.1 ENSP00000288490 O75912.188 UPI000012DD23 20 NA NA PASS SITE 48,58|43,47 NA NA 1 93 20,20 164,179 60,60 29 1.76 NA 16.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 229.48 20 137577331 HCC1395_HCC1395T 21 0.803 111 3,18 9,29 12,52 NA 0/1 NA NA NA NA 11,10,43,47 G/A PANCANCER NA FALSE DGKI chr7:137577331:137577332:G:A SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 138116854 138116855 C G 38 48 0.791666666666667 MODIFIER AKR1D1 ENSG00000122787 G 3_prime_UTR_variant Transcript ENST00000242375 protein_coding 9/9 ENST00000242375.8:c.*192C>G NA 1233 1 SNV HGNC HGNC:388 YES NM_005989.4 1 P1 CCDS5846.1 ENSP00000242375 P51857.178 UPI0000125764 P51857-1 1 20 NA NA PASS SITE 10,30|2,36 NA NA 1 77 38,39 195,239 60,60 25 1.44 NA 7.83 NA FALSE 6.00 93 NA NA NA FALSE NA NA 149.33 20 138116854 HCC1395_HCC1395T 10 0.780 48 4,14 6,21 10,38 NA 0/1 NA NA NA NA 1,9,2,36 C/G PANCANCER NA FALSE AKR1D1 chr7:138116854:138116855:C:G SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 138583927 138583928 C T 20 124 0.161290322580645 LOW TRIM24 ENSG00000122779 T synonymous_variant Transcript ENST00000343526 protein_coding 18/19 ENST00000343526.9:c.2871C>T ENSP00000340507.4:p.S957= ENSP00000340507.4 p.S957= 3161 2871 957 S tcC/tcT COSV58969752 1 SNV HGNC HGNC:11812 YES NM_015905.3 1 P4 CCDS5847.1 ENSP00000340507 O15164.219 UPI00000012CB O15164-1 1 PDB-ENSP_mappings:2yyn.A&PDB-ENSP_mappings:2yyn.B&PDB-ENSP_mappings:2yyn.C&PDB-ENSP_mappings:2yyn.D&PDB-ENSP_mappings:3o33.A&PDB-ENSP_mappings:3o33.B&PDB-ENSP_mappings:3o33.C&PDB-ENSP_mappings:3o33.D&PDB-ENSP_mappings:3o34.A&PDB-ENSP_mappings:3o35.A&PDB-ENSP_mappings:3o35.B&PDB-ENSP_mappings:3o36.A&PDB-ENSP_mappings:3o36.B&PDB-ENSP_mappings:3o37.A&PDB-ENSP_mappings:3o37.B&PDB-ENSP_mappings:3o37.C&PDB-ENSP_mappings:3o37.D&PDB-ENSP_mappings:4yab.A&PDB-ENSP_mappings:4yab.B&PDB-ENSP_mappings:4yad.A&PDB-ENSP_mappings:4yad.B&PDB-ENSP_mappings:4yat.A&PDB-ENSP_mappings:4yat.B&PDB-ENSP_mappings:4yax.A&PDB-ENSP_mappings:4yax.B&PDB-ENSP_mappings:4ybm.A&PDB-ENSP_mappings:4ybm.B&PDB-ENSP_mappings:4ybs.A&PDB-ENSP_mappings:4ybt.A&PDB-ENSP_mappings:4yc9.A&PDB-ENSP_mappings:4zql.A&PDB-ENSP_mappings:4zql.B&PDB-ENSP_mappings:5h1t.A&PDB-ENSP_mappings:5h1t.B&PDB-ENSP_mappings:5h1t.C&PDB-ENSP_mappings:5h1t.D&PDB-ENSP_mappings:5h1u.A&PDB-ENSP_mappings:5h1u.B&PDB-ENSP_mappings:5h1u.C&PDB-ENSP_mappings:5h1u.D&PDB-ENSP_mappings:5h1v.A&PDB-ENSP_mappings:5h1v.B&PDB-ENSP_mappings:7b9x.A&CDD:cd05502&Pfam:PF00439&Gene3D:1.20.920.10&SMART:SM00297&Superfamily:SSF47370&PROSITE_profiles:PS50014&PROSITE_patterns:PS00633&AlphaFold_DB_import:AF-O15164-F1 1 1 20 NA NA PASS SITE 102,55|13,7 NA NA 1 93 20,20 167,172 60,60 40 1.59 NA 11.05 NA FALSE 6.00 53 NA NA NA FALSE NA NA 44.42 20 138583927 HCC1395_HCC1395T 104 0.169 124 24,8 41,5 68,13 NA 0/1 NA NA NA NA 65,39,13,7 C/T PANCANCER NA FALSE TRIM24_p.S957= chr7:138583927:138583928:C:T SNV 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 140024672 140024673 TCAAAGATCA T 35 178 0.196629213483146 MODERATE PARP12 ENSG00000059378 - inframe_deletion Transcript ENST00000263549 protein_coding 12/12 ENST00000263549.8:c.1985_1993del ENSP00000263549.3:p.VIF662del ENSP00000263549.3 p.VIF662del 2089-2097 1985-1993 662-665 VIFE/E gTGATCTTTGag/gag -1 deletion HGNC HGNC:21919 YES NM_022750.4 1 P1 CCDS5857.1 ENSP00000263549 Q9H0J9.170 A4D1T0.128 UPI000006F644 PDB-ENSP_mappings:2pqf.A&PDB-ENSP_mappings:2pqf.B&PDB-ENSP_mappings:2pqf.C&PDB-ENSP_mappings:2pqf.D&PDB-ENSP_mappings:2pqf.E&PDB-ENSP_mappings:2pqf.F&Gene3D:3.90.228.10&PDB-ENSP_mappings:6v3w.A&AlphaFold_DB_import:AF-Q9H0J9-F1&Pfam:PF00644&PROSITE_profiles:PS51059&PANTHER:PTHR45740&Superfamily:SSF56399&CDD:cd01439 20 NA NA PASS SITE 126,132|14,21 NA NA 1 93 20,20 162,167 60,60 33 1.90 NA 23.40 NA FALSE 6.00 93 NA NA NA FALSE NA NA 130.53 20 140024672 HCC1395_HCC1395T 143 0.211 178 34,7 40,10 93,24 NA 0/1 NA NA NA NA 71,72,14,21 TCAAAGATCA/T PANCANCER NA FALSE PARP12_p.VIF662del chr7:140024672:140024673:TCAAAGATCA:T indel 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 142482926 142482928 TC GA 7 692 0.0101156069364162 MODERATE TRBV5-5 ENSG00000211725 GA missense_variant Transcript ENST00000390372 TR_V_gene 2/2 ENST00000390372.3:c.250_251inv ENSP00000374895.3:p.S84E ENSP00000374895.3 p.S84E 257-258 250-251 84 S/E TCa/GAa 1 cds_end_NF substitution HGNC HGNC:12222 YES P1 ENSP00000374895 A0A597.81 UPI00001140E8 deleterious(0) probably_damaging(0.945) AlphaFold_DB_import:AF-A0A597-F1 20 NA NA PASS SITE 509,485|4,3 NA NA 1 93 20,20 158,157 60,60 46 2.30 NA 58.69 NA FALSE 6.00 15 NA NA NA FALSE NA NA 19.66 20 142482926 HCC1395_HCC1395T 685 0.011 692 247,3 165,1 437,4 NA 0/1 NA NA NA NA 353,332,4,3 TC/GA PANCANCER NA FALSE TRBV5-5_p.S84E chr7:142482926:142482928:TC:GA indel 4:1 chr7:75533848:144623121:4:1:1 NA NA 0.96 +chr7 150795289 150795290 C T 257 326 0.788343558282209 MODIFIER TMEM176B ENSG00000106565 T intron_variant Transcript ENST00000326442 protein_coding 2/6 ENST00000326442.10:c.204+1077G>A NA -1 SNV HGNC HGNC:29596 YES NM_001101312.2 1 P1 CCDS5908.1 ENSP00000318409 Q3YBM2.123 A0A090N7V7.44 UPI000013C82B Q3YBM2-1 20 NA NA PASS SITE 116,100|133,124 NA NA 1 93 20,20 163,164 60,60 32 1.99 NA 28.55 NA FALSE 6.00 93 NA NA NA FALSE NA NA 714.34 20 150795289 HCC1395_HCC1395T 69 0.785 326 21,62 23,101 46,171 NA 0/1 NA NA NA NA 37,32,133,124 C/T PANCANCER NA FALSE TMEM176B chr7:150795289:150795290:C:T SNV 5:1 chr7:144765858:152852022:5:1:1 NA NA 0.96 +chr7 150856421 150856422 G A 17 597 0.0284757118927973 MODIFIER AOC1 ENSG00000002726 A intron_variant Transcript ENST00000360937 protein_coding 1/4 ENST00000360937.9:c.-16-34G>A NA rs1308258765 1 SNV HGNC HGNC:80 YES NM_001091.4 1 P4 CCDS43679.1 ENSP00000354193 P19801.213 UPI00001AF136 P19801-1 20 NA NA PASS SITE 496,292|11,6 NA NA 1 93 20,20 164,152 60,60 35 2.14 NA 40.94 NA FALSE 6.00 49 NA NA NA FALSE NA NA 25.06 20 150856421 HCC1395_HCC1395T 580 0.029 597 159,5 224,6 403,11 NA 0/1 NA NA NA NA 375,205,11,6 G/A PANCANCER NA FALSE AOC1 chr7:150856421:150856422:G:A SNV 5:1 chr7:144765858:152852022:5:1:1 NA NA 0.96 +chr7 151000647 151000648 G A 34 158 0.215189873417722 MODIFIER NOS3 ENSG00000164867 A intron_variant Transcript ENST00000297494 protein_coding 10/26 ENST00000297494.8:c.1233+48G>A NA 1 SNV HGNC HGNC:7876 YES NM_000603.5 1 P1 CCDS5912.1 ENSP00000297494 P29474.248 UPI000013E417 P29474-1 1 20 NA NA PASS SITE 88,100|16,18 NA NA 1 93 20,20 156,169 60,60 32 1.66 NA 13.19 NA FALSE 6.00 88 NA NA NA FALSE NA NA 71.35 20 151000647 HCC1395_HCC1395T 124 0.209 158 31,10 48,9 82,21 NA 0/1 NA NA NA NA 61,63,16,18 G/A PANCANCER NA FALSE NOS3 chr7:151000647:151000648:G:A SNV 5:1 chr7:144765858:152852022:5:1:1 NA NA 0.96 +chr7 151115391 151115392 G A 10 53 0.188679245283019 LOW AGAP3 ENSG00000133612 A synonymous_variant Transcript ENST00000335367 protein_coding 1/9 ENST00000335367.7:c.621G>A ENSP00000335589.3:p.L207= ENSP00000335589.3 p.L207= 714 621 207 L ctG/ctA rs1368208483 1 SNV HGNC HGNC:16923 1 CCDS78287.1 ENSP00000335589 E7ESL9.80 UPI0000246FFA MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-E7ESL9-F1 0 0 0 0 0 0 gnomADe_AMR&gnomADe_NFE&gnomADe_OTH&gnomADe_SAS 20 NA NA PASS SITE 41,57|5,5 NA NA 1 93 20,20 144,146 60,60 45 1.57 NA 10.84 NA FALSE 6.00 29 NA NA NA FALSE NA NA 17.63 20 151115391 HCC1395_HCC1395T 43 0.194 53 7,2 12,3 24,5 NA 0/1 NA NA NA NA 19,24,5,5 G/A PANCANCER NA FALSE AGAP3_p.L207= chr7:151115391:151115392:G:A SNV 5:1 chr7:144765858:152852022:5:1:1 NA NA 0.96 +chr7 154587903 154587904 G A 59 426 0.13849765258216 MODIFIER DPP6 ENSG00000130226 A intron_variant Transcript ENST00000332007 protein_coding 5/25 ENST00000332007.7:c.441+20987G>A NA rs267601431 1 SNV HGNC HGNC:3010 1 P1 CCDS75684.1 ENSP00000328226 P42658.189 UPI000059DA00 P42658-2 1 20 NA NA PASS SITE 198,292|22,37 NA NA 1 93 20,20 173,177 60,60 29 1.92 NA 24.64 NA FALSE 6.00 90 NA NA NA FALSE NA NA 133.96 20 154587903 HCC1395_HCC1395T 367 0.141 426 102,14 137,23 268,43 NA 0/1 NA NA NA NA 144,223,22,37 G/A PANCANCER NA FALSE DPP6 chr7:154587903:154587904:G:A SNV 7:1 chr7:154587524:159110050:7:1:1 NA NA 0.96 +chr7 155395399 155395400 C T 45 227 0.198237885462555 MODIFIER LINC03010 ENSG00000218672 T non_coding_transcript_exon_variant Transcript ENST00000401499 lncRNA 2/2 ENST00000401499.1:n.594C>T NA 594 1 SNV HGNC HGNC:56135 YES 1 20 NA NA PASS SITE 140,152|22,23 NA NA 1 93 20,33 176,175 60,60 26 1.88 NA 22.58 NA FALSE 6.00 88 NA NA NA FALSE NA NA 109.42 20 155395399 HCC1395_HCC1395T 182 0.211 227 39,14 82,19 134,35 NA 0/1 NA NA NA NA 83,99,22,23 C/T PANCANCER NA FALSE LINC03010 chr7:155395399:155395400:C:T SNV 7:1 chr7:154587524:159110050:7:1:1 NA NA 0.96 +chr7 155776266 155776267 A G 113 760 0.148684210526316 MODIFIER RBM33 ENSG00000184863 G 3_prime_UTR_variant Transcript ENST00000341148 protein_coding 5/5 ENST00000341148.7:c.*1225A>G NA 1839 rs539003179 1 SNV HGNC HGNC:27223 1 A2 ENSP00000341583 A0A0C4DFS3.40 UPI0000251F77 0.0004 0.0015 0 0 0 0 2.628e-05 9.649e-05 0 0 0 0 0 0 0 0 0 0.0015 AFR 20 NA NA PASS SITE 441,444|58,55 NA NA 1 93 20,20 171,168 60,60 36 2.19 NA 45.75 NA FALSE 6.00 93 NA NA NA FALSE NA NA 239.32 20 155776266 HCC1395_HCC1395T 647 0.133 760 174,27 261,43 474,72 NA 0/1 NA NA NA NA 324,323,58,55 A/G PANCANCER NA FALSE RBM33 chr7:155776266:155776267:A:G SNV 7:1 chr7:154587524:159110050:7:1:1 NA NA 0.96 +chr7 157618002 157618003 C G 62 536 0.115671641791045 MODIFIER PTPRN2 ENSG00000155093 G intron_variant Transcript ENST00000389413 protein_coding 14/21 ENST00000389413.7:c.2257+3360G>C NA -1 SNV HGNC HGNC:9677 1 CCDS5949.1 ENSP00000374064 Q92932.194 UPI00001AF931 Q92932-2 20 NA NA PASS SITE 281,327|30,32 NA NA 1 93 20,20 179,176 60,60 32 1.99 NA 28.25 NA FALSE 6.00 83 NA NA NA FALSE NA NA 138.23 20 157618002 HCC1395_HCC1395T 474 0.120 536 133,12 178,28 330,44 NA 0/1 NA NA NA NA 221,253,30,32 C/G PANCANCER NA FALSE PTPRN2 chr7:157618002:157618003:C:G SNV 7:1 chr7:154587524:159110050:7:1:1 NA NA 0.96 +chr8 6757635 6757636 C G 115 115 1 MODIFIER AGPAT5 ENSG00000155189 G 3_prime_UTR_variant Transcript ENST00000285518 protein_coding 8/8 ENST00000285518.11:c.*247C>G NA 1369 1 SNV HGNC HGNC:20886 YES NM_018361.5 1 P1 CCDS34796.1 ENSP00000285518 Q9NUQ2.170 A0A024R640.56 UPI000003B4CB 21 NA NA PASS SITE 47,55|45,70 NA NA 1 93 39,39 198,197 60,60 30 1.95 NA 26.05 NA FALSE 6.00 93 NA NA NA FALSE NA NA 433.18 21 6757635 HCC1395_HCC1395T 0 0.990 115 0,27 0,61 0,99 NA 0/1 NA NA NA NA 0,0,45,70 C/G PANCANCER NA FALSE AGPAT5 chr8:6757635:6757636:C:G SNV 2:0 chr8:219366:38516406:2:0:1 TRUE NA 0.96 +chr8 8020044 8020045 A G 9 552 0.016304347826087 MODIFIER FAM90A11P ENSG00000233115 G upstream_gene_variant Transcript ENST00000518378 protein_coding NA 3033 -1 SNV HGNC HGNC:32259 YES P1 ENSP00000514266 A0A8V8TNH8.1 UPI000041944D 21 NA NA PASS SITE 657,254|7,2 NA NA 1 93 20,38 149,164 35,35 24 2.44 NA 80.88 NA FALSE 6.00 31 NA NA NA FALSE NA NA 12.28 21 8020044 HCC1395_HCC1395T 543 0.020 552 165,3 219,4 390,7 NA 0/1 NA NA NA NA 390,153,7,2 A/G PANCANCER NA FALSE FAM90A11P chr8:8020044:8020045:A:G SNV 2:0 chr8:219366:38516406:2:0:1 TRUE NA 0.96 +chr8 12388099 12388100 G T 19 55 0.345454545454545 MODIFIER FAM66A ENSG00000227888 T intron_variant&non_coding_transcript_variant Transcript ENST00000602658 lncRNA 5/5 ENST00000602658.1:n.500+80G>T NA 1 SNV HGNC HGNC:30444 YES 5 21 NA NA PASS SITE 26,56|4,15 NA NA 1 93 23,38 179,184 60,60 24 1.55 NA 10.23 NA FALSE 6.00 72 NA NA NA FALSE NA NA 57.05 21 12388099 HCC1395_HCC1395T 36 0.381 55 8,5 14,8 28,17 NA 0/1 NA NA NA NA 11,25,4,15 G/T PANCANCER NA FALSE FAM66A chr8:12388099:12388100:G:T SNV 2:0 chr8:219366:38516406:2:0:1 TRUE NA 0.96 +chr8 20204334 20204335 T C 10 10 1 MODIFIER ATP6V1B2 ENSG00000147416 C intron_variant Transcript ENST00000276390 protein_coding 1/13 ENST00000276390.7:c.137-150T>C NA 1 SNV HGNC HGNC:854 YES NM_001693.4 1 P1 CCDS6014.1 ENSP00000276390 P21281.217 A0A140VK65.36 UPI00001380AD 1 21 NA NA PASS SITE 10,0|5,5 NA NA 1 40 35,38 215,237 60,60 25 1.07 NA 3.01 NA FALSE 6.00 80 NA NA NA FALSE NA NA 41.29 21 20204334 HCC1395_HCC1395T 0 0.917 10 0,2 0,8 0,10 NA 0/1 NA NA NA NA 0,0,5,5 T/C PANCANCER NA FALSE ATP6V1B2 chr8:20204334:20204335:T:C SNV 2:0 chr8:219366:38516406:2:0:1 TRUE NA 0.96 +chr8 23368189 23368190 TGGCCACGTTGGCGGGGGCCTG T 174 174 1 MODERATE LOXL2 ENSG00000134013 - inframe_deletion Transcript ENST00000389131 protein_coding 2/14 ENST00000389131.8:c.142_162del ENSP00000373783.3:p.Q48_A54del ENSP00000373783.3 p.Q48_A54del 392-412 142-162 48-54 QAPANVA/- CAGGCCCCCGCCAACGTGGCC/- -1 deletion HGNC HGNC:6666 YES NM_002318.3 1 P1 CCDS34864.1 ENSP00000373783 Q9Y4K0.197 UPI000012E7AB PANTHER:PTHR45817&Gene3D:3.10.250.10&AlphaFold_DB_import:AF-Q9Y4K0-F1 21 NA NA PASS SITE 203,194|84,90 NA NA 1 93 20,20 157,182 60,60 29 2.41 NA 75.61 NA FALSE 6.00 93 NA NA NA FALSE NA NA 761.72 21 23368189 HCC1395_HCC1395T 0 0.992 174 0,47 0,56 0,125 NA 0/1 NA NA NA NA 0,0,84,90 TGGCCACGTTGGCGGGGGCCTG/T PANCANCER NA FALSE LOXL2_p.Q48_A54del chr8:23368189:23368190:TGGCCACGTTGGCGGGGGCCTG:T indel 2:0 chr8:219366:38516406:2:0:1 TRUE NA 0.96 +chr8 24509496 24509497 A G 5 20 0.25 MODIFIER ADAM7 ENSG00000069206 G 3_prime_UTR_variant Transcript ENST00000175238 protein_coding 22/22 ENST00000175238.10:c.*950A>G NA 3298 1 SNV HGNC HGNC:214 YES NM_003817.4 1 P2 CCDS6045.1 ENSP00000175238 Q9H2U9.160 A0A384MTL6.25 UPI000013C5CC Q9H2U9-1 21 NA NA PASS SITE 32,21|2,3 NA NA 1 78 20,40 193,176 60,60 12 1.43 NA 7.83 NA FALSE 6.00 35 NA NA NA FALSE NA NA 17.08 21 24509496 HCC1395_HCC1395T 15 0.316 20 7,2 4,3 12,5 NA 0/1 NA NA NA NA 10,5,2,3 A/G PANCANCER NA FALSE ADAM7 chr8:24509496:24509497:A:G SNV 2:0 chr8:219366:38516406:2:0:1 TRUE NA 0.96 +chr8 24913691 24913692 CCACGGGGCGGGGCCCTGGCCCGGGACCAGCGCCGCGGCTATAAATGGGCTGCGGCGAGGCCGGCAGAACGCTGTGACAGCCACACGCCCCAAGGCCTCCAAGATGAGCTA C 58 58 1 MODIFIER NEFM ENSG00000104722 - coding_sequence_variant&5_prime_UTR_variant Transcript ENST00000221166 protein_coding 1/3 NA ?-41 ?-8 ?-3 1 deletion HGNC HGNC:7734 YES NM_005382.2 1 P2 CCDS6046.1 ENSP00000221166 P07197.214 UPI000013C7A9 P07197-1 21 NA NA PASS SITE 112,99|36,28 NA NA 2 93 21,40 159,163 60,60 34 2.08 NA 35.58 NA FALSE 6.00 93 NA NA NA FALSE NA NA 176.49 21 24913691 HCC1395_HCC1395T 0 0.976 58 0,18 0,17 0,40 NA 0/1 NA NA NA NA 0,0,31,27 CCACGGGGCGGGGCCCTGGCCCGGGACCAGCGCCGCGGCTATAAATGGGCTGCGGCGAGGCCGGCAGAACGCTGTGACAGCCACACGCCCCAAGGCCTCCAAGATGAGCTA/C PANCANCER NA FALSE NEFM chr8:24913691:24913692:CCACGGGGCGGGGCCCTGGCCCGGGACCAGCGCCGCGGCTATAAATGGGCTGCGGCGAGGCCGGCAGAACGCTGTGACAGCCACACGCCCCAAGGCCTCCAAGATGAGCTA:C indel 2:0 chr8:219366:38516406:2:0:1 TRUE NA 0.96 +chr8 25332745 25332746 C T 25 25 1 MODIFIER DOCK5 ENSG00000147459 T intron_variant Transcript ENST00000276440 protein_coding 20/51 ENST00000276440.12:c.2091+53C>T NA rs948811416 1 SNV HGNC HGNC:23476 YES NM_024940.8 1 P1 CCDS6047.1 ENSP00000276440 Q9H7D0.166 UPI000022D4F3 Q9H7D0-1 6.572e-06 2.413e-05 0 0 0 0 0 0 0 0 0 2.413e-05 gnomADg_AFR 21 NA NA PASS SITE 6,22|2,23 NA NA 1 88 38,35 188,236 60,60 27 1.39 NA 6.62 NA FALSE 6.00 93 NA NA NA FALSE NA NA 92.20 21 25332745 HCC1395_HCC1395T 0 0.962 25 0,9 0,12 0,24 NA 0/1 NA NA NA NA 0,0,2,23 C/T PANCANCER NA FALSE DOCK5 chr8:25332745:25332746:C:T SNV 2:0 chr8:219366:38516406:2:0:1 TRUE NA 0.96 +chr8 27311439 27311440 T G 3 9 0.333333333333333 MODIFIER TRIM35 ENSG00000104228 G upstream_gene_variant Transcript ENST00000305364 protein_coding NA 167 -1 SNV HGNC HGNC:16285 YES NM_171982.5 1 P1 CCDS6056.2 ENSP00000301924 Q9UPQ4.175 UPI00001649FB Q9UPQ4-1 21 NA NA PASS SITE 7,9|2,1 NA NA 1 28 35,20 188,166 60,60 21 0.954 NA 2.41 NA FALSE 6.00 25 NA NA NA FALSE NA NA 7.03 21 27311439 HCC1395_HCC1395T 6 0.333 9 4,0 0,2 5,2 NA 0/1 NA NA NA NA 4,2,2,1 T/G PANCANCER NA FALSE TRIM35 chr8:27311439:27311440:T:G SNV 2:0 chr8:219366:38516406:2:0:1 TRUE NA 0.96 +chr8 27871429 27871430 G C 56 56 1 MODIFIER SCARA5 ENSG00000168079 C 3_prime_UTR_variant Transcript ENST00000354914 protein_coding 9/9 ENST00000354914.8:c.*505C>G NA 2425 -1 SNV HGNC HGNC:28701 YES NM_173833.6 2 P1 CCDS6064.1 ENSP00000346990 Q6ZMJ2.151 UPI000015FA6D Q6ZMJ2-1 21 NA NA PASS SITE 16,20|23,33 NA NA 1 93 28,20 167,169 60,60 26 1.45 NA 8.13 NA FALSE 6.00 93 NA NA NA FALSE NA NA 162.39 21 27871429 HCC1395_HCC1395T 0 0.976 56 0,17 0,18 0,40 NA 0/1 NA NA NA NA 0,0,23,33 G/C PANCANCER NA FALSE SCARA5 chr8:27871429:27871430:G:C SNV 2:0 chr8:219366:38516406:2:0:1 TRUE NA 0.96 +chr8 36888885 36888886 T C 18 18 1 MODIFIER KCNU1 ENSG00000215262 C intron_variant Transcript ENST00000399881 protein_coding 19/26 ENST00000399881.8:c.2010-16823T>C NA 1 SNV HGNC HGNC:18867 YES NM_001031836.3 2 P1 CCDS55220.1 ENSP00000382770 A8MYU2.129 UPI0000F079EF 21 NA NA PASS SITE 9,15|8,10 NA NA 1 64 20,20 165,175 60,60 47 1.23 NA 4.82 NA FALSE 6.00 73 NA NA NA FALSE NA NA 55.94 21 36888885 HCC1395_HCC1395T 0 0.933 18 0,2 0,10 0,13 NA 0/1 NA NA NA NA 0,0,8,10 T/C PANCANCER NA FALSE KCNU1 chr8:36888885:36888886:T:C SNV 2:0 chr8:219366:38516406:2:0:1 TRUE NA 0.96 +chr8 37754215 37754216 TTCCAGTTACTGTGGTGAAAAAGAAGAAATGAACTTAAATCCACTCCCTTTCTAGGGAAAGGAGGGTGGGGACTGATGA T 11 819 0.0134310134310134 MODIFIER ERLIN2 ENSG00000147475 - downstream_gene_variant Transcript ENST00000518526 protein_coding NA 2519 1 cds_end_NF deletion HGNC HGNC:1356 3 ENSP00000429229 E5RJ09.63 UPI0001E8F1A0 1 21 NA NA PASS SITE 853,764|7,4 NA NA 1 93 20,35 156,118 60,60 20 2.70 NA 145.91 NA FALSE 6.00 93 NA NA NA FALSE NA NA 28.08 21 37754215 HCC1395_HCC1395T 808 0.022 819 101,4 143,6 493,14 NA 0/1 NA NA NA NA 425,383,7,4 TTCCAGTTACTGTGGTGAAAAAGAAGAAATGAACTTAAATCCACTCCCTTTCTAGGGAAAGGAGGGTGGGGACTGATGA/T PANCANCER NA FALSE ERLIN2 chr8:37754215:37754216:TTCCAGTTACTGTGGTGAAAAAGAAGAAATGAACTTAAATCCACTCCCTTTCTAGGGAAAGGAGGGTGGGGACTGATGA:T indel 2:0 chr8:219366:38516406:2:0:1 TRUE NA 0.96 +chr8 38428420 38428421 G A 78 78 1 MODERATE FGFR1 ENSG00000077782 A missense_variant Transcript ENST00000326324 protein_coding 3/17 ENST00000326324.10:c.107C>T ENSP00000327229.6:p.S36L ENSP00000327229.6 p.S36L 831 107 36 S/L tCg/tTg rs121913473&COSV58332163 -1 SNV HGNC HGNC:3688 1 CCDS43731.1 ENSP00000327229 P11362.272 UPI0000167BB6 P11362-14 1 deleterious_low_confidence(0) benign(0.017) AlphaFold_DB_import:AF-P11362-F1&PIRSF:PIRSF000628&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg 1.223e-05 0 5.835e-05 0 5.619e-05 0 0 0 0 6.574e-06 0 0 0 0 0 0 0 1.47e-05 0 0 5.835e-05 gnomADe_AMR likely_pathogenic 0&1 1&1 21 NA NA PASS SITE 32,50|31,47 NA NA 1 93 20,20 164,160 60,60 37 1.76 NA 16.81 NA FALSE 6.00 93 NA NA NA FALSE NA NA 227.56 21 38428420 HCC1395_HCC1395T 0 0.981 78 0,21 0,25 0,51 NA 0/1 NA NA NA NA 0,0,31,47 G/A PANCANCER NA FALSE FGFR1_p.S36L chr8:38428420:38428421:G:A SNV 2:0 chr8:219366:38516406:2:0:1 TRUE NA 0.96 +chr8 41611677 41611678 C T 4 7 0.571428571428571 MODIFIER GPAT4 ENSG00000158669 T intron_variant Transcript ENST00000396987 protein_coding 5/12 ENST00000396987.7:c.612-226C>T NA 1 SNV HGNC HGNC:20880 YES NM_178819.4 1 P1 CCDS6117.1 ENSP00000380184 Q86UL3.156 UPI0000047FDD 21 NA NA PASS SITE 15,2|3,1 NA NA 1 42 37,20 205,161 60,60 16 1.11 NA 3.61 NA FALSE 6.00 30 NA NA NA FALSE NA NA 9.18 21 41611677 HCC1395_HCC1395T 3 0.499 7 1,1 2,1 3,3 NA 0/1 NA NA NA NA 3,0,3,1 C/T PANCANCER NA FALSE GPAT4 chr8:41611677:41611678:C:T SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 41687976 41687977 C T 53 53 1 MODIFIER ANK1 ENSG00000029534 T intron_variant Transcript ENST00000265709 protein_coding 36/42 ENST00000265709.14:c.4381+180G>A NA -1 SNV HGNC HGNC:492 1 A2 CCDS47849.1 ENSP00000265709 P16157.235 UPI0000E4453A P16157-21 1 21 NA NA PASS SITE 28,19|34,19 NA NA 1 93 20,20 190,170 60,60 27 1.56 NA 10.53 NA FALSE 6.00 93 NA NA NA FALSE NA NA 165.26 21 41687976 HCC1395_HCC1395T 0 0.976 53 0,13 0,24 0,39 NA 0/1 NA NA NA NA 0,0,34,19 C/T PANCANCER NA FALSE ANK1 chr8:41687976:41687977:C:T SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 54627056 54627057 A T 118 118 1 LOW RP1 ENSG00000104237 T synonymous_variant Transcript ENST00000220676 protein_coding 4/4 ENST00000220676.2:c.3174A>T ENSP00000220676.1:p.L1058= ENSP00000220676.1 p.L1058= 3293 3174 1058 L ctA/ctT 1 SNV HGNC HGNC:10263 YES NM_006269.2 1 CCDS6160.1 ENSP00000220676 P56715.171 UPI000013455B 1 AlphaFold_DB_import:AF-P56715-F1&PANTHER:PTHR23005 21 NA NA PASS SITE 37,29|49,69 NA NA 1 93 20,20 160,168 60,60 40 1.65 NA 12.94 NA FALSE 6.00 93 NA NA NA FALSE NA NA 361.15 21 54627056 HCC1395_HCC1395T 0 0.988 118 0,33 0,41 0,82 NA 0/1 NA NA NA NA 0,0,49,69 A/T PANCANCER NA FALSE RP1_p.L1058= chr8:54627056:54627057:A:T SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 55526145 55526146 C T 25 114 0.219298245614035 MODIFIER XKR4 ENSG00000206579 T 3_prime_UTR_variant Transcript ENST00000327381 protein_coding 3/3 ENST00000327381.7:c.*1918C>T NA 4332 1 SNV HGNC HGNC:29394 YES NM_052898.2 1 P1 CCDS34893.1 ENSP00000328326 Q5GH76.116 UPI000016098C 21 NA NA PASS SITE 52,135|4,21 NA NA 1 93 30,35 190,175 60,60 25 1.87 NA 21.32 NA FALSE 6.00 73 NA NA NA FALSE NA NA 63.38 21 55526145 HCC1395_HCC1395T 89 0.232 114 21,7 40,11 72,21 NA 0/1 NA NA NA NA 22,67,4,21 C/T PANCANCER NA FALSE XKR4 chr8:55526145:55526146:C:T SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 60866898 60866899 G C 12 32 0.375 MODIFIER CHD7 ENSG00000171316 C 3_prime_UTR_variant Transcript ENST00000423902 protein_coding 38/38 ENST00000423902.7:c.*965G>C NA 10476 1 SNV HGNC HGNC:20626 YES NM_017780.4 5 P1 CCDS47865.1 ENSP00000392028 Q9P2D1.202 UPI0000251DA6 Q9P2D1-1 1 21 NA NA PASS SITE 22,33|1,11 NA NA 1 87 20,40 188,218 60,60 22 1.41 NA 7.22 NA FALSE 6.00 90 NA NA NA FALSE NA NA 39.87 21 60866898 HCC1395_HCC1395T 20 0.400 32 10,5 7,6 17,11 NA 0/1 NA NA NA NA 6,14,1,11 G/C PANCANCER NA FALSE CHD7 chr8:60866898:60866899:G:C SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 64581002 64581003 AGGGGGCAGGGCTGCTGTTGCCGCCGCCTGGAGGAGGCGGCGGC A 35 195 0.179487179487179 HIGH BHLHE22 ENSG00000180828 - frameshift_variant Transcript ENST00000321870 protein_coding 1/1 ENST00000321870.3:c.215_257del ENSP00000318799.1:p.G72Afs*19 ENSP00000318799.1 p.G72Afs*19 639-681 213-255 71-85 EGAGLLLPPPGGGGG/X gaGGGGGCAGGGCTGCTGTTGCCGCCGCCTGGAGGAGGCGGCGGC/ga 1 deletion HGNC HGNC:11963 YES NM_152414.5 P1 CCDS6179.1 ENSP00000318799 Q8NFJ8.138 UPI0000070A3C AlphaFold_DB_import:AF-Q8NFJ8-F1&PANTHER:PTHR19290&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg 2 21 NA NA PASS SITE 173,134|23,12 NA NA 1 93 30,36 178,192 60,60 43 2.08 NA 34.03 NA FALSE 6.00 93 NA NA NA FALSE NA NA 129.81 21 64581002 HCC1395_HCC1395T 160 0.173 195 28,9 24,13 120,24 NA 0/1 NA NA NA NA 86,74,23,12 AGGGGGCAGGGCTGCTGTTGCCGCCGCCTGGAGGAGGCGGCGGC/A PANCANCER NA FALSE BHLHE22_p.G72Afs*19 chr8:64581002:64581003:AGGGGGCAGGGCTGCTGTTGCCGCCGCCTGGAGGAGGCGGCGGC:A indel 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 66134925 66134926 G A 73 162 0.450617283950617 MODIFIER TRIM55 ENSG00000147573 A intron_variant Transcript ENST00000276573 protein_coding 2/10 ENST00000276573.11:c.342-65G>A NA 1 SNV HGNC HGNC:14215 1 A1 CCDS6187.1 ENSP00000276573 Q9BYV6.181 UPI00001CE3B6 Q9BYV6-3 21 NA NA PASS SITE 145,65|50,23 NA NA 1 93 20,20 162,160 60,60 28 1.97 NA 27.09 NA FALSE 6.00 84 NA NA NA FALSE NA NA 197.27 21 66134925 HCC1395_HCC1395T 89 0.457 162 14,15 48,37 63,53 NA 0/1 NA NA NA NA 61,28,50,23 G/A PANCANCER NA FALSE TRIM55 chr8:66134925:66134926:G:A SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 66919984 66919985 C G 26 107 0.242990654205607 MODIFIER SNORD87 ENSG00000254341 G downstream_gene_variant Transcript ENST00000364849 snoRNA NA 2483 -1 SNV HGNC HGNC:32746 YES 21 NA NA PASS SITE 105,70|11,15 NA NA 1 93 37,39 197,209 60,60 15 1.89 NA 22.53 NA FALSE 6.00 60 NA NA NA FALSE NA NA 75.43 21 66919984 HCC1395_HCC1395T 81 0.247 107 20,5 47,15 72,23 NA 0/1 NA NA NA NA 49,32,11,15 C/G PANCANCER NA FALSE SNORD87 chr8:66919984:66919985:C:G SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 67086875 67086876 C A 22 83 0.265060240963855 MODIFIER CSPP1 ENSG00000104218 A intron_variant Transcript ENST00000262210 protein_coding 4/29 ENST00000262210.11:c.411+765C>A NA 1 SNV HGNC HGNC:26193 1 CCDS94301.1 ENSP00000262210 A0A7I2PHE7.7 UPI000387BE94 1 21 NA NA PASS SITE 49,59|5,17 NA NA 1 93 20,35 144,171 60,60 17 1.55 NA 10.23 NA FALSE 6.00 37 NA NA NA FALSE NA NA 58.37 21 67086875 HCC1395_HCC1395T 61 0.286 83 13,3 9,3 47,18 NA 0/1 NA NA NA NA 24,37,5,17 C/A PANCANCER NA FALSE CSPP1 chr8:67086875:67086876:C:A SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 67267309 67267310 A G 4 15 0.266666666666667 MODIFIER ARFGEF1 ENSG00000066777 G intron_variant Transcript ENST00000262215 protein_coding 11/38 ENST00000262215.8:c.1672+34T>C NA -1 SNV HGNC HGNC:15772 YES NM_006421.5 1 P1 CCDS6199.1 ENSP00000262215 Q9Y6D6.193 A0A024R7X0.61 UPI000013D275 1 21 NA NA PASS SITE 9,13|3,1 NA NA 1 29 37,30 202,169 60,60 35 1.000 NA 2.71 NA FALSE 6.00 24 NA NA NA FALSE NA NA 10.44 21 67267309 HCC1395_HCC1395T 11 0.307 15 0,2 7,1 8,3 NA 0/1 NA NA NA NA 6,5,3,1 A/G PANCANCER NA FALSE ARFGEF1 chr8:67267309:67267310:A:G SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 69466613 69466614 C G 14 37 0.378378378378378 MODIFIER SULF1 ENSG00000137573 G upstream_gene_variant Transcript ENST00000260128 protein_coding NA 11 1 SNV HGNC HGNC:20391 5 P1 CCDS6204.1 ENSP00000260128 Q8IWU6.155 A0A024R809.61 UPI000003FD82 21 NA NA PASS SITE 33,18|8,6 NA NA 1 69 20,20 158,150 60,60 46 1.26 NA 5.12 NA FALSE 6.00 31 NA NA NA FALSE NA NA 32.22 21 69466613 HCC1395_HCC1395T 23 0.387 37 6,1 10,7 16,10 NA 0/1 NA NA NA NA 16,7,8,6 C/G PANCANCER NA FALSE SULF1 chr8:69466613:69466614:C:G SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 71362098 71362099 C G 45 118 0.38135593220339 MODIFIER EYA1 ENSG00000104313 G upstream_gene_variant Transcript ENST00000303824 protein_coding NA 238 -1 SNV HGNC HGNC:3519 2 A1 CCDS75750.1 ENSP00000303221 A6NCB9.110 UPI000155D699 1 21 NA NA PASS SITE 67,114|22,23 NA NA 1 93 20,20 149,137 60,60 37 1.84 NA 20.17 NA FALSE 6.00 93 NA NA NA FALSE NA NA 98.12 21 71362098 HCC1395_HCC1395T 73 0.347 118 17,13 29,11 48,25 NA 0/1 NA NA NA NA 26,47,22,23 C/G PANCANCER NA FALSE EYA1 chr8:71362098:71362099:C:G SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 80518630 80518631 C G 8 26 0.307692307692308 MODIFIER ZBTB10 ENSG00000205189 G intron_variant Transcript ENST00000379091 protein_coding 4/5 ENST00000379091.8:c.1261+51C>G NA rs1050617640 1 SNV HGNC HGNC:30953 2 A2 CCDS64920.1 ENSP00000368384 Q96DT7.170 UPI000006E576 Q96DT7-4 21 NA NA PASS SITE 23,32|3,5 NA NA 1 83 20,39 174,238 60,60 53 1.44 NA 7.78 NA FALSE 6.00 35 NA NA NA FALSE NA NA 28.28 21 80518630 HCC1395_HCC1395T 18 0.391 26 6,1 6,7 13,8 NA 0/1 NA NA NA NA 6,12,3,5 C/G PANCANCER NA FALSE ZBTB10 chr8:80518630:80518631:C:G SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 85439106 85439107 C T 18 42 0.428571428571429 MODIFIER CA3 ENSG00000164879 T intron_variant Transcript ENST00000285381 protein_coding 1/6 ENST00000285381.3:c.34+163C>T NA 1 SNV HGNC HGNC:1374 YES NM_005181.4 1 P1 CCDS6238.1 ENSP00000285381 P07451.211 V9HWA3.51 UPI0000049C1A 21 NA NA PASS SITE 14,37|7,11 NA NA 1 89 20,20 174,169 60,60 20 1.32 NA 6.02 NA FALSE 6.00 63 NA NA NA FALSE NA NA 41.01 21 85439106 HCC1395_HCC1395T 24 0.400 42 7,4 10,6 17,11 NA 0/1 NA NA NA NA 7,17,7,11 C/T PANCANCER NA FALSE CA3 chr8:85439106:85439107:C:T SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 94543935 94543936 G A 21 123 0.170731707317073 MODERATE VIRMA ENSG00000164944 A missense_variant Transcript ENST00000297591 protein_coding 2/24 ENST00000297591.10:c.71C>T ENSP00000297591.5:p.S24F ENSP00000297591.5 p.S24F 93 71 24 S/F tCt/tTt -1 SNV HGNC HGNC:24500 YES NM_015496.5 1 P1 CCDS34923.1 ENSP00000297591 Q69YN4.140 UPI00001BBB23 Q69YN4-1 deleterious_low_confidence(0) benign(0.074) PDB-ENSP_mappings:7vf2.A&PDB-ENSP_mappings:7vf5.A&AlphaFold_DB_import:AF-Q69YN4-F1&Pfam:PF15912&PANTHER:PTHR23185 21 NA NA PASS SITE 76,125|9,12 NA NA 1 93 20,20 154,139 60,60 37 1.80 NA 18.66 NA FALSE 6.00 5 NA NA NA FALSE NA NA 40.42 21 94543935 HCC1395_HCC1395T 102 0.165 123 23,1 35,11 65,12 NA 0/1 NA NA NA NA 39,63,9,12 G/A PANCANCER NA FALSE VIRMA_p.S24F chr8:94543935:94543936:G:A SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 94930450 94930451 G C 51 184 0.277173913043478 MODIFIER TP53INP1 ENSG00000164938 C 3_prime_UTR_variant Transcript ENST00000342697 protein_coding 4/4 ENST00000342697.5:c.*29C>G NA 1127 -1 SNV HGNC HGNC:18022 YES NM_033285.4 1 P1 CCDS6265.1 ENSP00000344215 Q96A56.143 A0A024R9C8.48 UPI00000725F8 Q96A56-1 21 NA NA PASS SITE 164,120|24,27 NA NA 1 93 20,20 164,175 60,60 35 2.03 NA 31.30 NA FALSE 6.00 93 NA NA NA FALSE NA NA 121.66 21 94930450 HCC1395_HCC1395T 133 0.274 184 36,16 50,17 89,33 NA 0/1 NA NA NA NA 77,56,24,27 G/C PANCANCER NA FALSE TP53INP1 chr8:94930450:94930451:G:C SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 95247528 95247529 G T 83 332 0.25 MODIFIER CFAP418 ENSG00000156172 T 3_prime_UTR_variant Transcript ENST00000286688 protein_coding 6/6 ENST00000286688.6:c.*89C>A NA 725 -1 SNV HGNC HGNC:27232 YES NM_177965.4 1 P1 CCDS6268.1 ENSP00000286688 Q96NL8.124 UPI00000737D8 1 21 NA NA PASS SITE 286,225|47,36 NA NA 1 93 20,20 164,183 60,60 35 2.25 NA 52.32 NA FALSE 6.00 93 NA NA NA FALSE NA NA 196.66 21 95247528 HCC1395_HCC1395T 249 0.251 332 67,21 100,36 175,58 NA 0/1 NA NA NA NA 146,103,47,36 G/T PANCANCER NA FALSE CFAP418 chr8:95247528:95247529:G:T SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 98951689 98951690 G A 45 126 0.357142857142857 LOW OSR2 ENSG00000164920 A synonymous_variant Transcript ENST00000297565 protein_coding 4/4 ENST00000297565.9:c.927G>A ENSP00000297565.4:p.R309= ENSP00000297565.4 p.R309= 1423 927 309 R cgG/cgA 1 SNV HGNC HGNC:15830 YES NM_001142462.3 1 P1 CCDS47901.1 ENSP00000297565 Q8N2R0.161 UPI00001AEC4D Q8N2R0-1 AlphaFold_DB_import:AF-Q8N2R0-F1&PROSITE_profiles:PS50157&PANTHER:PTHR14196 21 NA NA PASS SITE 101,118|19,26 NA NA 1 93 20,20 171,170 60,60 33 2.00 NA 29.45 NA FALSE 6.00 83 NA NA NA FALSE NA NA 112.28 21 98951689 HCC1395_HCC1395T 81 0.351 126 26,12 27,18 62,33 NA 0/1 NA NA NA NA 39,42,19,26 G/A PANCANCER NA FALSE OSR2_p.R309= chr8:98951689:98951690:G:A SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 101688894 101688895 C T 26 77 0.337662337662338 MODIFIER NCALD ENSG00000104490 T 3_prime_UTR_variant Transcript ENST00000220931 protein_coding 4/4 ENST00000220931.11:c.*415G>A NA 1124 rs567946139&COSV99637620 -1 SNV HGNC HGNC:7655 YES NM_032041.3 1 P1 CCDS6292.1 ENSP00000220931 P61601.159 B2RB70.121 UPI0000004090 5.255e-05 0.0001447 0 0 0 0 0 0 2.939e-05 0 0 0.0001447 gnomADg_AFR 0&1 0&1 21 NA NA PASS SITE 55,68|13,13 NA NA 1 93 20,20 162,177 60,60 29 1.69 NA 14.40 NA FALSE 3.83 55 NA NA NA FALSE NA NA 61.27 21 101688894 HCC1395_HCC1395T 51 0.353 77 12,5 21,13 34,18 NA 0/1 NA NA NA NA 21,30,13,13 C/T PANCANCER NA FALSE NCALD chr8:101688894:101688895:C:T SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 107497939 107497940 G A 65 213 0.305164319248826 MODIFIER ANGPT1 ENSG00000154188 A 5_prime_UTR_variant Transcript ENST00000297450 protein_coding 1/9 ENST00000297450.7:c.-381C>T NA 117 rs746206813 -1 SNV HGNC HGNC:484 1 A1 CCDS56551.1 ENSP00000297450 Q15389.192 UPI0000169553 Q15389-2 1 21 NA NA PASS SITE 91,165|23,42 NA NA 1 93 36,20 172,167 60,60 33 1.96 NA 26.19 NA FALSE 6.00 93 NA NA NA FALSE NA NA 169.84 21 107497939 HCC1395_HCC1395T 148 0.300 213 48,15 56,28 116,49 NA 0/1 NA NA NA NA 51,97,23,42 G/A PANCANCER NA FALSE ANGPT1 chr8:107497939:107497940:G:A SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 108083619 108083620 C A 62 140 0.442857142857143 MODIFIER RSPO2 ENSG00000147655 A 5_prime_UTR_variant Transcript ENST00000276659 protein_coding 1/6 ENST00000276659.10:c.-592G>T NA 2 -1 SNV HGNC HGNC:28583 YES NM_178565.5 1 P1 CCDS6307.1 ENSP00000276659 Q6UXX9.147 UPI000021046F Q6UXX9-1 1 21 NA NA PASS SITE 62,107|25,37 NA NA 1 93 20,20 163,162 60,60 39 1.81 NA 18.61 NA FALSE 6.00 72 NA NA NA FALSE NA NA 156.68 21 108083619 HCC1395_HCC1395T 78 0.443 140 15,11 35,28 53,42 NA 0/1 NA NA NA NA 31,47,25,37 C/A PANCANCER TRUE FALSE RSPO2 chr8:108083619:108083620:C:A SNV 3:0 chr8:38968772:109406232:3:0:1 NA NA 0.96 +chr8 109440818 109440819 C T 50 171 0.292397660818713 LOW PKHD1L1 ENSG00000205038 T synonymous_variant Transcript ENST00000378402 protein_coding 33/78 ENST00000378402.10:c.4065C>T ENSP00000367655.5:p.F1355= ENSP00000367655.5 p.F1355= 4185 4065 1355 F ttC/ttT COSV65741313 1 SNV HGNC HGNC:20313 YES NM_177531.6 1 P1 CCDS47911.1 ENSP00000367655 Q86WI1.140 UPI0000E5B020 CDD:cd00603&PANTHER:PTHR46769&Gene3D:2.60.40.10&Pfam:PF01833&SMART:SM00429&Superfamily:SSF81296 1 1 21 NA NA PASS SITE 96,115|24,26 NA NA 1 93 20,20 156,153 60,60 36 1.76 NA 16.84 NA FALSE 6.00 93 NA NA NA FALSE NA NA 107.69 21 109440818 HCC1395_HCC1395T 121 0.284 171 25,12 47,16 75,29 NA 0/1 NA NA NA NA 54,67,24,26 C/T PANCANCER NA FALSE PKHD1L1_p.F1355= chr8:109440818:109440819:C:T SNV 4:0 chr8:109427290:109644043:4:0:1 NA NA 0.96 +chr8 112550908 112550909 A G 17 88 0.193181818181818 MODIFIER CSMD3 ENSG00000164796 G intron_variant Transcript ENST00000297405 protein_coding 26/70 ENST00000297405.10:c.4362-35T>C NA -1 SNV HGNC HGNC:19291 YES NM_198123.2 1 P1 CCDS6315.1 ENSP00000297405 Q7Z407.151 UPI00001E0584 Q7Z407-1 1 21 NA NA PASS SITE 23,79|2,15 NA NA 1 93 34,39 184,187 60,60 37 1.40 NA 6.92 NA FALSE 6.00 59 NA NA NA FALSE NA NA 46.34 21 112550908 HCC1395_HCC1395T 71 0.212 88 14,5 36,7 57,15 NA 0/1 NA NA NA NA 15,56,2,15 A/G PANCANCER TRUE FALSE CSMD3 chr8:112550908:112550909:A:G SNV 5:0 chr8:109646298:124562672:5:0:1 NA NA 0.96 +chr8 119557083 119557084 G C 12 35 0.342857142857143 MODIFIER ENPP2 ENSG00000136960 C downstream_gene_variant Transcript ENST00000075322 protein_coding NA 3 -1 SNV HGNC HGNC:3357 YES NM_001040092.3 1 P1 CCDS34936.1 ENSP00000075322 Q13822.195 UPI000013D05C Q13822-1 21 NA NA PASS SITE 38,1|11,1 NA NA 1 53 41,38 230,255 60,60 16 1.23 NA 4.82 NA FALSE 6.00 62 NA NA NA FALSE NA NA 37.49 21 119557083 HCC1395_HCC1395T 23 0.333 35 5,3 17,8 23,11 NA 0/1 NA NA NA NA 22,1,11,1 G/C PANCANCER NA FALSE ENPP2 chr8:119557083:119557084:G:C SNV 5:0 chr8:109646298:124562672:5:0:1 NA NA 0.96 +chr8 123182203 123182204 T C 79 260 0.303846153846154 MODIFIER FAM83A ENSG00000147689 C upstream_gene_variant Transcript ENST00000276699 protein_coding NA 478 1 SNV HGNC HGNC:28210 1 CCDS6339.1 ENSP00000276699 Q86UY5.136 UPI0000352C76 Q86UY5-3 21 NA NA PASS SITE 121,172|31,48 NA NA 1 93 20,29 169,195 60,60 33 1.89 NA 22.83 NA FALSE 6.00 93 NA NA NA FALSE NA NA 209.32 21 123182203 HCC1395_HCC1395T 181 0.313 260 55,26 70,28 134,61 NA 0/1 NA NA NA NA 72,109,31,48 T/C PANCANCER NA FALSE FAM83A chr8:123182203:123182204:T:C SNV 5:0 chr8:109646298:124562672:5:0:1 NA NA 0.96 +chr8 123209636 123209637 C T 56 168 0.333333333333333 MODIFIER FAM83A ENSG00000147689 T 3_prime_UTR_variant Transcript ENST00000276699 protein_coding 5/5 ENST00000276699.10:c.*140C>T NA 1420 1 SNV HGNC HGNC:28210 1 CCDS6339.1 ENSP00000276699 Q86UY5.136 UPI0000352C76 Q86UY5-3 21 NA NA PASS SITE 59,111|22,34 NA NA 1 93 30,20 177,178 60,60 29 1.64 NA 12.30 NA FALSE 6.00 93 NA NA NA FALSE NA NA 145.60 21 123209636 HCC1395_HCC1395T 112 0.323 168 37,20 43,19 89,42 NA 0/1 NA NA NA NA 39,73,22,34 C/T PANCANCER NA FALSE FAM83A chr8:123209636:123209637:C:T SNV 5:0 chr8:109646298:124562672:5:0:1 NA NA 0.96 +chr8 123220221 123220229 A AGGGCTAC 557 557 1 HIGH C8orf76 ENSG00000189376 GGGCTAC frameshift_variant Transcript ENST00000276704 protein_coding 6/6 ENST00000276704.6:c.1024_1025insGTAGCCC ENSP00000276704.4:p.L342Rfs*15 ENSP00000276704.4 p.L342Rfs*15 1055-1056 1024-1025 342 L/RSPX ctg/cGTAGCCCtg -1 insertion HGNC HGNC:25924 YES NM_032847.3 1 P1 CCDS6341.1 ENSP00000276704 Q96K31.138 UPI000006E851 Q96K31-1 PANTHER:PTHR31919&Pfam:PF17826&AlphaFold_DB_import:AF-Q96K31-F1 21 NA NA PASS SITE 69,124|196,361 NA NA 2 93 20,20 173,162 60,60 38 2.19 NA 42.20 NA FALSE 6.00 93 1,2 GGGCTAC NA TRUE NA 93 2481.21 21 123220221 HCC1395_HCC1395T 0 0.998 557 0,116 0,147 0,398 NA 0/1 NA NA NA NA 0,0,196,361 A/AGGGCTAC PANCANCER NA FALSE C8orf76_p.L342Rfs*15 chr8:123220221:123220229:A:AGGGCTAC indel 5:0 chr8:109646298:124562672:5:0:1 NA NA 0.96 +chr8 124973353 124973354 GAGGGGGTACCTTCCTCCCGGACCGCTGGGGGTGC G 71 426 0.166666666666667 MODIFIER ZNF572 ENSG00000180938 - 5_prime_UTR_variant Transcript ENST00000319286 protein_coding 1/3 ENST00000319286.6:c.-94_-61del NA 60-93 1 deletion HGNC HGNC:26758 YES NM_152412.3 1 P1 CCDS6354.1 ENSP00000319305 Q7Z3I7.156 UPI0000140576 4 21 NA NA PASS SITE 242,281|32,39 NA NA 1 93 20,35 161,205 60,60 39 1.99 NA 28.67 NA FALSE 6.00 93 NA NA NA FALSE NA NA 266.80 21 124973353 HCC1395_HCC1395T 355 0.180 426 70,21 98,18 220,47 NA 0/1 NA NA NA NA 166,189,32,39 GAGGGGGTACCTTCCTCCCGGACCGCTGGGGGTGC/G PANCANCER NA FALSE ZNF572 chr8:124973353:124973354:GAGGGGGTACCTTCCTCCCGGACCGCTGGGGGTGC:G indel 7:0 chr8:124562684:127416550:7:0:1 NA NA 0.96 +chr8 125102411 125102412 G C 235 911 0.257958287596048 MODERATE NSMCE2 ENSG00000156831 C missense_variant Transcript ENST00000287437 protein_coding 3/8 ENST00000287437.8:c.81G>C ENSP00000287437.3:p.L27F ENSP00000287437.3 p.L27F 290 81 27 L/F ttG/ttC COSV54906574 1 SNV HGNC HGNC:26513 YES NM_173685.4 1 P1 CCDS6356.1 ENSP00000287437 Q96MF7.149 A0A024R9J6.59 UPI0000039EC8 1 deleterious(0) probably_damaging(0.996) AlphaFold_DB_import:AF-Q96MF7-F1&PANTHER:PTHR21330 1 1 21 NA NA PASS SITE 416,543|94,141 NA NA 1 93 20,20 162,165 60,60 33 2.28 NA 55.68 NA FALSE 6.00 93 NA NA NA FALSE NA NA 571.17 21 125102411 HCC1395_HCC1395T 676 0.255 911 168,42 248,101 456,155 NA 0/1 NA NA NA NA 289,387,94,141 G/C PANCANCER NA FALSE NSMCE2_p.L27F chr8:125102411:125102412:G:C SNV 7:0 chr8:124562684:127416550:7:0:1 NA NA 0.96 +chr8 125436371 125436373 CC TT 47 286 0.164335664335664 MODERATE TRIB1 ENSG00000173334 TT missense_variant Transcript ENST00000311922 protein_coding 3/3 ENST00000311922.4:c.1019_1020delinsTT ENSP00000312150.3:p.S340F ENSP00000312150.3 p.S340F 1564-1565 1019-1020 340 S/F tCC/tTT 1 substitution HGNC HGNC:16891 YES NM_025195.4 1 P1 CCDS6357.1 ENSP00000312150 Q96RU8.168 UPI00000717B2 Q96RU8-1 deleterious(0.04) possibly_damaging(0.456) PDB-ENSP_mappings:5cek.A&PDB-ENSP_mappings:5cem.A&PDB-ENSP_mappings:6dc0.A&PDB-ENSP_mappings:6dc0.B&PANTHER:PTHR22961&Gene3D:1.10.510.10&Superfamily:SSF56112&AlphaFold_DB_import:AF-Q96RU8-F1 21 NA NA PASS SITE 188,161|30,17 NA NA 1 93 20,20 166,168 60,60 36 1.92 NA 24.08 NA FALSE 6.00 93 NA NA NA FALSE NA NA 169.97 21 125436371 HCC1395_HCC1395T 239 0.159 286 76,14 91,16 174,32 NA 0/1 NA NA NA NA 131,108,30,17 CC/TT PANCANCER NA FALSE TRIB1_p.S340F chr8:125436371:125436373:CC:TT indel 7:0 chr8:124562684:127416550:7:0:1 NA NA 0.96 +chr8 130443698 130443699 G A 8 22 0.363636363636364 MODIFIER ASAP1 ENSG00000153317 A upstream_gene_variant Transcript ENST00000357668 protein_coding NA rs573445333 38 -1 SNV HGNC HGNC:2720 5 A2 CCDS75788.1 ENSP00000350297 A0A0A0MRE5.67 UPI0000EE3232 0.0016 0.0045 0.0014 0 0.001 0 0.00135 0.004322 0 0.00118 0 0 0.0001903 0 1.472e-05 0.002395 0 0.0045 AFR 21 NA NA PASS SITE 4,23|1,7 NA NA 1 6 38,37 201,199 60,60 19 1.08 NA 3.31 NA FALSE 3.01 20 NA NA NA FALSE NA NA 22.64 21 130443698 HCC1395_HCC1395T 14 0.381 22 7,1 5,5 12,7 NA 0/1 NA NA NA NA 2,12,1,7 G/A PANCANCER NA FALSE ASAP1 chr8:130443698:130443699:G:A SNV 6:0 chr8:127416578:138153030:6:0:1 NA NA 0.96 +chr8 132100024 132100025 A G 47 425 0.110588235294118 MODIFIER HHLA1 ENSG00000132297 G intron_variant Transcript ENST00000414222 protein_coding 4/16 ENST00000414222.2:c.199+51T>C NA -1 SNV HGNC HGNC:4904 YES NM_001145095.3 5 P2 ENSP00000388322 C9JL84.75 UPI000192B909 C9JL84-1 21 NA NA PASS SITE 277,245|28,19 NA NA 1 93 20,20 160,167 60,60 23 1.69 NA 28.54 NA FALSE 6.00 69 NA NA NA FALSE NA NA 99.23 21 132100024 HCC1395_HCC1395T 378 0.115 425 93,11 154,21 262,33 NA 0/1 NA NA NA NA 199,179,28,19 A/G PANCANCER NA FALSE HHLA1 chr8:132100024:132100025:A:G SNV 6:0 chr8:127416578:138153030:6:0:1 NA NA 0.96 +chr8 132141243 132141244 C G 138 441 0.312925170068027 MODERATE KCNQ3 ENSG00000184156 G missense_variant Transcript ENST00000388996 protein_coding 10/15 ENST00000388996.10:c.1351G>C ENSP00000373648.3:p.D451H ENSP00000373648.3 p.D451H 1914 1351 451 D/H Gat/Cat -1 SNV HGNC HGNC:6297 YES NM_004519.4 1 P1 CCDS34943.1 ENSP00000373648 O43525.202 UPI00001279F0 O43525-1 1 deleterious(0) probably_damaging(0.976) AlphaFold_DB_import:AF-O43525-F1&Pfam:PF03520&PANTHER:PTHR47735 21 NA NA PASS SITE 229,221|76,62 NA NA 1 93 20,20 161,164 60,60 38 1.98 NA 28.59 NA FALSE 6.00 93 NA NA NA FALSE NA NA 359.28 21 132141243 HCC1395_HCC1395T 303 0.317 441 68,29 128,60 208,96 NA 0/1 NA NA NA NA 157,146,76,62 C/G PANCANCER NA FALSE KCNQ3_p.D451H chr8:132141243:132141244:C:G SNV 6:0 chr8:127416578:138153030:6:0:1 NA NA 0.96 +chr8 132948806 132948807 C G 223 223 1 MODERATE TG ENSG00000042832 G missense_variant Transcript ENST00000220616 protein_coding 27/48 ENST00000220616.9:c.5264C>G ENSP00000220616.4:p.P1755R ENSP00000220616.4 p.P1755R 5307 5264 1755 P/R cCc/cGc COSV55072692 1 SNV HGNC HGNC:11764 YES NM_003235.5 1 P1 CCDS34944.1 ENSP00000220616 P01266.227 UPI000013C79F P01266-1 1 deleterious(0) probably_damaging(0.948) PDB-ENSP_mappings:6scj.A&PDB-ENSP_mappings:6scj.B&PDB-ENSP_mappings:7b75.A&PDB-ENSP_mappings:7b75.B&PIRSF:PIRSF001831 1 1 21 NA NA PASS SITE 44,14|175,48 NA NA 1 93 20,31 171,178 60,60 24 1.66 NA 13.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 721.77 21 132948806 HCC1395_HCC1395T 0 0.995 223 0,71 0,107 0,183 NA 0/1 NA NA NA NA 0,0,175,48 C/G PANCANCER NA FALSE TG_p.P1755R chr8:132948806:132948807:C:G SNV 6:0 chr8:127416578:138153030:6:0:1 NA NA 0.96 +chr8 133256734 133256735 C G 37 97 0.381443298969072 MODIFIER NDRG1 ENSG00000104419 G intron_variant Transcript ENST00000323851 protein_coding 8/15 ENST00000323851.13:c.537+43G>C NA -1 SNV HGNC HGNC:7679 YES NM_006096.4 1 P1 CCDS34945.1 ENSP00000319977 Q92597.204 UPI000012FEDD Q92597-1 1 21 NA NA PASS SITE 86,23|33,4 NA NA 1 93 37,40 191,214 60,60 32 1.63 NA 12.04 NA FALSE 6.00 93 NA NA NA FALSE NA NA 124.25 21 133256734 HCC1395_HCC1395T 60 0.410 97 22,11 24,22 48,33 NA 0/1 NA NA NA NA 46,14,33,4 C/G PANCANCER NA FALSE NDRG1 chr8:133256734:133256735:C:G SNV 6:0 chr8:127416578:138153030:6:0:1 NA NA 0.96 +chr8 133459437 133459438 C T 64 380 0.168421052631579 MODIFIER ST3GAL1 ENSG00000008513 T 3_prime_UTR_variant Transcript ENST00000521180 protein_coding 9/9 ENST00000521180.5:c.*327G>A NA 2367 -1 SNV HGNC HGNC:10862 1 P1 CCDS6373.1 ENSP00000428540 Q11201.191 A0A024R9L6.61 UPI00000015E1 21 NA NA PASS SITE 242,254|35,29 NA NA 1 93 20,20 160,181 60,60 34 2.05 NA 33.11 NA FALSE 6.00 93 NA NA NA FALSE NA NA 143.28 21 133459437 HCC1395_HCC1395T 316 0.174 380 88,18 114,26 213,44 NA 0/1 NA NA NA NA 158,158,35,29 C/T PANCANCER NA FALSE ST3GAL1 chr8:133459437:133459438:C:T SNV 6:0 chr8:127416578:138153030:6:0:1 NA NA 0.96 +chr8 138619384 138619385 G T 13 78 0.166666666666667 MODIFIER COL22A1 ENSG00000169436 T intron_variant Transcript ENST00000303045 protein_coding 53/64 ENST00000303045.11:c.3825+71C>A NA -1 SNV HGNC HGNC:22989 YES NM_152888.3 1 P1 CCDS6376.1 ENSP00000303153 Q8NFW1.157 UPI00001C1EA1 Q8NFW1-1 21 NA NA PASS SITE 88,9|11,2 NA NA 1 93 40,37 200,181 60,60 24 1.50 NA 8.68 NA FALSE 6.00 46 NA NA NA FALSE NA NA 33.18 21 138619384 HCC1395_HCC1395T 65 0.165 78 17,6 42,5 60,11 NA 0/1 NA NA NA NA 59,6,11,2 G/T PANCANCER NA FALSE COL22A1 chr8:138619384:138619385:G:T SNV 5:0 chr8:138177259:138811814:5:0:1 NA NA 0.96 +chr8 138737577 138737578 C A 37 268 0.138059701492537 MODERATE COL22A1 ENSG00000169436 A missense_variant&splice_region_variant Transcript ENST00000303045 protein_coding 23/65 ENST00000303045.11:c.2086G>T ENSP00000303153.6:p.G696W ENSP00000303153.6 p.G696W 2581 2086 696 G/W Ggg/Tgg COSV57343769 -1 SNV HGNC HGNC:22989 YES NM_152888.3 1 P1 CCDS6376.1 ENSP00000303153 Q8NFW1.157 UPI00001C1EA1 Q8NFW1-1 deleterious(0.01) unknown(0) AlphaFold_DB_import:AF-Q8NFW1-F1&MobiDB_lite:mobidb-lite 1 1 21 NA NA PASS SITE 144,202|15,22 NA NA 1 93 20,20 162,157 60,60 33 1.87 NA 22.18 NA FALSE 6.00 88 NA NA NA FALSE NA NA 76.12 21 138737577 HCC1395_HCC1395T 231 0.149 268 52,13 86,10 148,25 NA 0/1 NA NA NA NA 95,136,15,22 C/A PANCANCER NA FALSE COL22A1_p.G696W chr8:138737577:138737578:C:A SNV 5:0 chr8:138177259:138811814:5:0:1 NA NA 0.96 +chr8 140818848 140818849 T C 36 253 0.142292490118577 MODIFIER PTK2 ENSG00000169398 C intron_variant Transcript ENST00000340930 protein_coding 9/32 ENST00000340930.7:c.789+32A>G NA -1 SNV HGNC HGNC:9611 2 CCDS56557.1 ENSP00000341189 Q05397.251 UPI0001E8F57E Q05397-5 21 NA NA PASS SITE 214,110|24,12 NA NA 1 93 20,20 162,162 60,60 30 1.86 NA 21.37 NA FALSE 6.00 55 NA NA NA FALSE NA NA 79.07 21 140818848 HCC1395_HCC1395T 217 0.150 253 35,7 111,17 146,25 NA 0/1 NA NA NA NA 145,72,24,12 T/C PANCANCER NA FALSE PTK2 chr8:140818848:140818849:T:C SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 141479057 141479058 C T 16 96 0.166666666666667 MODIFIER MROH5 ENSG00000226807 T intron_variant Transcript ENST00000430863 protein_coding_LoF 9/29 ENST00000430863.5:c.1095+150G>A NA -1 SNV HGNC HGNC:42976 YES 1 P5 ENSP00000431031 21 NA NA PASS SITE 106,17|12,4 NA NA 1 93 39,30 196,172 60,60 31 1.60 NA 11.44 NA FALSE 6.00 46 NA NA NA FALSE NA NA 38.97 21 141479057 HCC1395_HCC1395T 80 0.155 96 34,4 35,8 70,12 NA 0/1 NA NA NA NA 70,10,12,4 C/T PANCANCER NA FALSE MROH5 chr8:141479057:141479058:C:T SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 141480564 141480565 C T 15 93 0.161290322580645 MODIFIER MROH5 ENSG00000226807 T intron_variant Transcript ENST00000430863 protein_coding_LoF 6/29 ENST00000430863.5:c.751-116G>A NA -1 SNV HGNC HGNC:42976 YES 1 P5 ENSP00000431031 21 NA NA PASS SITE 8,115|3,12 NA NA 1 93 39,36 189,193 60,60 27 1.62 NA 11.99 NA FALSE 6.00 60 NA NA NA FALSE NA NA 35.19 21 141480564 HCC1395_HCC1395T 78 0.155 93 30,5 41,5 75,13 NA 0/1 NA NA NA NA 3,75,3,12 C/T PANCANCER NA FALSE MROH5 chr8:141480564:141480565:C:T SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 142489220 142489221 G A 22 67 0.328358208955224 MODIFIER ADGRB1 ENSG00000181790 A intron_variant Transcript ENST00000517894 protein_coding 15/30 ENST00000517894.6:c.2528+110G>A NA 1 SNV HGNC HGNC:943 YES NM_001702.3 5 P4 CCDS64985.1 ENSP00000430945 O14514.193 UPI00002109E8 21 NA NA PASS SITE 10,58|3,19 NA NA 1 83 39,37 233,242 60,60 20 1.39 NA 6.92 NA FALSE 6.00 88 NA NA NA FALSE NA NA 69.81 21 142489220 HCC1395_HCC1395T 45 0.333 67 14,9 29,12 45,22 NA 0/1 NA NA NA NA 6,39,3,19 G/A PANCANCER NA FALSE ADGRB1 chr8:142489220:142489221:G:A SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 142774705 142774706 G C 91 509 0.178781925343811 MODIFIER SLURP2 ENSG00000283992 C upstream_gene_variant Transcript ENST00000317543 protein_coding NA 4877 -1 SNV HGNC HGNC:25549 YES NM_177458.3 1 P1 CCDS34952.1 ENSP00000319846 P0DP57.35 UPI000000D72B 21 NA NA PASS SITE 332,319|49,42 NA NA 1 93 20,20 160,159 60,60 32 2.20 NA 46.91 NA FALSE 6.00 93 NA NA NA FALSE NA NA 196.49 21 142774705 HCC1395_HCC1395T 418 0.177 509 115,25 138,30 269,57 NA 0/1 NA NA NA NA 213,205,49,42 G/C PANCANCER NA FALSE SLURP2 chr8:142774705:142774706:G:C SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 142875211 142875212 C G 60 340 0.176470588235294 MODIFIER CYP11B1 ENSG00000160882 G intron_variant Transcript ENST00000292427 protein_coding 7/8 ENST00000292427.10:c.1200+23G>C NA rs1200321971 -1 SNV HGNC HGNC:2591 YES NM_000497.4 1 P1 CCDS6392.1 ENSP00000292427 P15538.219 UPI000013E0BA P15538-1 1 21 NA NA PASS SITE 133,277|19,41 NA NA 1 93 20,20 176,183 60,60 23 2.00 NA 29.79 NA FALSE 6.00 93 NA NA NA FALSE NA NA 139.68 21 142875211 HCC1395_HCC1395T 280 0.173 340 76,17 107,22 208,43 NA 0/1 NA NA NA NA 90,190,19,41 C/G PANCANCER NA FALSE CYP11B1 chr8:142875211:142875212:C:G SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 142879934 142879935 A G 59 204 0.28921568627451 MODIFIER CYP11B1 ENSG00000160882 G upstream_gene_variant Transcript ENST00000292427 protein_coding NA 109 -1 SNV HGNC HGNC:2591 YES NM_000497.4 1 P1 CCDS6392.1 ENSP00000292427 P15538.219 UPI000013E0BA P15538-1 1 21 NA NA PASS SITE 65,180|16,43 NA NA 1 93 34,20 168,162 60,60 17 1.86 NA 21.07 NA FALSE 6.00 93 NA NA NA FALSE NA NA 154.40 21 142879934 HCC1395_HCC1395T 145 0.276 204 47,20 52,19 117,44 NA 0/1 NA NA NA NA 33,112,16,43 A/G PANCANCER NA FALSE CYP11B1 chr8:142879934:142879935:A:G SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 143368852 143368853 G A 33 112 0.294642857142857 MODIFIER RHPN1 ENSG00000158106 A upstream_gene_variant Transcript ENST00000289013 protein_coding NA 24 1 SNV HGNC HGNC:19973 YES NM_052924.3 1 P1 CCDS47927.1 ENSP00000289013 Q8TCX5.157 UPI0000071870 21 NA NA PASS SITE 82,51|24,9 NA NA 1 93 20,33 164,169 60,60 22 1.60 NA 11.44 NA FALSE 6.00 93 NA NA NA FALSE NA NA 86.35 21 143368852 HCC1395_HCC1395T 79 0.318 112 26,12 23,11 52,24 NA 0/1 NA NA NA NA 46,33,24,9 G/A PANCANCER NA FALSE RHPN1 chr8:143368852:143368853:G:A SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 143558229 143558230 G C 25 64 0.390625 MODIFIER GSDMD ENSG00000104518 C upstream_gene_variant Transcript ENST00000262580 protein_coding NA 117 1 SNV HGNC HGNC:25697 YES NM_024736.7 1 P2 CCDS34956.1 ENSP00000262580 P57764.162 UPI00001291ED 21 NA NA PASS SITE 61,2|22,3 NA NA 1 70 40,39 223,202 60,60 35 1.38 NA 6.62 NA FALSE 6.00 93 NA NA NA FALSE NA NA 80.08 21 143558229 HCC1395_HCC1395T 39 0.368 64 19,8 17,14 39,22 NA 0/1 NA NA NA NA 39,0,22,3 G/C PANCANCER NA FALSE GSDMD chr8:143558229:143558230:G:C SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 143805314 143805315 A C 60 378 0.158730158730159 MODERATE SCRIB ENSG00000180900 C missense_variant Transcript ENST00000320476 protein_coding 19/36 ENST00000320476.7:c.2468T>G ENSP00000322938.3:p.V823G ENSP00000322938.3 p.V823G 2475 2468 823 V/G gTc/gGc rs1554636272 -1 SNV HGNC HGNC:30377 1 P2 CCDS6411.1 ENSP00000322938 Q14160.219 UPI000232E1C1 Q14160-1 1 deleterious_low_confidence(0) benign(0.073) PDB-ENSP_mappings:6esp.A&AlphaFold_DB_import:AF-Q14160-F1&PANTHER:PTHR23119 6.582e-06 0 0 0 0 0.0001932 0 0 0 0 0 0.0001932 gnomADg_EAS 21 NA NA PASS SITE 307,200|41,20 NA NA 2 93 20,39 161,180 60,60 29 2.15 NA 42.10 NA FALSE 4.61 93 NA NA NA FALSE NA NA 167.45 21 143805314 HCC1395_HCC1395T 318 0.182 378 91,19 133,30 228,50 NA 0/1 NA NA NA NA 195,123,41,19 A/C PANCANCER NA FALSE SCRIB_p.V823G chr8:143805314:143805315:A:C SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 144054726 144054727 G A 7 587 0.0119250425894378 MODIFIER OPLAH ENSG00000178814 A upstream_gene_variant Transcript ENST00000527993 retained_intron NA rs868921961 73 -1 SNV HGNC HGNC:8149 5 1 21 NA NA PASS SITE 337,490|3,5 NA NA 1 93 20,32 165,157 60,60 14 0.818 NA 49.50 NA FALSE 6.00 10 NA NA NA FALSE NA NA 9.55 21 144054726 HCC1395_HCC1395T 580 0.013 587 180,2 226,3 443,5 NA 0/1 NA NA NA NA 231,349,3,4 G/A PANCANCER NA FALSE OPLAH chr8:144054726:144054727:G:A SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 144105528 144105529 C T 16 90 0.177777777777778 MODIFIER MAF1 ENSG00000179632 T intron_variant Transcript ENST00000322428 protein_coding 1/7 ENST00000322428.10:c.-44-112C>T NA 1 SNV HGNC HGNC:24966 YES NM_032272.5 1 P1 CCDS6416.1 ENSP00000318604 Q9H063.158 UPI0000140E10 21 NA NA PASS SITE 87,16|12,4 NA NA 2 93 38,34 201,167 60,60 20 1.40 NA 6.92 NA FALSE 6.00 69 NA NA NA FALSE NA NA 38.78 21 144105528 HCC1395_HCC1395T 74 0.175 90 24,7 39,6 65,13 NA 0|1 0|1 144105528_C_T NA 144105528 64,10,12,4 C|T PANCANCER NA FALSE MAF1 chr8:144105528:144105529:C:T SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 144413906 144413907 C A 362 363 0.997245179063361 MODIFIER SLC39A4 ENSG00000147804 A intron_variant Transcript ENST00000276833 protein_coding 6/10 ENST00000276833.9:c.1213-25G>T NA -1 SNV HGNC HGNC:17129 2 CCDS43782.1 ENSP00000276833 Q6P5W5.155 UPI0002064DC5 Q6P5W5-2 1 21 NA NA PASS SITE 89,76|209,153 NA NA 1 93 20,20 168,161 60,60 27 2.06 NA 34.31 NA FALSE 6.00 93 NA NA NA FALSE NA NA 1076.44 21 144413906 HCC1395_HCC1395T 1 0.996 363 0,108 0,117 1,243 NA 0/1 NA NA NA NA 0,1,209,153 C/A PANCANCER NA FALSE SLC39A4 chr8:144413906:144413907:C:A SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 144474144 144474145 C G 86 486 0.176954732510288 MODIFIER KIFC2 ENSG00000167702 G downstream_gene_variant Transcript ENST00000301332 protein_coding NA 29 1 SNV HGNC HGNC:29530 1 CCDS6427.1 ENSP00000301332 Q96AC6.154 UPI000006D3B2 Q96AC6-1 21 NA NA PASS SITE 209,408|31,55 NA NA 1 93 37,35 178,175 60,60 23 2.24 NA 51.38 NA FALSE 6.00 93 NA NA NA FALSE NA NA 213.52 21 144474144 HCC1395_HCC1395T 400 0.176 486 118,15 149,35 320,69 NA 0/1 NA NA NA NA 129,271,31,55 C/G PANCANCER NA FALSE KIFC2 chr8:144474144:144474145:C:G SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 144500974 144500975 G A 19 138 0.13768115942029 LOW PPP1R16A ENSG00000160972 A splice_donor_region_variant&intron_variant Transcript ENST00000292539 protein_coding 9/10 ENST00000292539.8:c.1037+3G>A NA rs1226173475 1 SNV HGNC HGNC:14941 2 P1 CCDS6429.1 ENSP00000292539 Q96I34.165 UPI0000132057 0 0 0 0 0 0 0 0 0 0 gnomADe_AFR&gnomADe_AMR&gnomADe_ASJ&gnomADe_EAS&gnomADe_FIN&gnomADe_NFE&gnomADe_OTH&gnomADe_SAS 21 NA NA PASS SITE 65,141|4,15 NA NA 1 93 37,35 187,162 60,60 13 1.86 NA 21.37 NA FALSE 6.00 69 NA NA NA FALSE NA NA 47.40 21 144500974 HCC1395_HCC1395T 119 0.159 138 48,6 38,6 94,17 NA 0/1 NA NA NA NA 39,80,4,15 G/A PANCANCER NA FALSE PPP1R16A chr8:144500974:144500975:G:A SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 144811108 144811109 C G 56 317 0.176656151419558 MODIFIER ZNF517 ENSG00000197363 G downstream_gene_variant Transcript ENST00000359971 protein_coding NA 1024 1 SNV HGNC HGNC:27984 YES NM_213605.3 4 P1 CCDS6434.1 ENSP00000353058 Q6ZMY9.154 UPI000045770F 21 NA NA PASS SITE 179,220|24,32 NA NA 1 93 20,20 158,174 60,60 40 1.96 NA 27.08 NA FALSE 6.00 93 NA NA NA FALSE NA NA 133.67 21 144811108 HCC1395_HCC1395T 261 0.178 317 66,16 93,18 179,38 NA 0/1 NA NA NA NA 114,147,24,32 C/G PANCANCER NA FALSE ZNF517 chr8:144811108:144811109:C:G SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 144847587 144847588 C T 65 158 0.411392405063291 MODIFIER COMMD5 ENSG00000170619 T downstream_gene_variant Transcript ENST00000305103 protein_coding NA 2589 -1 SNV HGNC HGNC:17902 YES NM_014066.4 1 P1 CCDS6436.1 ENSP00000304544 Q9GZQ3.149 UPI000004A08E 21 NA NA PASS SITE 34,126|9,56 NA NA 1 93 38,39 194,204 60,60 36 1.75 NA 16.25 NA FALSE 6.00 93 NA NA NA FALSE NA NA 206.04 21 144847587 HCC1395_HCC1395T 93 0.423 158 30,27 36,21 77,56 NA 0/1 NA NA NA NA 20,73,9,56 C/T PANCANCER NA FALSE COMMD5 chr8:144847587:144847588:C:T SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr8 144878996 144878997 C G 39 114 0.342105263157895 MODIFIER ZNF250 ENSG00000196150 G 3_prime_UTR_variant Transcript ENST00000292579 protein_coding 6/6 ENST00000292579.11:c.*2519G>C NA 4319 -1 SNV HGNC HGNC:13044 1 P4 CCDS34972.1 ENSP00000292579 P15622.211 UPI0000197F51 P15622-1 21 NA NA PASS SITE 51,71|16,23 NA NA 1 93 20,20 168,168 60,60 25 1.53 NA 9.93 NA FALSE 6.00 93 NA NA NA FALSE NA NA 97.62 21 144878996 HCC1395_HCC1395T 75 0.338 114 23,11 28,15 52,26 NA 0/1 NA NA NA NA 31,44,16,23 C/G PANCANCER NA FALSE ZNF250 chr8:144878996:144878997:C:G SNV 6:0 chr8:138833277:145004146:6:0:1 NA NA 0.96 +chr9 3287998 3287999 G C 24 49 0.489795918367347 MODIFIER RFX3 ENSG00000080298 C intron_variant Transcript ENST00000302303 protein_coding 8/10 ENST00000302303.5:c.851+133C>G NA -1 SNV HGNC HGNC:9984 1 CCDS75809.1 ENSP00000303847 P48380.184 UPI0000424FCD P48380-3 22 NA NA PASS SITE 56,3|23,1 NA NA 1 93 39,39 218,217 60,60 25 1.54 NA 9.63 NA FALSE 6.00 93 NA NA NA FALSE NA NA 87.83 22 3287998 HCC1395_HCC1395T 25 0.500 49 6,11 18,13 24,24 NA 0/1 NA NA NA NA 24,1,23,1 G/C PANCANCER NA FALSE RFX3 chr9:3287998:3287999:G:C SNV 3:1 chr9:213291:4844459:3:1:1 NA NA 0.96 +chr9 3825257 3825258 G T 287 613 0.468189233278956 MODIFIER GLIS3 ENSG00000107249 T 3_prime_UTR_variant Transcript ENST00000324333 protein_coding 10/10 ENST00000324333.14:c.*3015C>A NA 5537 -1 SNV HGNC HGNC:28510 1 CCDS6451.1 ENSP00000325494 Q8NEA6.162 A0A0S2Z689.37 UPI00003675FE Q8NEA6-1 1 22 NA NA PASS SITE 326,308|142,145 NA NA 2 93 20,20 170,170 60,60 29 2.35 NA 65.13 NA FALSE 6.00 93 NA NA NA FALSE NA NA 777.02 22 3825257 HCC1395_HCC1395T 326 0.466 613 52,48 110,101 243,211 NA 0/1 NA NA NA NA 167,159,142,145 G/T PANCANCER NA FALSE GLIS3 chr9:3825257:3825258:G:T SNV 3:1 chr9:213291:4844459:3:1:1 NA NA 0.96 +chr9 3825296 3825297 G C 332 687 0.483260553129549 MODIFIER GLIS3 ENSG00000107249 C 3_prime_UTR_variant Transcript ENST00000324333 protein_coding 10/10 ENST00000324333.14:c.*2976C>G NA 5498 -1 SNV HGNC HGNC:28510 1 CCDS6451.1 ENSP00000325494 Q8NEA6.162 A0A0S2Z689.37 UPI00003675FE Q8NEA6-1 1 22 NA NA PASS SITE 361,326|183,149 NA NA 2 93 20,32 170,166 60,60 26 2.38 NA 70.30 NA FALSE 6.00 93 NA NA NA FALSE NA NA 978.75 22 3825296 HCC1395_HCC1395T 355 0.499 687 64,63 121,121 253,252 NA 0/1 NA NA NA NA 186,169,183,149 G/C PANCANCER NA FALSE GLIS3 chr9:3825296:3825297:G:C SNV 3:1 chr9:213291:4844459:3:1:1 NA NA 0.96 +chr9 4985358 4985359 C G 63 131 0.480916030534351 MODIFIER JAK2 ENSG00000096968 G 5_prime_UTR_variant Transcript ENST00000381652 protein_coding 1/25 ENST00000381652.4:c.-381C>G NA 87 1 SNV HGNC HGNC:6192 YES NM_004972.4 1 P1 CCDS6457.1 ENSP00000371067 O60674.234 UPI000012DA9E 1 22 NA NA PASS SITE 83,81|29,34 NA NA 1 93 20,20 169,164 60,60 20 1.83 NA 19.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 183.38 22 4985358 HCC1395_HCC1395T 68 0.480 131 19,20 31,23 51,47 NA 0/1 NA NA NA NA 36,32,29,34 C/G PANCANCER TRUE FALSE JAK2 chr9:4985358:4985359:C:G SNV 3:0 chr9:4844704:5231712:3:0:1 NA NA 0.96 +chr9 5769270 5769271 C T 78 146 0.534246575342466 LOW RIC1 ENSG00000107036 T synonymous_variant Transcript ENST00000251879 protein_coding 22/22 ENST00000251879.10:c.3438C>T ENSP00000251879.6:p.F1146= ENSP00000251879.6 p.F1146= 3723 3438 1146 F ttC/ttT COSV52613639&COSV52616400 1 SNV HGNC HGNC:17686 1 CCDS47949.2 ENSP00000251879 Q4ADV7.133 UPI00002110E0 Q4ADV7-2 1 AlphaFold_DB_import:AF-Q4ADV7-F1 1&1 1&1 22 NA NA PASS SITE 67,92|27,51 NA NA 1 93 20,34 182,186 60,60 27 1.85 NA 20.77 NA FALSE 6.00 93 NA NA NA FALSE NA NA 225.56 22 5769270 HCC1395_HCC1395T 68 0.555 146 21,23 24,36 51,64 NA 0/1 NA NA NA NA 28,40,27,51 C/T PANCANCER NA FALSE RIC1_p.F1146= chr9:5769270:5769271:C:T SNV 3:1 chr9:5335470:13175988:3:1:1 NA NA 0.96 +chr9 5922534 5922535 G C 222 466 0.476394849785408 LOW KIAA2026 ENSG00000183354 C synonymous_variant Transcript ENST00000381461 protein_coding 7/7 ENST00000381461.6:c.3372C>G ENSP00000370870.2:p.V1124= ENSP00000370870.2 p.V1124= 3372 3372 1124 V gtC/gtG rs1283886929 -1 SNV HGNC HGNC:23378 5 A2 ENSP00000370870 Q5HYC2.122 UPI0001D322F2 Q5HYC2-2 AlphaFold_DB_import:AF-Q5HYC2-F1&PANTHER:PTHR31095 6.569e-06 0 0 0 0 0 0 0 0 0.0004776 0 0.0004776 gnomADg_OTH 22 NA NA PASS SITE 225,242|102,120 NA NA 1 93 20,20 163,167 60,60 31 2.17 NA 43.35 NA FALSE 4.61 93 NA NA NA FALSE NA NA 578.30 22 5922534 HCC1395_HCC1395T 244 0.468 466 58,41 100,92 167,147 NA 0/1 NA NA NA NA 115,129,102,120 G/C PANCANCER NA FALSE KIAA2026_p.V1124= chr9:5922534:5922535:G:C SNV 3:1 chr9:5335470:13175988:3:1:1 NA NA 0.96 +chr9 12695920 12695921 G A 27 76 0.355263157894737 MODIFIER TYRP1 ENSG00000107165 A intron_variant Transcript ENST00000381136 protein_coding 1/4 ENST00000381136.2:c.43+83G>A NA 1 SNV HGNC HGNC:12450 2 ENSP00000370528 E7EQI3.71 UPI000048D7E8 1 22 NA NA PASS SITE 17,61|7,20 NA NA 1 64 36,20 183,162 60,60 19 1.35 NA 6.32 NA FALSE 6.00 37 NA NA NA FALSE NA NA 70.77 22 12695920 HCC1395_HCC1395T 49 0.333 76 14,4 21,15 41,20 NA 0/1 NA NA NA NA 9,40,7,20 G/A PANCANCER NA FALSE TYRP1 chr9:12695920:12695921:G:A SNV 3:1 chr9:5335470:13175988:3:1:1 NA NA 0.96 +chr9 14784671 14784672 C G 97 171 0.567251461988304 MODIFIER FREM1 ENSG00000164946 G intron_variant&NMD_transcript_variant Transcript ENST00000380875 nonsense_mediated_decay 23/30 ENST00000380875.7:c.3981+8072G>C NA -1 SNV HGNC HGNC:23399 1 ENSP00000370257 F8WE85.65 UPI000048D7EC 1 22 NA NA PASS SITE 58,88|39,58 NA NA 1 93 20,20 159,163 60,60 37 1.67 NA 13.75 NA FALSE 6.00 93 NA NA NA FALSE NA NA 253.55 22 14784671 HCC1395_HCC1395T 74 0.569 171 14,17 29,41 46,61 NA 0/1 NA NA NA NA 31,43,39,58 C/G PANCANCER NA FALSE FREM1 chr9:14784671:14784672:C:G SNV 4:1 chr9:13176313:15468482:4:1:1 NA NA 0.96 +chr9 19049363 19049364 C T 85 85 1 MODIFIER HAUS6 ENSG00000147874 T downstream_gene_variant Transcript ENST00000380502 protein_coding NA 3778 -1 SNV HGNC HGNC:25948 YES NM_017645.5 1 P1 CCDS6489.1 ENSP00000369871 Q7Z4H7.152 UPI00000740C7 Q7Z4H7-1 22 NA NA PASS SITE 117,53|58,27 NA NA 1 93 20,20 166,169 60,60 24 2.10 NA 36.98 NA FALSE 6.00 93 NA NA NA FALSE NA NA 262.80 22 19049363 HCC1395_HCC1395T 0 0.984 85 0,27 0,32 0,60 NA 0/1 NA NA NA NA 0,0,58,27 C/T PANCANCER NA FALSE HAUS6 chr9:19049363:19049364:C:T SNV 2:0 chr9:15486352:42894371:2:0:1 TRUE NA 0.96 +chr9 27294444 27294445 C A 4 9 0.444444444444444 MODIFIER EQTN ENSG00000120160 A intron_variant Transcript ENST00000380031 protein_coding 2/3 ENST00000380031.2:c.203-42G>T NA -1 SNV HGNC HGNC:1359 1 ENSP00000369370 Q9NQ60.127 UPI000007278A Q9NQ60-2 22 NA NA PASS SITE 2,30|0,4 NA NA 1 76 39,37 189,246 60,60 42 1.42 NA 7.53 NA FALSE 6.00 43 NA NA NA FALSE NA NA 13.59 22 27294444 HCC1395_HCC1395T 5 0.454 9 0,2 4,2 5,4 NA 0/1 NA NA NA NA 0,5,0,4 C/A PANCANCER NA FALSE EQTN chr9:27294444:27294445:C:A SNV 2:0 chr9:15486352:42894371:2:0:1 TRUE NA 0.96 +chr9 32974337 32974339 GG AA 7 19 0.368421052631579 MODIFIER APTX ENSG00000137074 AA intron_variant Transcript ENST00000309615 protein_coding 6/6 ENST00000309615.8:c.712+120_712+121delinsTT NA -1 substitution HGNC HGNC:15984 1 CCDS75827.1 ENSP00000311547 Q7Z2E3.191 UPI00002318C3 Q7Z2E3-5 1 22 NA NA PASS SITE 36,7|5,2 NA NA 1 73 38,20 208,145 60,60 9 1.41 NA 7.22 NA FALSE 6.00 39 NA NA NA FALSE NA NA 25.68 22 32974337 HCC1395_HCC1395T 12 0.316 19 3,2 9,3 12,5 NA 0/1 NA NA NA NA 12,0,5,2 GG/AA PANCANCER NA FALSE APTX chr9:32974337:32974339:GG:AA indel 2:0 chr9:15486352:42894371:2:0:1 TRUE NA 0.96 +chr9 35091097 35091098 C A 14 20 0.7 MODIFIER PIGO ENSG00000165282 A intron_variant Transcript ENST00000298004 protein_coding 9/12 ENST00000298004.9:c.1396+143G>T NA -1 SNV HGNC HGNC:23215 1 CCDS6576.1 ENSP00000298004 Q8TEQ8.173 UPI000013E47F Q8TEQ8-2 1 22 NA NA PASS SITE 15,4|11,3 NA NA 1 30 36,39 202,196 60,60 28 1.04 NA 3.01 NA FALSE 6.00 72 NA NA NA FALSE NA NA 43.89 22 35091097 HCC1395_HCC1395T 6 0.679 20 1,5 3,6 5,11 NA 0/1 NA NA NA NA 5,1,11,3 C/A PANCANCER NA FALSE PIGO chr9:35091097:35091098:C:A SNV 2:0 chr9:15486352:42894371:2:0:1 TRUE NA 0.96 +chr9 35609476 35609477 C T 155 155 1 MODIFIER CD72 ENSG00000137101 T downstream_gene_variant Transcript ENST00000259633 protein_coding NA rs1373248755&COSV52412662 506 -1 SNV HGNC HGNC:1696 YES NM_001782.3 1 P1 CCDS6581.1 ENSP00000259633 P21854.191 Q5TLG3.147 UPI00001273AA 0 0 0 0 0 0 0 0 0 0 gnomADe_AFR&gnomADe_AMR&gnomADe_ASJ&gnomADe_EAS&gnomADe_FIN&gnomADe_NFE&gnomADe_OTH&gnomADe_SAS 0&1 0&1 22 NA NA PASS SITE 128,121|77,78 NA NA 1 93 20,20 162,156 60,60 34 2.21 NA 47.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 429.17 22 35609476 HCC1395_HCC1395T 0 0.990 155 0,36 0,58 0,97 NA 0/1 NA NA NA NA 0,0,77,78 C/T PANCANCER NA FALSE CD72 chr9:35609476:35609477:C:T SNV 2:0 chr9:15486352:42894371:2:0:1 TRUE NA 0.96 +chr9 35750918 35750919 C T 106 106 1 MODERATE RGP1 ENSG00000107185 T missense_variant Transcript ENST00000378078 protein_coding 5/9 ENST00000378078.5:c.416C>T ENSP00000367318.4:p.T139I ENSP00000367318.4 p.T139I 557 416 139 T/I aCc/aTc 1 SNV HGNC HGNC:21965 YES NM_001080496.3 1 P1 CCDS47964.2 ENSP00000367318 Q92546.156 UPI0000139519 tolerated(0.08) possibly_damaging(0.843) PANTHER:PTHR12507&Pfam:PF08737&AlphaFold_DB_import:AF-Q92546-F1 22 NA NA PASS SITE 52,64|52,54 NA NA 1 93 20,20 164,172 60,60 30 1.92 NA 24.68 NA FALSE 6.00 93 NA NA NA FALSE NA NA 324.24 22 35750918 HCC1395_HCC1395T 0 0.987 106 0,28 0,37 0,74 NA 0/1 NA NA NA NA 0,0,52,54 C/T PANCANCER NA FALSE RGP1_p.T139I chr9:35750918:35750919:C:T SNV 2:0 chr9:15486352:42894371:2:0:1 TRUE NA 0.96 +chr9 37784016 37784017 T A 27 59 0.457627118644068 MODERATE EXOSC3 ENSG00000107371 A missense_variant Transcript ENST00000327304 protein_coding 2/4 ENST00000327304.10:c.372A>T ENSP00000323046.4:p.K124N ENSP00000323046.4 p.K124N 392 372 124 K/N aaA/aaT COSV59203684 -1 SNV HGNC HGNC:17944 YES NM_016042.4 1 P1 CCDS35016.1 ENSP00000323046 Q9NQT5.198 UPI0000134936 Q9NQT5-1 1 deleterious(0) probably_damaging(0.954) Gene3D:2.40.50.140&PDB-ENSP_mappings:2nn6.G&PDB-ENSP_mappings:6d6q.G&PDB-ENSP_mappings:6d6r.G&PDB-ENSP_mappings:6h25.G&AlphaFold_DB_import:AF-Q9NQT5-F1&PANTHER:PTHR21321&Superfamily:SSF50249&CDD:cd05790 1 1 22 NA NA PASS SITE 62,43|18,9 NA NA 1 93 20,20 166,199 60,60 31 1.67 NA 13.80 NA FALSE 6.00 70 NA NA NA FALSE NA NA 70.44 22 37784016 HCC1395_HCC1395T 32 0.463 59 7,5 14,13 21,18 NA 0/1 NA NA NA NA 19,13,18,9 T/A PANCANCER NA FALSE EXOSC3_p.K124N chr9:37784016:37784017:T:A SNV 2:0 chr9:15486352:42894371:2:0:1 TRUE NA 0.96 +chr9 68483583 68483584 G T 4 7 0.571428571428571 MODIFIER PGM5 ENSG00000154330 T intron_variant Transcript ENST00000396396 protein_coding 8/10 ENST00000396396.6:c.1296-282G>T NA 1 SNV HGNC HGNC:8908 YES NM_021965.4 2 P1 CCDS6622.2 ENSP00000379678 Q15124.177 UPI0000210ABF Q15124-1 22 NA NA PASS SITE 12,1|3,1 NA NA 1 31 40,24 188,168 60,60 25 1.04 NA 3.01 NA FALSE 6.00 20 NA NA NA FALSE NA NA 10.60 22 68483583 HCC1395_HCC1395T 3 0.571 7 0,2 2,1 2,3 NA 0/1 NA NA NA NA 2,1,3,1 G/T PANCANCER NA FALSE PGM5 chr9:68483583:68483584:G:T SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 74739227 74739228 G A 34 62 0.548387096774194 MODIFIER TRPM6 ENSG00000119121 A intron_variant Transcript ENST00000360774 protein_coding 35/38 ENST00000360774.6:c.5570+140C>T NA rs537385803&COSV62521253 -1 SNV HGNC HGNC:17995 YES NM_017662.5 1 P2 CCDS6647.1 ENSP00000354006 Q9BX84.169 UPI000006E041 Q9BX84-1 1 3.288e-05 2.416e-05 0 0 0 0.0001933 0 0 1.47e-05 0 0.0004149 0.0004149 gnomADg_SAS 0&1 0&1 22 NA NA PASS SITE 58,16|27,7 NA NA 1 93 29,37 187,172 60,60 21 1.59 NA 11.13 NA FALSE 4.13 62 NA NA NA FALSE NA NA 106.35 22 74739227 HCC1395_HCC1395T 28 0.558 62 4,7 18,21 22,28 NA 0/1 NA NA NA NA 22,6,27,7 G/A PANCANCER NA FALSE TRPM6 chr9:74739227:74739228:G:A SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 77358275 77358276 C T 25 99 0.252525252525253 MODIFIER VPS13A ENSG00000197969 T downstream_gene_variant Transcript ENST00000355766 retained_intron NA 4644 1 SNV HGNC HGNC:1908 3 1 22 NA NA PASS SITE 106,88|13,12 NA NA 1 93 20,20 169,180 60,60 45 1.90 NA 23.43 NA FALSE 6.00 46 NA NA NA FALSE NA NA 60.84 22 77358275 HCC1395_HCC1395T 74 0.268 99 28,4 23,12 51,18 NA 0/1 NA NA NA NA 39,35,13,12 C/T PANCANCER NA FALSE VPS13A chr9:77358275:77358276:C:T SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 81992223 81992224 C G 261 402 0.649253731343284 MODERATE SPATA31D1 ENSG00000214929 G missense_variant Transcript ENST00000344803 protein_coding 4/4 ENST00000344803.3:c.1753C>G ENSP00000341988.2:p.Q585E ENSP00000341988.2 p.Q585E 1800 1753 585 Q/E Caa/Gaa COSV61203084 1 SNV HGNC HGNC:37283 YES NM_001001670.3 2 P1 CCDS47986.1 ENSP00000341988 Q6ZQQ2.113 UPI00001C10A6 deleterious(0.01) possibly_damaging(0.841) Pfam:PF14650&AlphaFold_DB_import:AF-Q6ZQQ2-F1 1 1 22 NA NA PASS SITE 217,161|151,110 NA NA 1 93 20,20 157,161 60,60 35 2.18 NA 45.45 NA FALSE 6.00 93 NA NA NA FALSE NA NA 676.44 22 81992223 HCC1395_HCC1395T 141 0.635 402 35,62 53,94 92,161 NA 0/1 NA NA NA NA 83,58,151,110 C/G PANCANCER NA FALSE SPATA31D1_p.Q585E chr9:81992223:81992224:C:G SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 89065521 89065522 C T 50 184 0.271739130434783 LOW SHC3 ENSG00000148082 T splice_region_variant&intron_variant Transcript ENST00000375835 protein_coding 6/11 ENST00000375835.9:c.835+8G>A NA -1 SNV HGNC HGNC:18181 YES NM_016848.6 1 P1 CCDS6681.1 ENSP00000364995 Q92529.178 UPI0000073E1F Q92529-1 22 NA NA PASS SITE 107,141|20,30 NA NA 1 93 20,20 158,163 60,60 34 1.86 NA 21.07 NA FALSE 6.00 52 NA NA NA FALSE NA NA 116.03 22 89065521 HCC1395_HCC1395T 134 0.275 184 32,7 52,23 93,35 NA 0/1 NA NA NA NA 58,76,20,30 C/T PANCANCER NA FALSE SHC3 chr9:89065521:89065522:C:T SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 90864820 90864821 C T 8 25 0.32 MODIFIER SYK ENSG00000165025 T intron_variant Transcript ENST00000375746 protein_coding 5/13 ENST00000375746.1:c.796+153C>T NA rs137917566 1 SNV HGNC HGNC:11491 1 P1 CCDS6688.1 ENSP00000364898 P43405.241 A0A024R244.69 UPI000012E0DD P43405-1 1 0.0004 0 0.0014 0 0.001 0 0.001329 0.0003141 0 0.002688 0.0005767 0 0 0 0.002088 0.001914 0 0.002688 gnomADg_AMR 22 NA NA PASS SITE 9,35|2,6 NA NA 1 39 30,29 220,143 60,60 18 1.38 NA 6.88 NA FALSE 3.00 20 NA NA NA FALSE NA NA 20.93 22 90864820 HCC1395_HCC1395T 17 0.318 25 6,4 8,1 14,6 NA 0/1 NA NA NA NA 3,14,2,6 C/T PANCANCER NA FALSE SYK chr9:90864820:90864821:C:T SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 92600415 92600416 C G 7 316 0.0221518987341772 MODIFIER CENPP ENSG00000188312 G 5_prime_UTR_variant Transcript ENST00000375579 protein_coding 1/4 ENST00000375579.7:c.-49C>G NA 159 COSV100980531 1 SNV HGNC HGNC:32933 1 CCDS69618.1 ENSP00000364729 Q6IPU0.150 UPI0000211A50 Q6IPU0-2 1 1 22 NA NA PASS SITE 267,261|4,3 NA NA 1 93 20,20 161,170 60,60 31 2.17 NA 43.04 NA FALSE 6.00 51 NA NA NA FALSE NA NA 8.90 22 92600415 HCC1395_HCC1395T 309 0.028 316 62,3 135,2 207,5 NA 0/1 NA NA NA NA 156,153,4,3 C/G PANCANCER NA FALSE CENPP chr9:92600415:92600416:C:G SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 92884541 92884542 TGCCCTAACCC T 30 44 0.681818181818182 LOW ENSG00000291169 - splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant Transcript ENST00000411450 lncRNA 2/3 ENST00000411450.5:n.319-23_319-14del NA 1 deletion 4 1 22 NA NA PASS SITE 48,47|13,17 NA NA 1 93 20,20 155,181 60,55 34 1.71 NA 15.02 NA FALSE 6.00 93 NA NA NA FALSE NA NA 126.81 22 92884541 HCC1395_HCC1395T 14 0.691 44 2,6 4,7 8,19 NA 0/1 NA NA NA NA 6,8,13,17 TGCCCTAACCC/T PANCANCER NA FALSE chr9:92884541:92884542:TGCCCTAACCC:T indel 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 92885181 92885182 T A 31 131 0.236641221374046 MODIFIER ENSG00000291169 A downstream_gene_variant Transcript ENST00000411450 lncRNA NA 130 1 SNV 4 22 NA NA PASS SITE 112,84|16,15 NA NA 1 93 22,20 187,171 60,60 28 1.87 NA 21.93 NA FALSE 6.00 63 NA NA NA FALSE NA NA 67.94 22 92885181 HCC1395_HCC1395T 100 0.222 131 36,6 39,15 76,21 NA 0/1 NA NA NA NA 61,39,16,15 T/A PANCANCER NA FALSE chr9:92885181:92885182:T:A SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 97365646 97365647 C T 206 318 0.647798742138365 MODIFIER MIR1302-8 ENSG00000221269 T upstream_gene_variant Transcript ENST00000408342 miRNA NA 1965 -1 SNV HGNC HGNC:35300 YES 22 NA NA PASS SITE 168,182|96,110 NA NA 1 93 20,20 160,163 60,60 36 2.20 NA 46.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 537.21 22 97365646 HCC1395_HCC1395T 112 0.633 318 28,55 43,68 78,134 NA 0/1 NA NA NA NA 54,58,96,110 C/T PANCANCER NA FALSE MIR1302-8 chr9:97365646:97365647:C:T SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 97480757 97480758 A T 20 35 0.571428571428571 MODIFIER TDRD7 ENSG00000196116 T intron_variant Transcript ENST00000355295 protein_coding 13/16 ENST00000355295.5:c.2302-71A>T NA 1 SNV HGNC HGNC:30831 YES NM_014290.3 1 P1 CCDS6725.1 ENSP00000347444 Q8NHU6.161 UPI00002114B5 Q8NHU6-1 1 22 NA NA PASS SITE 47,2|18,2 NA NA 1 93 34,37 196,205 60,60 16 1.54 NA 9.89 NA FALSE 6.00 86 NA NA NA FALSE NA NA 69.64 22 97480757 HCC1395_HCC1395T 15 0.556 35 4,7 11,12 15,19 NA 0/1 NA NA NA NA 15,0,18,2 A/T PANCANCER NA FALSE TDRD7 chr9:97480757:97480758:A:T SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 99826856 99826857 C A 24 120 0.2 MODIFIER NR4A3 ENSG00000119508 A intron_variant Transcript ENST00000330847 protein_coding 1/6 ENST00000330847.1:c.31+55C>A NA 1 SNV HGNC HGNC:7982 5 CCDS6742.1 ENSP00000333122 Q92570.210 UPI0000160FE4 Q92570-3 1 22 NA NA PASS SITE 74,98|10,14 NA NA 1 93 20,20 159,176 60,60 29 1.73 NA 15.30 NA FALSE 6.00 27 NA NA NA FALSE NA NA 53.29 22 99826856 HCC1395_HCC1395T 96 0.220 120 22,3 38,11 63,17 NA 0/1 NA NA NA NA 41,55,10,14 C/A PANCANCER NA FALSE NR4A3 chr9:99826856:99826857:C:A SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 101399290 101399291 G T 16 45 0.355555555555556 MODIFIER ZNF189 ENSG00000136870 T intron_variant Transcript ENST00000259395 protein_coding 1/3 ENST00000259395.4:c.-188+101G>T NA 1 SNV HGNC HGNC:12980 1 CCDS6755.1 ENSP00000259395 O75820.190 UPI00001696BC O75820-4 22 NA NA PASS SITE 16,51|2,14 NA NA 1 93 35,35 193,187 60,60 30 1.55 NA 9.63 NA FALSE 6.00 78 NA NA NA FALSE NA NA 42.08 22 101399290 HCC1395_HCC1395T 29 0.380 45 8,6 15,7 23,14 NA 0/1 NA NA NA NA 6,23,2,14 G/T PANCANCER NA FALSE ZNF189 chr9:101399290:101399291:G:T SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 101546744 101546745 C G 17 38 0.447368421052632 MODIFIER RNF20 ENSG00000155827 G intron_variant Transcript ENST00000389120 protein_coding 6/19 ENST00000389120.8:c.748-76C>G NA 1 SNV HGNC HGNC:10062 YES NM_019592.7 1 P1 CCDS35084.1 ENSP00000373772 Q5VTR2.176 UPI00001CE3B5 22 NA NA PASS SITE 37,6|12,5 NA NA 1 60 37,39 195,210 60,60 24 1.31 NA 5.72 NA FALSE 6.00 56 NA NA NA FALSE NA NA 48.73 22 101546744 HCC1395_HCC1395T 21 0.424 38 5,3 12,10 18,13 NA 0/1 NA NA NA NA 18,3,12,5 C/G PANCANCER NA FALSE RNF20 chr9:101546744:101546745:C:G SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 105548555 105548556 C G 54 80 0.675 MODIFIER FSD1L ENSG00000106701 G 3_prime_UTR_variant Transcript ENST00000374707 protein_coding 8/8 ENST00000374707.1:c.*2072C>G NA 3184 1 SNV HGNC HGNC:13753 1 ENSP00000363839 Q8N450.172 UPI0000072A47 22 NA NA PASS SITE 52,31|26,28 NA NA 1 93 26,25 165,179 60,60 24 1.66 NA 13.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 164.66 22 105548555 HCC1395_HCC1395T 26 0.682 80 4,18 14,18 19,42 NA 0/1 NA NA NA NA 14,12,26,28 C/G PANCANCER NA FALSE FSD1L chr9:105548555:105548556:C:G SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 105598001 105598002 G A 12 21 0.571428571428571 MODIFIER FKTN ENSG00000106692 A intron_variant Transcript ENST00000223528 protein_coding 3/9 ENST00000223528.6:c.165+1344G>A NA 1 SNV HGNC HGNC:3622 1 P1 CCDS6766.1 ENSP00000223528 O75072.173 UPI000012A5A6 O75072-1 1 22 NA NA PASS SITE 24,3|11,1 NA NA 1 48 40,35 218,220 60,60 22 1.23 NA 4.82 NA FALSE 6.00 48 NA NA NA FALSE NA NA 40.54 22 105598001 HCC1395_HCC1395T 9 0.571 21 1,3 7,9 9,12 NA 0/1 NA NA NA NA 8,1,11,1 G/A PANCANCER NA FALSE FKTN chr9:105598001:105598002:G:A SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 105607844 105607845 G A 206 330 0.624242424242424 MODERATE FKTN ENSG00000106692 A missense_variant Transcript ENST00000223528 protein_coding 6/10 ENST00000223528.6:c.673G>A ENSP00000223528.2:p.D225N ENSP00000223528.2 p.D225N 797 673 225 D/N Gat/Aat rs1298422772&COSV56308550&COSV56312746 1 SNV HGNC HGNC:3622 1 P1 CCDS6766.1 ENSP00000223528 O75072.173 UPI000012A5A6 O75072-1 1 deleterious(0) probably_damaging(0.992) AlphaFold_DB_import:AF-O75072-F1&Pfam:PF19737&PANTHER:PTHR15407 6.604e-06 2.431e-05 0 0 0 0 0 0 0 0 0 2.431e-05 gnomADg_AFR 0&1&1 0&1&1 22 NA NA PASS SITE 173,170|105,101 NA NA 2 93 20,20 155,158 60,60 35 2.14 NA 41.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 862.79 22 105607844 HCC1395_HCC1395T 124 0.623 330 27,42 43,80 77,128 NA 0|1 0|1 105607844_G_A NA 105607844 60,64,105,101 G|A PANCANCER NA FALSE FKTN_p.D225N chr9:105607844:105607845:G:A SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 105607846 105607847 T A 206 330 0.624242424242424 MODERATE FKTN ENSG00000106692 A missense_variant Transcript ENST00000223528 protein_coding 6/10 ENST00000223528.6:c.675T>A ENSP00000223528.2:p.D225E ENSP00000223528.2 p.D225E 799 675 225 D/E gaT/gaA rs779298204&COSV56312762 1 SNV HGNC HGNC:3622 1 P1 CCDS6766.1 ENSP00000223528 O75072.173 UPI000012A5A6 O75072-1 1 deleterious(0.02) probably_damaging(0.989) AlphaFold_DB_import:AF-O75072-F1&Pfam:PF19737&PANTHER:PTHR15407 3.979e-06 0 0 0 0 0 8.799e-06 0 0 8.799e-06 gnomADe_NFE 0&1 0&1 22 NA NA PASS SITE 173,170|105,101 NA NA 2 93 20,20 155,158 60,60 35 2.14 NA 41.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 862.79 22 105607846 HCC1395_HCC1395T 124 0.623 330 28,42 45,81 77,128 NA 0|1 0|1 105607844_G_A NA 105607844 60,64,105,101 T|A PANCANCER NA FALSE FKTN_p.D225E chr9:105607846:105607847:T:A SNV 2:1 chr9:68479292:106929395:2:1:1 TRUE NA 0.96 +chr9 112275987 112275988 T C 20 165 0.121212121212121 MODERATE PTBP3 ENSG00000119314 C missense_variant Transcript ENST00000210227 protein_coding 3/5 ENST00000210227.4:c.163A>G ENSP00000210227.4:p.K55E ENSP00000210227.4 p.K55E 349 163 55 K/E Aaa/Gaa -1 cds_end_NF SNV HGNC HGNC:10253 2 ENSP00000210227 X6R242.59 UPI0003F48366 deleterious_low_confidence(0) probably_damaging(0.981) Gene3D:3.30.70.330&AlphaFold_DB_import:AF-X6R242-F1&PANTHER:PTHR15592&MobiDB_lite:mobidb-lite 22 NA NA PASS SITE 117,148|10,10 NA NA 1 93 20,20 156,188 60,60 31 1.89 NA 22.88 NA FALSE 6.00 65 NA NA NA FALSE NA NA 37.98 22 112275987 HCC1395_HCC1395T 145 0.125 165 39,5 48,6 93,13 NA 0/1 NA NA NA NA 66,79,10,10 T/C PANCANCER NA FALSE PTBP3_p.K55E chr9:112275987:112275988:T:C SNV 2:0 chr9:107318737:128937930:2:0:1 TRUE NA 0.96 +chr9 113369792 113369793 G A 52 88 0.590909090909091 MODIFIER HDHD3 ENSG00000119431 A downstream_gene_variant Transcript ENST00000238379 protein_coding NA COSV53056927 3627 -1 SNV HGNC HGNC:28171 1 P1 CCDS6793.1 ENSP00000238379 Q9BSH5.160 UPI0000073CC1 1 1 22 NA NA PASS SITE 62,82|23,30 NA NA 1 93 37,20 187,174 60,60 23 0.201 NA 22.16 NA FALSE 6.00 93 NA NA NA FALSE NA NA 139.85 22 113369792 HCC1395_HCC1395T 36 0.557 88 15,21 12,13 30,38 NA 0/1 NA NA NA NA 12,24,23,29 G/A PANCANCER NA FALSE HDHD3 chr9:113369792:113369793:G:A SNV 2:0 chr9:107318737:128937930:2:0:1 TRUE NA 0.96 +chr9 113387662 113387663 C G 50 50 1 MODIFIER ALAD ENSG00000148218 G 3_prime_UTR_variant Transcript ENST00000409155 protein_coding 12/12 ENST00000409155.8:c.*638G>C NA 1779 -1 SNV HGNC HGNC:395 YES NM_000031.6 1 P1 CCDS6794.2 ENSP00000386284 P13716.224 A0A140VJL9.30 UPI0000037431 P13716-1 1 22 NA NA PASS SITE 27,24|27,23 NA NA 1 93 20,20 166,160 60,60 32 1.57 NA 10.84 NA FALSE 6.00 93 NA NA NA FALSE NA NA 152.69 22 113387662 HCC1395_HCC1395T 0 0.972 50 0,10 0,23 0,33 NA 0/1 NA NA NA NA 0,0,27,23 C/G PANCANCER NA FALSE ALAD chr9:113387662:113387663:C:G SNV 2:0 chr9:107318737:128937930:2:0:1 TRUE NA 0.96 +chr9 113387776 113387777 C T 42 42 1 MODIFIER ALAD ENSG00000148218 T 3_prime_UTR_variant Transcript ENST00000409155 protein_coding 12/12 ENST00000409155.8:c.*524G>A NA 1665 -1 SNV HGNC HGNC:395 YES NM_000031.6 1 P1 CCDS6794.2 ENSP00000386284 P13716.224 A0A140VJL9.30 UPI0000037431 P13716-1 1 22 NA NA PASS SITE 29,35|19,23 NA NA 1 93 20,20 160,180 60,60 26 1.66 NA 13.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 127.52 22 113387776 HCC1395_HCC1395T 0 0.969 42 0,11 0,14 0,30 NA 0/1 NA NA NA NA 0,0,19,23 C/T PANCANCER NA FALSE ALAD chr9:113387776:113387777:C:T SNV 2:0 chr9:107318737:128937930:2:0:1 TRUE NA 0.96 +chr9 113485515 113485516 A T 63 63 1 MODIFIER RGS3 ENSG00000138835 T intron_variant Transcript ENST00000317613 protein_coding 4/17 ENST00000317613.10:c.285-110A>T NA 1 SNV HGNC HGNC:9999 2 CCDS35113.1 ENSP00000312844 P49796.219 UPI0000246E00 P49796-5 22 NA NA PASS SITE 56,30|43,20 NA NA 1 93 20,20 165,167 60,60 23 1.80 NA 18.31 NA FALSE 6.00 93 NA NA NA FALSE NA NA 204.75 22 113485515 HCC1395_HCC1395T 0 0.980 63 0,14 0,32 0,47 NA 0/1 NA NA NA NA 0,0,43,20 A/T PANCANCER NA FALSE RGS3 chr9:113485515:113485516:A:T SNV 2:0 chr9:107318737:128937930:2:0:1 TRUE NA 0.96 +chr9 120858191 120858192 G A 81 193 0.419689119170984 MODERATE PHF19 ENSG00000119403 A missense_variant Transcript ENST00000373896 protein_coding 15/15 ENST00000373896.8:c.1496C>T ENSP00000363003.3:p.P499L ENSP00000363003.3 p.P499L 1609 1496 499 P/L cCc/cTc COSV65877998 -1 SNV HGNC HGNC:24566 YES NM_015651.3 2 P1 CCDS35116.1 ENSP00000363003 Q5T6S3.156 UPI000016050A Q5T6S3-1 tolerated(0.17) benign(0.007) AlphaFold_DB_import:AF-Q5T6S3-F1&PANTHER:PTHR12628&MobiDB_lite:mobidb-lite 1 1 22 NA NA PASS SITE 129,183|31,50 NA NA 1 93 20,20 163,167 60,60 30 2.15 NA 41.49 NA FALSE 6.00 93 NA NA NA FALSE NA NA 212.96 22 120858191 HCC1395_HCC1395T 112 0.414 193 30,25 42,24 80,56 NA 0/1 NA NA NA NA 47,65,31,50 G/A PANCANCER NA FALSE PHF19_p.P499L chr9:120858191:120858192:G:A SNV 2:0 chr9:107318737:128937930:2:0:1 TRUE NA 0.96 +chr9 121046216 121046217 T A 3 12 0.25 MODERATE C5 ENSG00000106804 A missense_variant Transcript ENST00000223642 protein_coding 2/41 ENST00000223642.3:c.233A>T ENSP00000223642.1:p.K78I ENSP00000223642.1 p.K78I 262 233 78 K/I aAa/aTa -1 SNV HGNC HGNC:1331 YES NM_001735.3 1 P1 CCDS6826.1 ENSP00000223642 P01031.237 UPI000013C838 1 deleterious(0) possibly_damaging(0.901) Gene3D:2.60.40.1930&PDB-ENSP_mappings:3cu7.A&PDB-ENSP_mappings:3cu7.B&PDB-ENSP_mappings:3kls.A&PDB-ENSP_mappings:3kls.B&PDB-ENSP_mappings:3km9.A&PDB-ENSP_mappings:3km9.B&PDB-ENSP_mappings:3prx.A&PDB-ENSP_mappings:3prx.C&PDB-ENSP_mappings:3pvm.A&PDB-ENSP_mappings:3pvm.C&PDB-ENSP_mappings:4a5w.A&PDB-ENSP_mappings:4e0s.A&PDB-ENSP_mappings:5b71.E&PDB-ENSP_mappings:5b71.F&PDB-ENSP_mappings:5hcc.B&PDB-ENSP_mappings:5hcd.B&PDB-ENSP_mappings:5hce.B&PDB-ENSP_mappings:5i5k.A&PDB-ENSP_mappings:5i5k.B&PDB-ENSP_mappings:6h03.A&PDB-ENSP_mappings:6h04.A&PDB-ENSP_mappings:6rqj.B&PDB-ENSP_mappings:7ad6.A&PDB-ENSP_mappings:7ad6.B&PDB-ENSP_mappings:7ad7.A&PDB-ENSP_mappings:7ad7.B&PDB-ENSP_mappings:7nyc.A&PDB-ENSP_mappings:7nyd.A&PDB-ENSP_mappings:7op0.B&PDB-ENSP_mappings:8ayh.C&AlphaFold_DB_import:AF-P01031-F1&Pfam:PF17790&PANTHER:PTHR11412 22 NA NA PASS SITE 19,1|2,1 NA NA 1 30 36,34 204,186 60,60 14 1.04 NA 2.96 NA FALSE 6.00 27 NA NA NA FALSE NA NA 9.09 22 121046216 HCC1395_HCC1395T 9 0.229 12 6,0 3,1 9,2 NA 0/1 NA NA NA NA 9,0,2,1 T/A PANCANCER NA FALSE C5_p.K78I chr9:121046216:121046217:T:A SNV 2:0 chr9:107318737:128937930:2:0:1 TRUE NA 0.96 +chr9 121328765 121328766 T G 11 26 0.423076923076923 MODIFIER GSN ENSG00000148180 G intron_variant&NMD_transcript_variant Transcript ENST00000373806 nonsense_mediated_decay 2/5 ENST00000373806.1:c.*184-126T>G NA 1 cds_start_NF SNV HGNC HGNC:4620 2 ENSP00000362912 Q5T0H8.98 UPI000719A1B4 1 22 NA NA PASS SITE 39,18|8,3 NA NA 1 93 20,20 167,160 60,60 32 1.49 NA 9.03 NA FALSE 6.00 65 NA NA NA FALSE NA NA 30.34 22 121328765 HCC1395_HCC1395T 15 0.454 26 3,6 5,2 10,8 NA 0/1 NA NA NA NA 10,5,8,3 T/G PANCANCER NA FALSE GSN chr9:121328765:121328766:T:G SNV 2:0 chr9:107318737:128937930:2:0:1 TRUE NA 0.96 +chr9 121759150 121759151 G A 108 108 1 MODIFIER DAB2IP ENSG00000136848 A intron_variant Transcript ENST00000259371 protein_coding 5/16 ENST00000259371.7:c.531+154G>A NA 1 SNV HGNC HGNC:17294 5 CCDS6833.2 ENSP00000259371 Q5VWQ8.171 UPI0000D77E70 Q5VWQ8-5 22 NA NA PASS SITE 50,51|57,51 NA NA 1 93 20,20 154,163 60,60 36 1.83 NA 19.55 NA FALSE 6.00 93 NA NA NA FALSE NA NA 291.25 22 121759150 HCC1395_HCC1395T 0 0.985 108 0,27 0,36 0,65 NA 0/1 NA NA NA NA 0,0,57,51 G/A PANCANCER NA FALSE DAB2IP chr9:121759150:121759151:G:A SNV 2:0 chr9:107318737:128937930:2:0:1 TRUE NA 0.96 +chr9 122378980 122378981 G A 13 69 0.188405797101449 MODIFIER PTGS1 ENSG00000095303 A intron_variant Transcript ENST00000223423 protein_coding 5/10 ENST00000223423.8:c.496+62G>A NA 1 SNV HGNC HGNC:9604 1 CCDS6843.1 ENSP00000223423 P23219.225 UPI0000160640 P23219-2 22 NA NA PASS SITE 39,87|6,7 NA NA 1 93 20,34 175,191 60,60 41 1.71 NA 14.75 NA FALSE 6.00 56 NA NA NA FALSE NA NA 29.92 22 122378980 HCC1395_HCC1395T 56 0.193 69 19,6 21,4 45,10 NA 0/1 NA NA NA NA 13,43,6,7 G/A PANCANCER NA FALSE PTGS1 chr9:122378980:122378981:G:A SNV 2:0 chr9:107318737:128937930:2:0:1 TRUE NA 0.96 +chr9 123375485 123375486 C G 19 20 0.95 MODIFIER CRB2 ENSG00000148204 G downstream_gene_variant Transcript ENST00000359999 protein_coding NA 1386 1 SNV HGNC HGNC:18688 2 ENSP00000353092 Q5IJ48.159 UPI00004577AA Q5IJ48-2 1 22 NA NA PASS SITE 0,21|1,18 NA NA 1 75 40,39 239,226 60,60 21 1.32 NA 6.02 NA FALSE 6.00 93 NA NA NA FALSE NA NA 75.74 22 123375485 HCC1395_HCC1395T 1 0.945 20 0,7 0,11 1,19 NA 0/1 NA NA NA NA 0,1,1,18 C/G PANCANCER NA FALSE CRB2 chr9:123375485:123375486:C:G SNV 2:0 chr9:107318737:128937930:2:0:1 TRUE NA 0.96 +chr9 128422202 128422203 C T 50 50 1 MODIFIER CERCAM ENSG00000167123 T intron_variant Transcript ENST00000372838 protein_coding 1/12 ENST00000372838.9:c.198-666C>T NA 1 SNV HGNC HGNC:23723 YES NM_016174.5 1 P1 CCDS6901.2 ENSP00000361929 Q5T4B2.144 UPI000046FF85 Q5T4B2-1 22 NA NA PASS SITE 20,30|22,28 NA NA 1 93 20,20 174,172 60,60 35 1.59 NA 11.14 NA FALSE 6.00 93 NA NA NA FALSE NA NA 145.10 22 128422202 HCC1395_HCC1395T 0 0.971 50 0,8 0,23 0,33 NA 0/1 NA NA NA NA 0,0,22,28 C/T PANCANCER NA FALSE CERCAM chr9:128422202:128422203:C:T SNV 2:0 chr9:107318737:128937930:2:0:1 TRUE NA 0.96 +chr9 129102404 129102405 T C 22 113 0.194690265486726 MODERATE CRAT ENSG00000095321 C missense_variant Transcript ENST00000318080 protein_coding 5/14 ENST00000318080.7:c.626A>G ENSP00000315013.2:p.Y209C ENSP00000315013.2 p.Y209C 910 626 209 Y/C tAc/tGc -1 SNV HGNC HGNC:2342 YES NM_000755.5 1 P1 CCDS6919.1 ENSP00000315013 P43155.203 UPI000014021A P43155-1 1 tolerated(0.11) probably_damaging(0.938) PDB-ENSP_mappings:1nm8.A&PDB-ENSP_mappings:1s5o.A&PANTHER:PTHR22589&Gene3D:3.30.559.70&Gene3D:3.30.559.10&Pfam:PF00755&Superfamily:SSF52777&AlphaFold_DB_import:AF-P43155-F1 22 NA NA PASS SITE 106,43|16,6 NA NA 1 93 20,20 161,151 60,60 24 1.66 NA 12.94 NA FALSE 6.00 76 NA NA NA FALSE NA NA 53.49 22 129102404 HCC1395_HCC1395T 91 0.202 113 29,7 35,9 66,16 NA 0/1 NA NA NA NA 63,28,16,6 T/C PANCANCER NA FALSE CRAT_p.Y209C chr9:129102404:129102405:T:C SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 130307566 130307567 G A 16 110 0.145454545454545 LOW HMCN2 ENSG00000148357 A splice_region_variant&5_prime_UTR_variant Transcript ENST00000611173 protein_coding 1/10 ENST00000611173.1:c.-12G>A NA 48 1 SNV HGNC HGNC:21293 1 ENSP00000481543 A0A087WY63.45 UPI0004E4C9B4 22 NA NA PASS SITE 85,114|6,10 NA NA 1 93 20,20 166,161 60,60 47 1.84 NA 20.16 NA FALSE 6.00 51 NA NA NA FALSE NA NA 35.25 22 130307566 HCC1395_HCC1395T 94 0.160 110 18,4 34,6 62,11 NA 0/1 NA NA NA NA 39,55,6,10 G/A PANCANCER NA FALSE HMCN2 chr9:130307566:130307567:G:A SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 131094351 131094352 A G 13 78 0.166666666666667 MODIFIER AIF1L ENSG00000126878 G upstream_gene_variant Transcript ENST00000247291 protein_coding NA 2180 1 SNV HGNC HGNC:28904 YES NM_031426.4 1 P1 CCDS6939.1 ENSP00000247291 Q9BQI0.181 UPI0000047811 Q9BQI0-1 22 NA NA PASS SITE 51,47|6,7 NA NA 1 68 20,35 161,166 60,60 20 1.38 NA 6.92 NA FALSE 6.00 9 NA NA NA FALSE NA NA 33.42 22 131094351 HCC1395_HCC1395T 65 0.196 78 16,1 26,6 44,10 NA 0/1 NA NA NA NA 36,29,6,7 A/G PANCANCER NA FALSE AIF1L chr9:131094351:131094352:A:G SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 131120337 131120338 C T 44 239 0.184100418410042 MODIFIER AIF1L ENSG00000126878 T 3_prime_UTR_variant Transcript ENST00000247291 protein_coding 6/6 ENST00000247291.8:c.*15C>T NA 567 1 SNV HGNC HGNC:28904 YES NM_031426.4 1 P1 CCDS6939.1 ENSP00000247291 Q9BQI0.181 UPI0000047811 Q9BQI0-1 22 NA NA PASS SITE 167,173|21,23 NA NA 1 93 20,27 180,179 60,60 31 2.02 NA 31.00 NA FALSE 6.00 93 NA NA NA FALSE NA NA 110.05 22 131120337 HCC1395_HCC1395T 195 0.198 239 58,16 70,13 137,33 NA 0/1 NA NA NA NA 100,95,21,23 C/T PANCANCER NA FALSE AIF1L chr9:131120337:131120338:C:T SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 133344292 133344293 G C 27 33 0.818181818181818 MODIFIER RPL7A ENSG00000148303 C upstream_gene_variant Transcript ENST00000315731 protein_coding NA COSV59300977 4630 1 SNV HGNC HGNC:10364 2 ENSP00000361071 Q5T8U2.123 UPI000046FDFF 1 1 22 NA NA PASS SITE 34,37|10,17 NA NA 1 93 20,20 145,186 60,60 21 1.61 NA 11.99 NA FALSE 6.00 93 NA NA NA FALSE NA NA 77.35 22 133344292 HCC1395_HCC1395T 6 0.828 33 0,5 3,11 3,18 NA 0/1 NA NA NA NA 3,3,10,17 G/C PANCANCER NA FALSE RPL7A chr9:133344292:133344293:G:C SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 133354715 133354716 G C 21 32 0.65625 MODIFIER RPL7A ENSG00000148303 C downstream_gene_variant Transcript ENST00000315731 protein_coding NA COSV59871863 3289 1 SNV HGNC HGNC:10364 2 ENSP00000361071 Q5T8U2.123 UPI000046FDFF 1 1 22 NA NA PASS SITE 29,18|15,6 NA NA 1 72 20,20 167,150 60,60 29 1.40 NA 7.18 NA FALSE 6.00 83 NA NA NA FALSE NA NA 57.65 22 133354715 HCC1395_HCC1395T 11 0.640 32 4,5 4,9 8,15 NA 0/1 NA NA NA NA 7,4,15,6 G/C PANCANCER NA FALSE RPL7A chr9:133354715:133354716:G:C SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 133405468 133405469 G C 172 429 0.400932400932401 MODIFIER REXO4 ENSG00000148300 C downstream_gene_variant Transcript ENST00000371935 protein_coding NA 591 -1 SNV HGNC HGNC:12820 3 CCDS65179.1 ENSP00000361003 Q9GZR2.173 UPI0000551C9E Q9GZR2-2 22 NA NA PASS SITE 287,253|96,76 NA NA 1 93 20,20 157,158 60,60 39 2.25 NA 52.98 NA FALSE 6.00 93 NA NA NA FALSE NA NA 437.98 22 133405468 HCC1395_HCC1395T 257 0.413 429 68,59 76,40 163,115 NA 0/1 NA NA NA NA 139,118,96,76 G/C PANCANCER NA FALSE REXO4 chr9:133405468:133405469:G:C SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 133474130 133474131 G C 52 79 0.658227848101266 MODIFIER CACFD1 ENSG00000160325 C downstream_gene_variant Transcript ENST00000291722 protein_coding NA 3282 1 SNV HGNC HGNC:1365 2 CCDS48051.1 ENSP00000291722 Q9UGQ2.163 UPI000003B0B1 Q9UGQ2-2 22 NA NA PASS SITE 19,68|15,37 NA NA 1 93 36,34 180,167 60,60 19 1.69 NA 14.45 NA FALSE 6.00 93 NA NA NA FALSE NA NA 160.00 22 133474130 HCC1395_HCC1395T 27 0.661 79 7,17 10,18 20,40 NA 0/1 NA NA NA NA 7,20,15,37 G/C PANCANCER NA FALSE CACFD1 chr9:133474130:133474131:G:C SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 136008117 136008118 A T 21 89 0.235955056179775 MODIFIER NACC2 ENSG00000148411 T 3_prime_UTR_variant Transcript ENST00000277554 protein_coding 6/6 ENST00000277554.4:c.*3399T>A NA 5323 -1 SNV HGNC HGNC:23846 YES NM_144653.5 1 P1 CCDS6993.1 ENSP00000277554 Q96BF6.156 A0A024R8I0.63 UPI0000073EEB 22 NA NA PASS SITE 82,73|10,11 NA NA 1 93 20,20 156,170 60,60 35 1.78 NA 17.46 NA FALSE 6.00 71 NA NA NA FALSE NA NA 47.84 22 136008117 HCC1395_HCC1395T 68 0.246 89 21,5 21,8 45,14 NA 0/1 NA NA NA NA 37,31,10,11 A/T PANCANCER NA FALSE NACC2 chr9:136008117:136008118:A:T SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 136115760 136115761 C G 92 136 0.676470588235294 MODIFIER TMEM250 ENSG00000238227 G 3_prime_UTR_variant Transcript ENST00000418388 protein_coding 2/2 ENST00000418388.6:c.*721G>C NA 1656 rs1245039579 -1 SNV HGNC HGNC:31009 YES NM_152833.3 1 P1 CCDS59155.1 ENSP00000453019 H0YL14.70 UPI0000210F31 22 NA NA PASS SITE 69,68|44,48 NA NA 1 93 20,20 149,154 60,60 34 1.78 NA 17.76 NA FALSE 6.00 93 NA NA NA FALSE NA NA 253.60 22 136115760 HCC1395_HCC1395T 44 0.700 136 10,25 15,28 25,60 NA 0/1 NA NA NA NA 24,20,44,48 C/G PANCANCER NA FALSE TMEM250 chr9:136115760:136115761:C:G SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 136754586 136754587 G A 53 122 0.434426229508197 MODIFIER LCN8 ENSG00000204001 A intron_variant Transcript ENST00000371688 protein_coding 6/6 ENST00000371688.8:c.448-77C>T NA -1 SNV HGNC HGNC:27038 YES NM_178469.4 1 P2 CCDS35183.1 ENSP00000360753 Q6JVE9.144 A0A384MDK0.17 UPI00000498C5 Q6JVE9-2 22 NA NA PASS SITE 52,120|18,35 NA NA 1 93 20,20 172,163 60,60 18 1.91 NA 22.58 NA FALSE 6.00 87 NA NA NA FALSE NA NA 132.97 22 136754586 HCC1395_HCC1395T 69 0.435 122 17,12 28,17 48,37 NA 0/1 NA NA NA NA 24,45,18,35 G/A PANCANCER NA FALSE LCN8 chr9:136754586:136754587:G:A SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 136764600 136764601 G A 9 27 0.333333333333333 MODIFIER LCN15 ENSG00000177984 A upstream_gene_variant Transcript ENST00000316144 protein_coding NA 82 -1 SNV HGNC HGNC:33777 YES NM_203347.2 1 P1 CCDS7006.1 ENSP00000313833 Q6UWW0.130 UPI000004C645 22 NA NA PASS SITE 4,41|2,7 NA NA 1 77 38,34 196,197 60,60 26 1.42 NA 7.52 NA FALSE 6.00 49 NA NA NA FALSE NA NA 22.80 22 136764600 HCC1395_HCC1395T 18 0.320 27 7,3 7,4 16,7 NA 0/1 NA NA NA NA 2,16,2,7 G/A PANCANCER NA FALSE LCN15 chr9:136764600:136764601:G:A SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 136994920 136994921 C T 50 65 0.769230769230769 MODIFIER PAXX ENSG00000148362 T downstream_gene_variant Transcript ENST00000371620 protein_coding NA rs1394670129 944 1 SNV HGNC HGNC:27849 YES NM_183241.3 1 P1 CCDS7020.1 ENSP00000360682 Q9BUH6.146 UPI00001BD908 Q9BUH6-1 2.776e-05 7.479e-05 0 6.861e-05 0 0 0 0 0 0 0 7.479e-05 gnomADg_AFR 22 NA NA PASS SITE 30,28|23,27 NA NA 1 68 20,20 133,155 60,60 27 1.48 NA 8.73 NA FALSE 4.31 93 NA NA NA FALSE NA NA 132.89 22 136994920 HCC1395_HCC1395T 15 0.773 65 3,16 6,17 9,33 NA 0/1 NA NA NA NA 8,7,23,27 C/T PANCANCER NA FALSE PAXX chr9:136994920:136994921:C:T SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 137008691 137008692 G C 44 202 0.217821782178218 MODIFIER ABCA2 ENSG00000107331 C intron_variant Transcript ENST00000341511 protein_coding 47/48 ENST00000341511.11:c.7068+40C>G NA -1 SNV HGNC HGNC:32 YES NM_001606.5 5 P3 CCDS43909.1 ENSP00000344155 Q9BZC7.177 UPI0000049F97 Q9BZC7-3 1 22 NA NA PASS SITE 139,145|19,25 NA NA 1 93 20,33 161,188 60,60 29 1.97 NA 26.75 NA FALSE 6.00 87 NA NA NA FALSE NA NA 112.80 22 137008691 HCC1395_HCC1395T 158 0.231 202 38,8 60,17 111,33 NA 0/1 NA NA NA NA 80,78,19,25 G/C PANCANCER NA FALSE ABCA2 chr9:137008691:137008692:G:C SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 137086862 137086863 T C 70 220 0.318181818181818 MODIFIER UAP1L1 ENSG00000197355 C downstream_gene_variant Transcript ENST00000360271 protein_coding NA 2323 1 SNV HGNC HGNC:28082 2 ENSP00000353409 Q3KQV9.122 UPI00004577E9 Q3KQV9-2 22 NA NA PASS SITE 180,159|37,33 NA NA 1 93 20,20 158,156 60,60 37 2.08 NA 36.02 NA FALSE 6.00 93 NA NA NA FALSE NA NA 166.16 22 137086862 HCC1395_HCC1395T 150 0.313 220 44,17 46,26 98,44 NA 0/1 NA NA NA NA 81,69,37,33 T/C PANCANCER NA FALSE UAP1L1 chr9:137086862:137086863:T:C SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 137181620 137181621 C G 59 74 0.797297297297297 MODIFIER ANAPC2 ENSG00000176248 G intron_variant Transcript ENST00000323927 protein_coding 7/12 ENST00000323927.3:c.1468+61G>C NA COSV60570847 -1 SNV HGNC HGNC:19989 YES NM_013366.4 1 P1 CCDS7033.1 ENSP00000314004 Q9UJX6.196 UPI0000043E1B Q9UJX6-1 1 1 22 NA NA PASS SITE 44,33|39,20 NA NA 1 93 20,20 157,170 60,60 29 1.62 NA 12.04 NA FALSE 6.00 93 NA NA NA FALSE NA NA 175.51 22 137181620 HCC1395_HCC1395T 15 0.808 74 3,14 6,27 9,41 NA 0/1 NA NA NA NA 9,6,39,20 C/G PANCANCER NA FALSE ANAPC2 chr9:137181620:137181621:C:G SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 137255474 137255475 G C 207 253 0.818181818181818 MODERATE NELFB ENSG00000188986 C missense_variant Transcript ENST00000343053 protein_coding 1/13 ENST00000343053.6:c.109G>C ENSP00000339495.6:p.G37R ENSP00000339495.6 p.G37R 148 109 37 G/R Ggg/Cgg 1 SNV HGNC HGNC:24324 YES NM_015456.5 1 P1 CCDS7040.2 ENSP00000339495 Q8WX92.187 A0A5H1ZRP4.11 UPI0006573AD6 Q8WX92-2 deleterious_low_confidence(0) unknown(0) AlphaFold_DB_import:AF-A0A5H1ZRP4-F1&AlphaFold_DB_import:AF-Q8WX92-F1&PANTHER:PTHR13503&MobiDB_lite:mobidb-lite 22 NA NA PASS SITE 149,79|130,77 NA NA 1 93 20,20 155,164 60,60 25 2.12 NA 39.08 NA FALSE 6.00 93 NA NA NA FALSE NA NA 608.53 22 137255474 HCC1395_HCC1395T 46 0.810 253 14,60 17,80 33,144 NA 0/1 NA NA NA NA 29,17,130,77 G/C PANCANCER NA FALSE NELFB_p.G37R chr9:137255474:137255475:G:C SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 137280377 137280378 C T 185 240 0.770833333333333 MODIFIER TOR4A ENSG00000198113 T 3_prime_UTR_variant Transcript ENST00000357503 protein_coding 2/2 ENST00000357503.3:c.*416C>T NA 1907 1 SNV HGNC HGNC:25981 YES NM_017723.3 2 P1 CCDS7041.1 ENSP00000350102 Q9NXH8.153 UPI00004577EC 22 NA NA PASS SITE 110,80|106,79 NA NA 1 93 20,20 170,164 60,60 31 1.98 NA 28.59 NA FALSE 6.00 93 NA NA NA FALSE NA NA 510.29 22 137280377 HCC1395_HCC1395T 55 0.747 240 18,37 23,84 42,126 NA 0/1 NA NA NA NA 36,19,106,79 C/T PANCANCER NA FALSE TOR4A chr9:137280377:137280378:C:T SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 137436072 137436073 C T 190 543 0.349907918968692 MODIFIER NOXA1 ENSG00000188747 T downstream_gene_variant Transcript ENST00000341349 protein_coding NA rs757636531 1666 1 SNV HGNC HGNC:10668 1 CCDS7042.1 ENSP00000342848 Q86UR1.162 UPI0000074717 Q86UR1-2 1.2e-05 0 0 0 0 0 1.775e-05 0.0001636 0 6.569e-06 0 0 0 0 0 0 0 1.47e-05 0 0 0.0001636 gnomADe_OTH 22 NA NA PASS SITE 442,301|118,72 NA NA 1 93 20,20 159,164 60,60 35 2.43 NA 78.51 NA FALSE 4.61 93 NA NA NA FALSE NA NA 471.60 22 137436072 HCC1395_HCC1395T 353 0.347 543 99,51 131,74 243,129 NA 0/1 NA NA NA NA 216,137,118,72 C/T PANCANCER NA FALSE NOXA1 chr9:137436072:137436073:C:T SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 137498347 137498348 C T 10 39 0.256410256410256 MODIFIER PNPLA7 ENSG00000130653 T intron_variant Transcript ENST00000277531 protein_coding 15/33 ENST00000277531.8:c.1683-102G>A NA -1 SNV HGNC HGNC:24768 2 A2 CCDS7045.1 ENSP00000277531 Q6ZV29.154 UPI000443805E Q6ZV29-1 22 NA NA PASS SITE 5,56|0,10 NA NA 1 81 38,34 194,202 60,60 23 1.47 NA 8.39 NA FALSE 6.00 41 NA NA NA FALSE NA NA 24.96 22 137498347 HCC1395_HCC1395T 29 0.269 39 9,3 19,6 28,10 NA 0/1 NA NA NA NA 1,28,0,10 C/T PANCANCER NA FALSE PNPLA7 chr9:137498347:137498348:C:T SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr9 137879161 137879162 T C 139 519 0.267822736030829 HIGH CACNA1B ENSG00000148408 C splice_donor_variant Transcript ENST00000277551 protein_coding 2/46 ENST00000277551.6:c.390+2T>C NA rs201604190&COSV53116736&COSV53125946 1 SNV HGNC HGNC:1389 5 A2 CCDS59523.1 ENSP00000277551 Q00975.203 UPI0000470351 Q00975-2 1 0.008276 0.004854 0.003072 0.004343 0.004753 0.02103 0.00979 0.004803 0.01409 0.02103 gnomADe_FIN 0&1&1 0&1&1 22 NA NA PASS SITE 413,373|78,61 NA NA 1 93 20,20 157,162 60,60 31 2.42 NA 77.00 NA FALSE 3.91 93 NA NA NA FALSE NA NA 333.22 22 137879161 HCC1395_HCC1395T 380 0.274 519 90,41 131,44 248,93 NA 0/1 NA NA NA NA 206,174,78,61 T/C PANCANCER NA FALSE CACNA1B chr9:137879161:137879162:T:C SNV 2:1 chr9:128973280:138123517:2:1:1 TRUE NA 0.96 +chr10 5882953 5882954 G C 24 89 0.269662921348315 MODIFIER ANKRD16 ENSG00000134461 C intron_variant Transcript ENST00000191063 protein_coding 5/5 ENST00000191063.8:c.849+53C>G NA -1 SNV HGNC HGNC:23471 3 CCDS31137.1 ENSP00000352361 Q6P6B7.161 UPI00004C9B0D Q6P6B7-2 2 NA NA PASS SITE 83,74|12,12 NA NA 1 93 20,20 164,146 60,60 39 1.79 NA 17.76 NA FALSE 6.00 93 NA NA NA FALSE NA NA 51.09 2 5882953 HCC1395_HCC1395T 65 0.263 89 11,7 27,7 44,15 NA 0/1 NA NA NA NA 34,31,12,12 G/C PANCANCER NA FALSE ANKRD16 chr10:5882953:5882954:G:C SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 5956497 5956498 C G 40 40 1 MODIFIER IL15RA ENSG00000134470 G intron_variant Transcript ENST00000379971 protein_coding 3/4 ENST00000379971.5:c.323-43G>C NA -1 SNV HGNC HGNC:5978 3 ENSP00000369306 Q13261.182 UPI00004A3A4A Q13261-9 2 NA NA PASS SITE 32,38|21,19 NA NA 1 93 20,20 164,173 60,60 43 1.67 NA 13.75 NA FALSE 6.00 93 NA NA NA FALSE NA NA 127.02 2 5956497 HCC1395_HCC1395T 0 0.968 40 0,16 0,11 0,28 NA 0/1 NA NA NA NA 0,0,21,19 C/G PANCANCER NA FALSE IL15RA chr10:5956497:5956498:C:G SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 6216956 6216957 G C 29 29 1 MODIFIER PFKFB3 ENSG00000170525 C intron_variant Transcript ENST00000317350 protein_coding 5/14 ENST00000317350.8:c.441+176G>C NA 1 SNV HGNC HGNC:8874 5 A1 ENSP00000369105 Q5W015.125 UPI0000458882 2 NA NA PASS SITE 30,5|29,0 NA NA 1 93 38,39 230,230 60,60 37 1.56 NA 10.53 NA FALSE 6.00 93 NA NA NA FALSE NA NA 123.67 2 6216956 HCC1395_HCC1395T 0 0.969 29 0,9 0,20 0,29 NA 0/1 NA NA NA NA 0,0,29,0 G/C PANCANCER NA FALSE PFKFB3 chr10:6216956:6216957:G:C SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 7161282 7161283 G T 51 51 1 MODIFIER SFMBT2 ENSG00000198879 T 3_prime_UTR_variant Transcript ENST00000361972 protein_coding 21/21 ENST00000361972.8:c.*2488C>A NA 5264 -1 SNV HGNC HGNC:20256 1 P4 CCDS31138.1 ENSP00000355109 Q5VUG0.150 UPI00001C1EDF 2 NA NA PASS SITE 33,30|26,25 NA NA 1 93 20,20 150,149 60,60 24 1.63 NA 12.34 NA FALSE 6.00 93 NA NA NA FALSE NA NA 152.64 2 7161282 HCC1395_HCC1395T 0 0.973 51 0,15 0,18 0,34 NA 0/1 NA NA NA NA 0,0,26,25 G/T PANCANCER NA FALSE SFMBT2 chr10:7161282:7161283:G:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 11330539 11330540 T C 96 96 1 MODIFIER CELF2 ENSG00000048740 C downstream_gene_variant Transcript ENST00000354897 protein_coding NA 1260 1 SNV HGNC HGNC:2550 5 ENSP00000346971 Q5VZZ6.140 UPI00001F8B3A 1 2 NA NA PASS SITE 46,37|51,45 NA NA 1 93 20,34 182,180 60,60 31 1.80 NA 18.36 NA FALSE 6.00 93 NA NA NA FALSE NA NA 327.90 2 11330539 HCC1395_HCC1395T 0 0.987 96 0,19 0,50 0,73 NA 0/1 NA NA NA NA 0,0,51,45 T/C PANCANCER NA FALSE CELF2 chr10:11330539:11330540:T:C SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 11823264 11823265 G A 7 7 1 MODIFIER PROSER2 ENSG00000148426 A upstream_gene_variant Transcript ENST00000277570 protein_coding NA rs974817002 92 1 SNV HGNC HGNC:23728 YES NM_153256.4 1 P2 CCDS7085.1 ENSP00000277570 Q86WR7.135 UPI00001F8B49 Q86WR7-1 2 NA NA PASS SITE 16,0|6,1 NA NA 1 63 32,38 193,209 60,60 15 1.24 NA 4.81 NA FALSE 6.00 76 NA NA NA FALSE NA NA 28.32 2 11823264 HCC1395_HCC1395T 0 0.888 7 0,3 0,3 0,6 NA 0/1 NA NA NA NA 0,0,6,1 G/A PANCANCER NA FALSE PROSER2 chr10:11823264:11823265:G:A SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 13481024 13481025 C G 158 159 0.993710691823899 MODERATE BEND7 ENSG00000165626 G missense_variant Transcript ENST00000341083 protein_coding 6/9 ENST00000341083.7:c.782G>C ENSP00000345773.3:p.R261T ENSP00000345773.3 p.R261T 1079 782 261 R/T aGa/aCa COSV105242965&COSV61991707 -1 SNV HGNC HGNC:23514 2 A2 CCDS7099.1 ENSP00000345773 Q8N7W2.146 UPI000013FFEA Q8N7W2-3 deleterious(0) probably_damaging(0.99) PROSITE_profiles:PS51457&PANTHER:PTHR35068&Gene3D:1.10.10.2590&Pfam:PF10523&SMART:SM01025&AlphaFold_DB_import:AF-Q8N7W2-F1 1&1 1&1 2 NA NA PASS SITE 92,108|69,89 NA NA 1 93 20,20 152,164 60,60 37 2.11 NA 37.62 NA FALSE 6.00 93 NA NA NA FALSE NA NA 479.35 2 13481024 HCC1395_HCC1395T 1 0.982 159 0,37 1,63 1,105 NA 0/1 NA NA NA NA 0,1,69,89 C/G PANCANCER NA FALSE BEND7_p.R261T chr10:13481024:13481025:C:G SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 13740500 13740501 G A 23 50 0.46 MODIFIER FRMD4A ENSG00000151474 A intron_variant Transcript ENST00000264546 protein_coding 9/16 ENST00000264546.10:c.713+12C>T NA rs758038748 -1 cds_end_NF SNV HGNC HGNC:25491 2 ENSP00000264546 Q5T376.159 UPI000013E4DA 1 0 0 0 0 0 0 0 0 0 0 gnomADe_AFR&gnomADe_AMR&gnomADe_ASJ&gnomADe_EAS&gnomADe_FIN&gnomADe_NFE&gnomADe_OTH&gnomADe_SAS 2 NA NA PASS SITE 60,31|15,8 NA NA 1 93 20,20 171,151 60,60 30 1.67 NA 13.84 NA FALSE 6.00 49 NA NA NA FALSE NA NA 59.90 2 13740500 HCC1395_HCC1395T 27 0.447 50 7,4 12,12 20,16 NA 0/1 NA NA NA NA 18,9,15,8 G/A PANCANCER NA FALSE FRMD4A chr10:13740500:13740501:G:A SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 18680490 18680491 G A 49 50 0.98 MODIFIER ARL5B ENSG00000165997 A 3_prime_UTR_variant Transcript ENST00000377275 protein_coding 6/6 ENST00000377275.4:c.*5274G>A NA 6021 1 SNV HGNC HGNC:23052 YES NM_178815.5 1 P1 CCDS7131.1 ENSP00000366487 Q96KC2.165 B0YIW9.118 UPI000006F7A5 2 NA NA PASS SITE 90,64|30,19 NA NA 1 93 20,35 159,207 60,60 24 2.03 NA 31.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 169.89 2 18680490 HCC1395_HCC1395T 1 0.960 50 0,16 1,27 1,44 NA 0/1 NA NA NA NA 0,1,30,19 G/A PANCANCER NA FALSE ARL5B chr10:18680490:18680491:G:A SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 23442124 23442126 GA AT 3 16 0.1875 MODIFIER OTUD1 ENSG00000165312 AT 3_prime_UTR_variant Transcript ENST00000376495 protein_coding 1/1 ENST00000376495.5:c.*1221_*1222delinsAT NA 3050-3051 1 substitution HGNC HGNC:27346 YES NM_001145373.3 P1 CCDS44366.1 ENSP00000365678 Q5VV17.122 UPI0000458A32 2 NA NA PASS SITE 23,22|2,1 NA NA 1 93 39,39 216,199 60,60 16 1.52 NA 9.63 NA FALSE 6.00 24 NA NA NA FALSE NA NA 9.52 2 23442124 HCC1395_HCC1395T 13 0.222 16 4,1 8,2 13,3 NA 0/1 NA NA NA NA 6,7,2,1 GA/AT PANCANCER NA FALSE OTUD1 chr10:23442124:23442126:GA:AT indel 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 32567833 32567834 C T 26 76 0.342105263157895 MODERATE CCDC7 ENSG00000216937 T missense_variant Transcript ENST00000277657 protein_coding 16/18 ENST00000277657.12:c.1361C>T ENSP00000277657.6:p.S454L ENSP00000277657.6 p.S454L 1670 1361 454 S/L tCa/tTa 1 SNV HGNC HGNC:26533 1 P2 CCDS7173.1 ENSP00000277657 Q96M83.143 A0A384NKY2.17 UPI00000745EB Q96M83-3 tolerated(0.17) benign(0.171) AlphaFold_DB_import:AF-Q96M83-F1&PANTHER:PTHR22035&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite 2 NA NA PASS SITE 44,49|10,16 NA NA 1 84 20,20 166,174 60,60 29 1.46 NA 8.43 NA FALSE 6.00 68 NA NA NA FALSE NA NA 60.23 2 32567833 HCC1395_HCC1395T 50 0.340 76 7,5 20,6 34,17 NA 0/1 NA NA NA NA 23,27,10,16 C/T PANCANCER NA FALSE CCDC7_p.S454L chr10:32567833:32567834:C:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 35607697 35607698 G T 17 1003 0.0169491525423729 MODERATE GJD4 ENSG00000177291 T missense_variant Transcript ENST00000321660 protein_coding 2/2 ENST00000321660.2:c.184G>T ENSP00000315070.1:p.A62S ENSP00000315070.1 p.A62S 411 184 62 A/S Gcc/Tcc rs1347303151&COSV58703453 1 SNV HGNC HGNC:23296 YES NM_153368.3 1 P1 CCDS7191.1 ENSP00000315070 Q96KN9.150 UPI000007118B tolerated(0.87) benign(0.068) PANTHER:PTHR11984&PROSITE_patterns:PS00407&Gene3D:1.20.1440.80&Pfam:PF00029&SMART:SM00037&Prints:PR00206&AlphaFold_DB_import:AF-Q96KN9-F1 3.979e-06 0 0 0 0 0 0 0.000163 0 0.000163 gnomADe_OTH 0&1 0&1 2 NA NA PASS SITE 862,783|9,8 NA NA 1 93 20,20 155,142 60,60 20 2.63 NA 125.03 NA FALSE 6.00 29 NA NA NA FALSE NA NA 23.02 2 35607697 HCC1395_HCC1395T 986 0.017 1003 257,2 335,8 630,10 NA 0/1 NA NA NA NA 523,463,9,8 G/T PANCANCER NA FALSE GJD4_p.A62S chr10:35607697:35607698:G:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 37858179 37858180 G A 26 50 0.52 MODIFIER ZNF248 ENSG00000198105 A upstream_gene_variant Transcript ENST00000357328 protein_coding NA rs974984278 95 -1 SNV HGNC HGNC:13041 2 P1 CCDS7194.1 ENSP00000349882 Q8NDW4.165 A2RUI7.134 UPI000006CF12 Q8NDW4-1 2 NA NA PASS SITE 16,36|6,20 NA NA 1 65 20,33 186,159 60,60 23 1.33 NA 6.02 NA FALSE 6.00 53 NA NA NA FALSE NA NA 73.16 2 37858179 HCC1395_HCC1395T 24 0.553 50 6,5 9,11 16,20 NA 0/1 NA NA NA NA 8,16,6,20 G/A PANCANCER NA FALSE ZNF248 chr10:37858179:37858180:G:A SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 37957501 37957502 C T 133 275 0.483636363636364 MODERATE ZNF25 ENSG00000175395 T missense_variant Transcript ENST00000302609 protein_coding 3/6 ENST00000302609.8:c.61G>A ENSP00000302222.7:p.E21K ENSP00000302222.7 p.E21K 288 61 21 E/K Gaa/Aaa COSV56924601 -1 SNV HGNC HGNC:13043 YES NM_145011.4 1 P1 CCDS7195.1 ENSP00000302222 P17030.202 UPI0000071FFD P17030-1 deleterious(0.01) possibly_damaging(0.631) PROSITE_profiles:PS50805&CDD:cd07765&Gene3D:6.10.140.140&Pfam:PF01352&SMART:SM00349&Superfamily:SSF109640&AlphaFold_DB_import:AF-P17030-F1 1 1 2 NA NA PASS SITE 115,145|62,71 NA NA 1 93 20,20 150,155 60,60 35 1.85 NA 21.07 NA FALSE 6.00 93 NA NA NA FALSE NA NA 319.30 2 37957501 HCC1395_HCC1395T 142 0.493 275 30,30 44,48 86,83 NA 0/1 NA NA NA NA 62,80,62,71 C/T PANCANCER NA FALSE ZNF25_p.E21K chr10:37957501:37957502:C:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 43128682 43128683 C A 26 105 0.247619047619048 MODIFIER RET ENSG00000165731 A downstream_gene_variant Transcript ENST00000340058 protein_coding NA 1178 1 SNV HGNC HGNC:9967 1 A2 CCDS53525.1 ENSP00000344798 P07949.269 UPI0000160664 P07949-2 1 2 NA NA PASS SITE 63,58|14,12 NA NA 1 88 20,20 160,161 60,60 31 1.48 NA 8.68 NA FALSE 6.00 66 NA NA NA FALSE NA NA 59.30 2 43128682 HCC1395_HCC1395T 79 0.234 105 21,7 34,10 58,17 NA 0/1 NA NA NA NA 39,40,14,12 C/A PANCANCER TRUE FALSE RET chr10:43128682:43128683:C:A SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 48743018 48743019 C T 50 151 0.33112582781457 LOW WDFY4 ENSG00000128815 T synonymous_variant Transcript ENST00000325239 protein_coding 12/62 ENST00000325239.12:c.1929C>T ENSP00000320563.5:p.V643= ENSP00000320563.5 p.V643= 2075 1929 643 V gtC/gtT 1 SNV HGNC HGNC:29323 YES NM_001394531.1 5 P1 CCDS44385.1 ENSP00000320563 Q6ZS81.147 UPI000176ADB8 Q6ZS81-1 Gene3D:1.25.10.10&PANTHER:PTHR46108&Superfamily:SSF48371&Superfamily:SSF48371 2 NA NA PASS SITE 146,83|32,18 NA NA 1 93 20,20 166,170 60,60 34 1.96 NA 27.08 NA FALSE 6.00 93 NA NA NA FALSE NA NA 124.50 2 48743018 HCC1395_HCC1395T 101 0.316 151 40,16 32,18 75,34 NA 0/1 NA NA NA NA 65,36,32,18 C/T PANCANCER NA FALSE WDFY4_p.V643= chr10:48743018:48743019:C:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 48823499 48823500 T C 20 56 0.357142857142857 MODIFIER WDFY4 ENSG00000128815 C intron_variant Transcript ENST00000325239 protein_coding 35/61 ENST00000325239.12:c.5982+962T>C NA rs903786385 1 SNV HGNC HGNC:29323 YES NM_001394531.1 5 P1 CCDS44385.1 ENSP00000320563 Q6ZS81.147 UPI000176ADB8 Q6ZS81-1 1.314e-05 0 0 0 0 0 0 0 2.939e-05 0 0 2.939e-05 gnomADg_NFE 2 NA NA PASS SITE 42,36|8,12 NA NA 1 82 20,20 160,155 60,60 30 1.45 NA 8.13 NA FALSE 6.00 47 NA NA NA FALSE NA NA 47.41 2 48823499 HCC1395_HCC1395T 36 0.359 56 6,8 18,4 24,13 NA 0/1 NA NA NA NA 21,15,8,12 T/C PANCANCER NA FALSE WDFY4 chr10:48823499:48823500:T:C SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 48963723 48963724 C T 9 19 0.473684210526316 MODIFIER WDFY4 ENSG00000128815 T intron_variant Transcript ENST00000325239 protein_coding 53/61 ENST00000325239.12:c.8224-119C>T NA 1 SNV HGNC HGNC:29323 YES NM_001394531.1 5 P1 CCDS44385.1 ENSP00000320563 Q6ZS81.147 UPI000176ADB8 Q6ZS81-1 2 NA NA PASS SITE 27,3|9,0 NA NA 1 56 39,38 211,217 60,60 27 1.29 NA 5.42 NA FALSE 6.00 53 NA NA NA FALSE NA NA 32.02 2 48963723 HCC1395_HCC1395T 10 0.500 19 4,3 5,6 9,9 NA 0/1 NA NA NA NA 9,1,9,0 C/T PANCANCER NA FALSE WDFY4 chr10:48963723:48963724:C:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 49942257 49942258 C G 123 470 0.261702127659574 MODIFIER PARG ENSG00000227345 G intron_variant Transcript ENST00000402038 protein_coding 1/18 ENST00000402038.7:c.-99-433G>C NA -1 SNV HGNC HGNC:8605 1 P1 CCDS73130.1 ENSP00000384408 Q86W56.158 UPI000018CEA9 Q86W56-1 2 NA NA PASS SITE 361,382|63,60 NA NA 1 93 20,20 157,164 60,60 31 2.43 NA 79.11 NA FALSE 6.00 93 NA NA NA FALSE NA NA 280.13 2 49942257 HCC1395_HCC1395T 347 0.273 470 103,42 111,35 223,83 NA 0/1 NA NA NA NA 170,177,63,60 C/G PANCANCER NA FALSE PARG chr10:49942257:49942258:C:G SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 53802984 53802985 C A 3 10 0.3 MODIFIER PCDH15 ENSG00000150275 A 3_prime_UTR_variant Transcript ENST00000373965 protein_coding 35/35 ENST00000373965.6:c.*3595G>T NA 9024 -1 SNV HGNC HGNC:14674 5 A1 CCDS73135.1 ENSP00000363076 A9Z1W1.111 UPI0001884907 1 2 NA NA PASS SITE 7,18|2,1 NA NA 1 40 31,20 175,111 60,60 7 1.16 NA 3.92 NA FALSE 6.00 20 NA NA NA FALSE NA NA 5.96 2 53802984 HCC1395_HCC1395T 7 0.300 10 2,1 4,1 6,2 NA 0/1 NA NA NA NA 1,6,2,1 C/A PANCANCER NA FALSE PCDH15 chr10:53802984:53802985:C:A SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 70784663 70784664 C T 16 27 0.592592592592593 MODIFIER TBATA ENSG00000166220 T 5_prime_UTR_variant Transcript ENST00000299290 protein_coding 2/11 ENST00000299290.5:c.-163G>A NA 228 -1 SNV HGNC HGNC:23511 1 P4 CCDS7308.1 ENSP00000299290 Q96M53.126 UPI000013E57C Q96M53-1 2 NA NA PASS SITE 15,12|9,7 NA NA 1 32 20,20 158,171 60,60 28 1.09 NA 3.31 NA FALSE 6.00 69 NA NA NA FALSE NA NA 39.56 2 70784663 HCC1395_HCC1395T 11 0.550 27 2,4 5,6 8,10 NA 0/1 NA NA NA NA 7,4,9,7 C/T PANCANCER NA FALSE TBATA chr10:70784663:70784664:C:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 71762019 71762020 C T 79 137 0.576642335766423 MODIFIER CDH23 ENSG00000107736 T intron_variant Transcript ENST00000224721 protein_coding 38/69 ENST00000224721.12:c.4846-15661C>T NA COSV56457991&COSV56488435 1 SNV HGNC HGNC:13733 YES NM_022124.6 5 P1 CCDS86100.1 ENSP00000224721 Q9H251.206 UPI000175EE48 Q9H251-1 1 1&1 1&1 2 NA NA PASS SITE 120,138|37,42 NA NA 1 93 20,20 156,168 60,60 36 2.11 NA 38.23 NA FALSE 6.00 93 NA NA NA FALSE NA NA 207.78 2 71762019 HCC1395_HCC1395T 58 0.591 137 15,19 22,33 37,54 NA 0/1 NA NA NA NA 27,31,37,42 C/T PANCANCER NA FALSE CDH23 chr10:71762019:71762020:C:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 72375880 72375881 A C 78 145 0.537931034482759 LOW MICU1 ENSG00000107745 C splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000361114 protein_coding 10/11 ENST00000361114.10:c.1181-8T>G NA -1 SNV HGNC HGNC:1530 YES NM_001195518.2 1 P4 CCDS55715.1 ENSP00000354415 Q9BPX6.184 UPI0000035D9A Q9BPX6-1 1 2 NA NA PASS SITE 110,118|37,41 NA NA 1 93 20,20 162,154 60,60 33 2.03 NA 31.60 NA FALSE 6.00 93 NA NA NA FALSE NA NA 205.46 2 72375880 HCC1395_HCC1395T 67 0.541 145 23,25 18,24 43,51 NA 0/1 NA NA NA NA 34,33,37,41 A/C PANCANCER NA FALSE MICU1 chr10:72375880:72375881:A:C SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 73438198 73438199 T C 13 52 0.25 MODIFIER MSS51 ENSG00000166343 C upstream_gene_variant Transcript ENST00000299432 protein_coding NA 4637 -1 SNV HGNC HGNC:21000 YES NM_001024593.2 1 P1 CCDS31221.1 ENSP00000299432 Q4VC12.118 UPI00004CA0F2 Q4VC12-1 2 NA NA PASS SITE 55,43|9,4 NA NA 1 93 20,39 172,175 60,60 13 1.34 NA 12.64 NA FALSE 6.00 47 NA NA NA FALSE NA NA 31.57 2 73438198 HCC1395_HCC1395T 39 0.272 52 9,7 22,4 31,11 NA 0/1 NA NA NA NA 23,16,9,4 T/C PANCANCER NA FALSE MSS51 chr10:73438198:73438199:T:C SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 73797261 73797262 G A 127 127 1 MODIFIER NDST2 ENSG00000166507 A downstream_gene_variant Transcript ENST00000299641 protein_coding NA COSV55213912 4650 -1 SNV HGNC HGNC:7681 1 P1 CCDS7335.1 ENSP00000299641 P52849.177 UPI0000001C41 P52849-1 1 1 2 NA NA PASS SITE 78,65|73,54 NA NA 1 93 20,20 167,176 60,60 29 1.99 NA 28.80 NA FALSE 6.00 93 NA NA NA FALSE NA NA 393.99 2 73797261 HCC1395_HCC1395T 0 0.989 127 0,35 0,50 0,89 NA 0/1 NA NA NA NA 0,0,73,54 G/A PANCANCER NA FALSE NDST2 chr10:73797261:73797262:G:A SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 80273375 80273376 G A 18 33 0.545454545454545 MODIFIER MAT1A ENSG00000151224 A 3_prime_UTR_variant Transcript ENST00000372213 protein_coding 9/9 ENST00000372213.8:c.*406C>T NA 1829 -1 SNV HGNC HGNC:6903 YES NM_000429.3 1 P1 CCDS7365.1 ENSP00000361287 Q00266.216 UPI000012EFF3 1 2 NA NA PASS SITE 25,43|6,12 NA NA 1 93 20,35 161,170 60,60 27 1.59 NA 11.14 NA FALSE 6.00 79 NA NA NA FALSE NA NA 55.10 2 80273375 HCC1395_HCC1395T 15 0.572 33 7,6 4,7 11,15 NA 0/1 NA NA NA NA 4,11,6,12 G/A PANCANCER NA FALSE MAT1A chr10:80273375:80273376:G:A SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 80609406 80609407 C T 11 24 0.458333333333333 MODIFIER SH2D4B ENSG00000178217 T intron_variant Transcript ENST00000313455 protein_coding 5/6 ENST00000313455.5:c.714-18C>T NA rs1333606162 1 SNV HGNC HGNC:31440 2 CCDS44449.1 ENSP00000314242 Q5SQS7.128 UPI00001C096B Q5SQS7-3 4.009e-06 6.289e-05 0 0 0 0 0 0 0 6.289e-05 gnomADe_AFR 2 NA NA PASS SITE 29,12|8,3 NA NA 1 72 38,31 173,166 60,60 20 1.39 NA 6.92 NA FALSE 6.00 49 NA NA NA FALSE NA NA 31.32 2 80609406 HCC1395_HCC1395T 13 0.429 24 8,3 3,5 11,8 NA 0/1 NA NA NA NA 9,4,8,3 C/T PANCANCER NA FALSE SH2D4B chr10:80609406:80609407:C:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 82232930 82232931 GAGTGTTCTCT G 66 133 0.496240601503759 MODIFIER NRG3 ENSG00000185737 - intron_variant Transcript ENST00000372141 protein_coding 1/8 ENST00000372141.7:c.824-125805_824-125796del NA 1 deletion HGNC HGNC:7999 YES NM_001010848.4 1 A2 CCDS31233.1 ENSP00000361214 P56975.180 UPI00003D64C0 P56975-4 3 2 NA NA PASS SITE 91,136|23,43 NA NA 2 93 20,20 171,184 60,60 31 2.02 NA 30.20 NA FALSE 6.00 93 NA NA NA FALSE NA NA 269.18 2 82232930 HCC1395_HCC1395T 67 0.501 133 12,14 15,18 46,46 NA 0|1 0|1 82232930_GAGTGTTCTCT_G NA 82232930 26,41,23,43 GAGTGTTCTCT|G PANCANCER NA FALSE NRG3 chr10:82232930:82232931:GAGTGTTCTCT:G indel 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 82232948 82232949 TG T 66 119 0.554621848739496 MODIFIER NRG3 ENSG00000185737 - intron_variant Transcript ENST00000372141 protein_coding 1/8 ENST00000372141.7:c.824-125789del NA 1 deletion HGNC HGNC:7999 YES NM_001010848.4 1 A2 CCDS31233.1 ENSP00000361214 P56975.180 UPI00003D64C0 P56975-4 1 2 NA NA PASS SITE 65,119|23,43 NA NA 2 93 20,37 172,184 60,60 25 1.97 NA 27.69 NA FALSE 6.00 93 2,1 G NA TRUE NA 93 271.66 2 82232948 HCC1395_HCC1395T 53 0.547 119 8,11 14,15 38,46 NA 0|1 0|1 82232930_GAGTGTTCTCT_G NA 82232930 20,33,23,43 TG|T PANCANCER NA FALSE NRG3 chr10:82232948:82232949:TG:T indel 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 84517520 84517521 C T 77 77 1 MODIFIER CCSER2 ENSG00000107771 T 3_prime_UTR_variant Transcript ENST00000224756 protein_coding 11/11 ENST00000224756.12:c.*3977C>T NA 6667 1 SNV HGNC HGNC:29197 5 A1 CCDS31235.1 ENSP00000224756 Q9H7U1.143 UPI00005E1AE0 Q9H7U1-1 2 NA NA PASS SITE 75,35|61,17 NA NA 1 93 20,35 156,158 60,60 19 0.774 NA 21.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 262.10 2 84517520 HCC1395_HCC1395T 0 0.984 77 0,22 0,38 0,60 NA 0/1 NA NA NA NA 0,0,60,17 C/T PANCANCER NA FALSE CCSER2 chr10:84517520:84517521:C:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 89420839 89420840 C G 222 222 1 MODIFIER IFIT5 ENSG00000152778 G 3_prime_UTR_variant Transcript ENST00000371795 protein_coding 2/2 ENST00000371795.5:c.*2191C>G NA 3871 1 SNV HGNC HGNC:13328 YES NM_012420.3 1 P1 CCDS7403.1 ENSP00000360860 Q13325.185 UPI000012D3E6 Q13325-1 2 NA NA PASS SITE 144,114|129,95 NA NA 1 93 20,20 170,172 60,60 35 -4.658e-01 NA 47.12 NA FALSE 6.00 93 NA NA NA FALSE NA NA 696.01 2 89420839 HCC1395_HCC1395T 0 0.994 222 0,60 0,85 0,152 NA 0/1 NA NA NA NA 0,0,128,94 C/G PANCANCER NA FALSE IFIT5 chr10:89420839:89420840:C:G SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 92050427 92050428 C T 232 232 1 MODIFIER CPEB3 ENSG00000107864 T 3_prime_UTR_variant Transcript ENST00000265997 protein_coding 10/10 ENST00000265997.5:c.*1785G>A NA 4046 -1 SNV HGNC HGNC:21746 YES NM_014912.5 1 CCDS31246.1 ENSP00000265997 Q8NE35.160 UPI000013F7DE Q8NE35-1 1 2 NA NA PASS SITE 150,134|113,119 NA NA 1 93 20,20 159,169 60,60 36 2.28 NA 56.29 NA FALSE 6.00 93 NA NA NA FALSE NA NA 696.16 2 92050427 HCC1395_HCC1395T 0 0.994 232 0,72 0,72 0,154 NA 0/1 NA NA NA NA 0,0,113,119 C/T PANCANCER NA FALSE CPEB3 chr10:92050427:92050428:C:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 98415129 98415130 C G 16 110 0.145454545454545 MODIFIER HPS1 ENSG00000107521 G downstream_gene_variant Transcript ENST00000325103 protein_coding NA 1069 -1 SNV HGNC HGNC:5163 5 P1 CCDS7475.1 ENSP00000326649 Q92902.189 UPI000006D5B0 Q92902-1 1 2 NA NA PASS SITE 104,180|6,10 NA NA 1 93 20,20 159,174 60,60 35 2.11 NA 37.62 NA FALSE 6.00 69 NA NA NA FALSE NA NA 32.83 2 98415129 HCC1395_HCC1395T 94 0.141 110 18,4 38,6 66,10 NA 0/1 NA NA NA NA 31,63,6,10 C/G PANCANCER NA FALSE HPS1 chr10:98415129:98415130:C:G SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 100164228 100164229 G C 62 62 1 MODIFIER ERLIN1 ENSG00000107566 C intron_variant Transcript ENST00000370408 protein_coding 8/10 ENST00000370408.2:c.564-133C>G NA -1 cds_end_NF SNV HGNC HGNC:16947 5 ENSP00000359436 B0QZ43.87 UPI0001611413 1 2 NA NA PASS SITE 26,49|19,43 NA NA 1 93 20,20 169,188 60,60 22 1.74 NA 15.65 NA FALSE 6.00 93 NA NA NA FALSE NA NA 199.96 2 100164228 HCC1395_HCC1395T 0 0.979 62 0,16 0,22 0,45 NA 0/1 NA NA NA NA 0,0,19,43 G/C PANCANCER NA FALSE ERLIN1 chr10:100164228:100164229:G:C SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 101845569 101845570 G C 4 4 1 MODIFIER KCNIP2 ENSG00000120049 C upstream_gene_variant Transcript ENST00000239117 protein_coding NA 2001 -1 cds_end_NF SNV HGNC HGNC:15522 1 CCDS7526.1 ENSP00000239117 Q9NS61.182 UPI000006EEFD Q9NS61-9 2 NA NA PASS SITE 10,1|4,0 NA NA 1 40 40,40 212,218 60,60 31 1.04 NA 3.01 NA FALSE 6.00 70 NA NA NA FALSE NA NA 16.71 2 101845569 HCC1395_HCC1395T 0 0.833 4 0,1 0,3 0,4 NA 0/1 NA NA NA NA 0,0,4,0 G/C PANCANCER NA FALSE KCNIP2 chr10:101845569:101845570:G:C SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 101849957 101849958 C G 7 7 1 MODIFIER ARMH3 ENSG00000120029 G intron_variant Transcript ENST00000370033 protein_coding 24/25 ENST00000370033.9:c.1861-65G>C NA rs1589897489 -1 SNV HGNC HGNC:25788 YES NM_024541.3 5 P1 CCDS41563.1 ENSP00000359050 Q5T2E6.119 UPI000047005B Q5T2E6-1 2 NA NA PASS SITE 1,9|0,7 NA NA 1 42 39,39 213,184 60,60 40 1.000 NA 2.71 NA FALSE 6.00 93 NA NA NA FALSE NA NA 28.51 2 101849957 HCC1395_HCC1395T 0 0.893 7 0,3 0,4 0,7 NA 0/1 NA NA NA NA 0,0,0,7 C/G PANCANCER NA FALSE ARMH3 chr10:101849957:101849958:C:G SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 103440731 103440732 C T 21 21 1 LOW PDCD11 ENSG00000148843 T splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000369797 protein_coding 29/35 ENST00000369797.8:c.4441-3C>T NA COSV63933652 1 SNV HGNC HGNC:13408 YES NM_014976.2 1 P4 CCDS31276.1 ENSP00000358812 Q14690.199 UPI00001C1ED1 1 1 2 NA NA PASS SITE 22,11|13,8 NA NA 1 93 29,20 156,186 60,60 30 1.42 NA 7.53 NA FALSE 6.00 93 NA NA NA FALSE NA NA 65.77 2 103440731 HCC1395_HCC1395T 0 0.944 21 0,10 0,5 0,16 NA 0/1 NA NA NA NA 0,0,13,8 C/T PANCANCER NA FALSE PDCD11 chr10:103440731:103440732:C:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 104046624 104046625 G C 21 21 1 MODIFIER COL17A1 ENSG00000065618 C intron_variant Transcript ENST00000369733 protein_coding 31/50 ENST00000369733.8:c.2362+123C>G NA rs144556796 -1 SNV HGNC HGNC:2194 5 A2 ENSP00000358748 Q9UMD9.189 UPI000046FD60 Q9UMD9-2 1 0.0028 0.0091 0.0029 0 0 0 0.003752 0.01248 0 0.002028 0.00173 0 0 0.006329 7.349e-05 0.004302 0.000207 0.01248 gnomADg_AFR 2 NA NA PASS SITE 34,16|10,11 NA NA 1 93 20,20 175,163 60,60 38 1.55 NA 10.44 NA FALSE 2.53 93 NA NA NA FALSE NA NA 68.32 2 104046624 HCC1395_HCC1395T 0 0.939 21 0,3 0,7 0,14 NA 0/1 NA NA NA NA 0,0,10,11 G/C PANCANCER NA FALSE COL17A1 chr10:104046624:104046625:G:C SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 119827430 119827431 T G 36 271 0.132841328413284 MODIFIER MCMBP ENSG00000197771 G downstream_gene_variant Transcript ENST00000360003 protein_coding NA 1974 -1 SNV HGNC HGNC:25782 2 A1 CCDS7617.1 ENSP00000353098 Q9BTE3.159 UPI0000070023 Q9BTE3-1 2 NA NA PASS SITE 295,259|21,15 NA NA 1 93 20,20 162,169 60,60 28 2.34 NA 64.11 NA FALSE 6.00 93 NA NA NA FALSE NA NA 73.67 2 119827430 HCC1395_HCC1395T 235 0.129 271 61,11 99,13 168,24 NA 0/1 NA NA NA NA 122,113,21,15 T/G PANCANCER NA FALSE MCMBP chr10:119827430:119827431:T:G SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 123154732 123154733 G C 11 11 1 MODIFIER HMX2 ENSG00000188816 C downstream_gene_variant Transcript ENST00000339992 protein_coding NA 4060 1 SNV HGNC HGNC:5018 YES NM_005519.2 1 P1 CCDS31305.1 ENSP00000341108 A2RU54.124 UPI0000251E4F 2 NA NA PASS SITE 16,5|11,0 NA NA 1 72 30,40 162,237 60,60 18 1.26 NA 5.12 NA FALSE 6.00 93 NA NA NA FALSE NA NA 47.41 2 123154732 HCC1395_HCC1395T 0 0.927 11 0,4 0,7 0,11 NA 0/1 NA NA NA NA 0,0,11,0 G/C PANCANCER NA FALSE HMX2 chr10:123154732:123154733:G:C SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 124021516 124021517 G C 14 35 0.4 MODIFIER CHST15 ENSG00000182022 C intron_variant Transcript ENST00000346248 protein_coding 5/7 ENST00000346248.7:c.1191-104C>G NA -1 SNV HGNC HGNC:18137 1 P1 CCDS7638.1 ENSP00000333947 Q7LFX5.163 UPI000004D06B Q7LFX5-1 2 NA NA PASS SITE 7,40|3,11 NA NA 1 65 38,40 196,160 60,60 20 1.36 NA 6.32 NA FALSE 6.00 76 NA NA NA FALSE NA NA 41.04 2 124021516 HCC1395_HCC1395T 21 0.353 35 9,5 8,4 21,11 NA 0/1 NA NA NA NA 2,19,3,11 G/C PANCANCER NA FALSE CHST15 chr10:124021516:124021517:G:C SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 124620619 124620620 C T 95 162 0.58641975308642 MODIFIER FAM53B ENSG00000189319 T 3_prime_UTR_variant Transcript ENST00000337318 protein_coding 5/5 ENST00000337318.8:c.*2623G>A NA 4432 -1 SNV HGNC HGNC:28968 YES NM_014661.4 1 P1 CCDS7641.1 ENSP00000338532 Q14153.149 UPI000013DC3C Q14153-1 2 NA NA PASS SITE 98,95|49,47 NA NA 1 93 20,20 159,157 60,60 30 1.94 NA 25.46 NA FALSE 6.00 93 NA NA NA FALSE NA NA 243.74 2 124620619 HCC1395_HCC1395T 67 0.581 162 18,23 26,37 45,63 NA 0/1 NA NA NA NA 37,30,49,46 C/T PANCANCER NA FALSE FAM53B chr10:124620619:124620620:C:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 125740509 125740510 C A 125 326 0.383435582822086 LOW EDRF1 ENSG00000107938 A synonymous_variant Transcript ENST00000337623 protein_coding 15/24 ENST00000337623.7:c.1926C>A ENSP00000336727.3:p.I642= ENSP00000336727.3 p.I642= 2031 1926 642 I atC/atA 1 SNV HGNC HGNC:24640 5 A2 CCDS7646.1 ENSP00000336727 Q3B7T1.136 UPI00001A962A Q3B7T1-5 PANTHER:PTHR15000&AlphaFold_DB_import:AF-Q3B7T1-F1 2 NA NA PASS SITE 229,195|67,58 NA NA 1 93 20,20 158,173 60,60 30 2.17 NA 43.66 NA FALSE 6.00 93 NA NA NA FALSE NA NA 301.67 2 125740509 HCC1395_HCC1395T 201 0.394 326 51,34 69,47 130,84 NA 0/1 NA NA NA NA 107,94,67,58 C/A PANCANCER NA FALSE EDRF1_p.I642= chr10:125740509:125740510:C:A SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 125859826 125859827 G C 268 268 1 MODERATE DHX32 ENSG00000089876 C missense_variant Transcript ENST00000284690 protein_coding 3/11 ENST00000284690.4:c.626C>G ENSP00000284690.3:p.P209R ENSP00000284690.3 p.P209R 1094 626 209 P/R cCa/cGa COSV52939818&COSV52943944&COSV99501881 -1 SNV HGNC HGNC:16717 YES NM_018180.3 1 P1 CCDS7652.1 ENSP00000284690 Q7L7V1.154 UPI00000467F4 Q7L7V1-1 1 deleterious(0.01) probably_damaging(0.969) PROSITE_profiles:PS51192&CDD:cd17977&PANTHER:PTHR18934&Gene3D:3.40.50.300&Superfamily:SSF52540&AlphaFold_DB_import:AF-Q7L7V1-F1 1&1&1 1&1&1 2 NA NA PASS SITE 74,76|133,135 NA NA 1 93 20,20 159,172 60,60 32 2.03 NA 31.60 NA FALSE 6.00 93 NA NA NA FALSE NA NA 836.07 2 125859826 HCC1395_HCC1395T 0 0.995 268 0,62 0,118 0,192 NA 0/1 NA NA NA NA 0,0,133,135 G/C PANCANCER NA FALSE DHX32_p.P209R chr10:125859826:125859827:G:C SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 127736565 127736566 C T 48 355 0.135211267605634 MODIFIER FOXI2 ENSG00000186766 T upstream_gene_variant Transcript ENST00000388920 protein_coding NA rs1458425817 620 1 SNV HGNC HGNC:32448 YES NM_207426.3 1 P1 CCDS7655.2 ENSP00000373572 Q6ZQN5.131 UPI0000253B9D 7.498e-06 0 0 0 0 0 0 0 4.492e-05 6.57e-06 0 0 0 0 0 0 0 1.47e-05 0 0 4.492e-05 gnomADe_SAS 2 NA NA PASS SITE 303,311|26,23 NA NA 1 93 20,20 160,163 60,60 26 0.746 NA 57.17 NA FALSE 6.00 93 NA NA NA FALSE NA NA 104.16 2 127736565 HCC1395_HCC1395T 307 0.141 355 97,15 101,17 212,34 NA 0/1 NA NA NA NA 156,151,25,23 C/T PANCANCER NA FALSE FOXI2 chr10:127736565:127736566:C:T SNV 2:0 chr10:48486:130145159:2:0:1 TRUE NA 0.96 +chr10 132163377 132163378 C G 31 50 0.62 MODERATE JAKMIP3 ENSG00000188385 G missense_variant Transcript ENST00000298622 protein_coding 19/24 ENST00000298622.9:c.2383C>G ENSP00000298622.4:p.R795G ENSP00000298622.4 p.R795G 2383 2383 795 R/G Cgg/Ggg COSV53827178 1 SNV HGNC HGNC:23523 5 P4 CCDS44494.1 ENSP00000298622 Q5VZ66.124 UPI000157482F deleterious_low_confidence(0) possibly_damaging(0.799) AlphaFold_DB_import:AF-Q5VZ66-F1&Coiled-coils_(Ncoils):Coil&PANTHER:PTHR18935 1 1 2 NA NA PASS SITE 18,49|8,23 NA NA 1 93 28,20 174,186 60,60 19 1.59 NA 11.39 NA FALSE 6.00 93 NA NA NA FALSE NA NA 90.29 2 132163377 HCC1395_HCC1395T 19 0.616 50 9,13 4,10 14,23 NA 0/1 NA NA NA NA 6,13,8,23 C/G PANCANCER NA FALSE JAKMIP3_p.R795G chr10:132163377:132163378:C:G SNV 3:0 chr10:130169429:133557962:3:0:1 NA NA 0.96 +chr11 695346 695347 G C 98 98 1 MODIFIER DEAF1 ENSG00000177030 C upstream_gene_variant Transcript ENST00000382409 protein_coding NA 124 -1 SNV HGNC HGNC:14677 YES NM_021008.4 1 P1 CCDS31327.1 ENSP00000371846 O75398.211 UPI00001290E6 O75398-1 1 3 NA NA PASS SITE 85,104|42,56 NA NA 1 93 20,20 158,170 60,60 33 2.12 NA 38.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 304.01 3 695346 HCC1395_HCC1395T 0 0.986 98 0,26 0,39 0,69 NA 0/1 NA NA NA NA 0,0,42,56 G/C PANCANCER NA FALSE DEAF1 chr11:695346:695347:G:C SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 862687 862688 C G 241 243 0.991769547325103 MODERATE TSPAN4 ENSG00000214063 G missense_variant Transcript ENST00000346501 protein_coding 3/7 ENST00000346501.8:c.201C>G ENSP00000324304.5:p.I67M ENSP00000324304.5 p.I67M 322 201 67 I/M atC/atG COSV60260988 1 SNV HGNC HGNC:11859 3 ENSP00000324304 J3KNL1.61 UPI0000E2281D deleterious(0) benign(0.06) PANTHER:PTHR19282&PROSITE_patterns:PS00421&Pfam:PF00335&PIRSF:PIRSF002419&Prints:PR00259&Transmembrane_helices:TMhelix&AlphaFold_DB_import:AF-J3KNL1-F1 1 1 3 NA NA PASS SITE 153,178|114,127 NA NA 1 93 20,20 150,155 60,60 36 2.31 NA 60.14 NA FALSE 6.00 93 NA NA NA FALSE NA NA 671.66 3 862687 HCC1395_HCC1395T 2 0.986 243 0,59 1,61 1,144 NA 0/1 NA NA NA NA 1,1,114,127 C/G PANCANCER NA FALSE TSPAN4_p.I67M chr11:862687:862688:C:G SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 1078020 1078021 CTA C 299 299 1 MODIFIER MUC2 ENSG00000198788 - non_coding_transcript_exon_variant Transcript ENST00000361558 protein_coding_CDS_not_defined 4/49 ENST00000361558.7:n.560_561del NA 559-560 1 deletion HGNC HGNC:7512 5 1 3 NA NA PASS SITE 231,200|168,131 NA NA 1 93 20,20 155,167 60,60 35 2.45 NA 84.26 NA FALSE 6.00 93 NA NA NA FALSE NA NA 987.22 3 1078020 HCC1395_HCC1395T 0 0.995 299 0,69 0,106 0,204 NA 0/1 NA NA NA NA 0,0,168,131 CTA/C PANCANCER NA FALSE MUC2 chr11:1078020:1078021:CTA:C indel 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 2146993 2146994 G T 35 77 0.454545454545455 MODIFIER IGF2-AS ENSG00000099869 T intron_variant&non_coding_transcript_variant Transcript ENST00000381361 lncRNA 2/2 ENST00000381361.4:n.715-325G>T NA rs1052617951 1 SNV HGNC HGNC:14062 YES 2 3 NA NA PASS SITE 50,78|18,17 NA NA 1 93 20,20 151,171 60,60 30 1.78 NA 17.71 NA FALSE 6.00 67 NA NA NA FALSE NA NA 85.22 3 2146993 HCC1395_HCC1395T 42 0.453 77 12,14 13,8 28,23 NA 0/1 NA NA NA NA 17,25,18,17 G/T PANCANCER NA FALSE IGF2-AS chr11:2146993:2146994:G:T SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 2418192 2418193 TCCCAAGAGAAATGCTTGCTGGGGAACTTCTCCTTAAACTGCTTCTCGGCCA T 24 89 0.269662921348315 MODERATE TRPM5 ENSG00000070985 - inframe_deletion Transcript ENST00000528453 protein_coding 6/24 ENST00000528453.1:c.830_880del ENSP00000436809.1:p.V277_W293del ENSP00000436809.1 p.V277_W293del 836-886 830-880 277-294 VAEKQFKEKFPSKHFSWE/E gTGGCCGAGAAGCAGTTTAAGGAGAAGTTCCCCAGCAAGCATTTCTCTTGGGag/gag -1 deletion HGNC HGNC:14323 1 A2 ENSP00000436809 E9PQF7.70 UPI0001F78505 AlphaFold_DB_import:AF-E9PQF7-F1&PANTHER:PTHR13800 3 NA NA PASS SITE 105,114|8,16 NA NA 1 93 20,35 158,204 60,60 45 1.94 NA 25.68 NA FALSE 6.00 93 NA NA NA FALSE NA NA 95.68 3 2418192 HCC1395_HCC1395T 65 0.296 89 9,6 18,5 36,16 NA 0/1 NA NA NA NA 31,34,8,16 TCCCAAGAGAAATGCTTGCTGGGGAACTTCTCCTTAAACTGCTTCTCGGCCA/T PANCANCER NA FALSE TRPM5_p.V277_W293del chr11:2418192:2418193:TCCCAAGAGAAATGCTTGCTGGGGAACTTCTCCTTAAACTGCTTCTCGGCCA:T indel 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 2919499 2919500 T C 5 11 0.454545454545455 MODIFIER SLC22A18 ENSG00000110628 C intron_variant Transcript ENST00000347936 protein_coding 8/10 ENST00000347936.6:c.864+92T>C NA rs570837003 1 SNV HGNC HGNC:10964 1 P1 CCDS7740.1 ENSP00000307859 Q96BI1.167 UPI0000070F3F 1 0.0004 0.0015 0 0 0 0 0.0005849 0.001955 0 0.0003927 0 0 0 0 0 0.0009551 0 0.001955 gnomADg_AFR 3 NA NA PASS SITE 0,21|0,5 NA NA 1 18 37,35 222,266 60,60 31 1.21 NA 4.47 NA FALSE 3.43 40 NA NA NA FALSE NA NA 15.63 3 2919499 HCC1395_HCC1395T 6 0.461 11 4,2 2,3 6,5 NA 0/1 NA NA NA NA 0,6,0,5 T/C PANCANCER NA FALSE SLC22A18 chr11:2919499:2919500:T:C SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 4367179 4367180 G A 33 65 0.507692307692308 MODIFIER OR52B4 ENSG00000221996 A downstream_gene_variant Transcript ENST00000624801 protein_coding NA 84 -1 SNV HGNC HGNC:15209 YES NM_001005161.3 P1 ENSP00000485530 Q8NGK2.154 A0A126GW82.32 UPI000013F0A2 3 NA NA PASS SITE 90,18|29,4 NA NA 1 93 39,38 197,171 60,60 24 1.83 NA 19.51 NA FALSE 6.00 60 NA NA NA FALSE NA NA 112.05 3 4367179 HCC1395_HCC1395T 32 0.517 65 7,7 20,22 27,29 NA 0/1 NA NA NA NA 27,5,29,4 G/A PANCANCER NA FALSE OR52B4 chr11:4367179:4367180:G:A SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 4999924 4999925 GTTTTAAGTA G 244 244 1 MODIFIER OR51L1 ENSG00000176798 - intron_variant&non_coding_transcript_variant Transcript ENST00000641624 protein_coding_CDS_not_defined 2/3 ENST00000641624.1:n.587+2342_587+2350del NA 1 deletion HGNC HGNC:14759 3 NA NA PASS SITE 106,120|106,138 NA NA 1 93 20,20 159,176 60,60 39 2.17 NA 43.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 1093.07 3 4999924 HCC1395_HCC1395T 0 0.994 244 0,43 0,75 0,162 NA 0/1 NA NA NA NA 0,0,106,138 GTTTTAAGTA/G PANCANCER NA FALSE OR51L1 chr11:4999924:4999925:GTTTTAAGTA:G indel 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 5968294 5968295 G C 70 70 1 MODERATE OR56A5 ENSG00000188691 C missense_variant Transcript ENST00000532411 protein_coding 1/1 ENST00000532411.2:c.201C>G ENSP00000481594.1:p.S67R ENSP00000481594.1 p.S67R 201 201 67 S/R agC/agG COSV60827549 -1 SNV HGNC HGNC:14792 YES NM_001146033.1 P1 CCDS73248.1 ENSP00000481594 P0C7T3.100 A0A126GWP3.27 UPI00006C10F9 deleterious(0.01) benign(0.012) Gene3D:1.20.1070.10&AlphaFold_DB_import:AF-P0C7T3-F1&Pfam:PF13853&Prints:PR00237&PROSITE_profiles:PS50262&PANTHER:PTHR26450&Superfamily:SSF81321&Transmembrane_helices:TMhelix&Low_complexity_(Seg):seg 1 1 3 NA NA PASS SITE 65,41|43,27 NA NA 1 93 20,38 168,189 60,60 30 1.89 NA 22.78 NA FALSE 6.00 93 NA NA NA FALSE NA NA 247.73 3 5968294 HCC1395_HCC1395T 0 0.983 70 0,24 0,30 0,55 NA 0/1 NA NA NA NA 0,0,43,27 G/C PANCANCER NA FALSE OR56A5_p.S67R chr11:5968294:5968295:G:C SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 6401001 6401002 C T 164 164 1 MODERATE APBB1 ENSG00000166313 T missense_variant Transcript ENST00000299402 protein_coding 11/14 ENST00000299402.10:c.1654G>A ENSP00000299402.6:p.A552T ENSP00000299402.6 p.A552T 1754 1654 552 A/T Gct/Act COSV54974702 -1 SNV HGNC HGNC:581 5 P4 CCDS31410.1 ENSP00000299402 O00213.201 UPI0000070BF7 O00213-2 tolerated(0.16) PDB-ENSP_mappings:3dxc.A&PDB-ENSP_mappings:3dxc.C&PDB-ENSP_mappings:3dxd.A&PDB-ENSP_mappings:3dxd.C&PDB-ENSP_mappings:3dxe.A&PDB-ENSP_mappings:3dxe.C&PDB-ENSP_mappings:5nqh.A&PDB-ENSP_mappings:5nqh.B&PDB-ENSP_mappings:5nqh.C&PDB-ENSP_mappings:5nqh.D&PROSITE_profiles:PS01179&CDD:cd01271&PANTHER:PTHR14058&Gene3D:2.30.29.30&SMART:SM00462&Superfamily:SSF50729&AlphaFold_DB_import:AF-O00213-F1 1 1 3 NA NA PASS SITE 110,94|89,75 NA NA 1 93 20,20 160,164 60,60 30 2.12 NA 39.09 NA FALSE 6.00 93 NA NA NA FALSE NA NA 469.26 3 6401001 HCC1395_HCC1395T 0 0.991 164 0,34 0,70 0,107 NA 0/1 NA NA NA NA 0,0,89,75 C/T PANCANCER NA FALSE APBB1_p.A552T chr11:6401001:6401002:C:T SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 6401237 6401238 C T 115 115 1 MODIFIER APBB1 ENSG00000166313 T intron_variant Transcript ENST00000299402 protein_coding 10/13 ENST00000299402.10:c.1582+108G>A NA -1 SNV HGNC HGNC:581 5 P4 CCDS31410.1 ENSP00000299402 O00213.201 UPI0000070BF7 O00213-2 3 NA NA PASS SITE 76,58|68,47 NA NA 1 93 20,20 158,169 60,60 30 1.96 NA 27.08 NA FALSE 6.00 93 NA NA NA FALSE NA NA 353.30 3 6401237 HCC1395_HCC1395T 0 0.988 115 0,27 0,53 0,83 NA 0/1 NA NA NA NA 0,0,68,47 C/T PANCANCER NA FALSE APBB1 chr11:6401237:6401238:C:T SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 6410518 6410519 C T 21 21 1 MODIFIER APBB1 ENSG00000166313 T intron_variant Transcript ENST00000299402 protein_coding 2/13 ENST00000299402.10:c.721+109G>A NA -1 SNV HGNC HGNC:581 5 P4 CCDS31410.1 ENSP00000299402 O00213.201 UPI0000070BF7 O00213-2 3 NA NA PASS SITE 9,7|13,8 NA NA 1 89 20,20 142,180 60,60 17 1.04 NA 3.01 NA FALSE 6.00 93 NA NA NA FALSE NA NA 64.97 3 6410518 HCC1395_HCC1395T 0 0.943 21 0,4 0,11 0,15 NA 0/1 NA NA NA NA 0,0,13,8 C/T PANCANCER NA FALSE APBB1 chr11:6410518:6410519:C:T SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 6410864 6410865 C T 57 57 1 MODERATE APBB1 ENSG00000166313 T missense_variant Transcript ENST00000299402 protein_coding 2/14 ENST00000299402.10:c.484G>A ENSP00000299402.6:p.E162K ENSP00000299402.6 p.E162K 584 484 162 E/K Gag/Aag rs943319518&COSV54974713 -1 SNV HGNC HGNC:581 5 P4 CCDS31410.1 ENSP00000299402 O00213.201 UPI0000070BF7 O00213-2 tolerated(0.23) Low_complexity_(Seg):seg&PANTHER:PTHR14058&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Coiled-coils_(Ncoils):Coil&AlphaFold_DB_import:AF-O00213-F1 0&1 0&1 3 NA NA PASS SITE 41,50|20,37 NA NA 1 93 34,33 170,172 60,60 27 1.85 NA 20.77 NA FALSE 6.00 93 NA NA NA FALSE NA NA 186.99 3 6410864 HCC1395_HCC1395T 0 0.979 57 0,23 0,20 0,45 NA 0/1 NA NA NA NA 0,0,20,37 C/T PANCANCER NA FALSE APBB1_p.E162K chr11:6410864:6410865:C:T SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 6458439 6458440 C T 103 103 1 MODIFIER TRIM3 ENSG00000110171 T intron_variant Transcript ENST00000345851 protein_coding 2/11 ENST00000345851.8:c.132-143G>A NA -1 SNV HGNC HGNC:10064 YES NM_033278.4 1 P1 CCDS7764.1 ENSP00000340797 O75382.199 UPI000013C8BA O75382-1 3 NA NA PASS SITE 52,56|45,58 NA NA 1 93 20,20 150,160 60,60 35 1.82 NA 19.57 NA FALSE 6.00 93 NA NA NA FALSE NA NA 312.07 3 6458439 HCC1395_HCC1395T 0 0.986 103 0,29 0,36 0,72 NA 0/1 NA NA NA NA 0,0,45,58 C/T PANCANCER NA FALSE TRIM3 chr11:6458439:6458440:C:T SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 12944198 12944199 G A 172 172 1 MODIFIER TEAD1 ENSG00000187079 A 3_prime_UTR_variant Transcript ENST00000526600 protein_coding 8/8 ENST00000526600.1:c.*6976G>A NA 8192 rs964415699 1 SNV HGNC HGNC:11714 1 ENSP00000435393 E9PKB7.67 UPI0000577847 1 1.315e-05 0 0 0 0 0 0 0 2.94e-05 0 0 2.94e-05 gnomADg_NFE 3 NA NA PASS SITE 71,54|100,73 NA NA 1 93 28,36 167,176 60,60 30 -8.323e-02 NA 25.33 NA FALSE 6.00 93 NA NA NA FALSE NA NA 591.96 3 12944198 HCC1395_HCC1395T 0 0.993 172 0,37 0,91 0,134 NA 0/1 NA NA NA NA 0,0,99,73 G/A PANCANCER NA FALSE TEAD1 chr11:12944198:12944199:G:A SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 14843826 14843827 GATTCTGATGGTAGAATTAACCATGGGCGAATTGCTTATATTTCTTCGA G 59 145 0.406896551724138 MODERATE PDE3B ENSG00000152270 - inframe_deletion&splice_region_variant Transcript ENST00000282096 protein_coding 12/16 ENST00000282096.9:c.2322_2369del ENSP00000282096.4:p.D774_K790delinsE ENSP00000282096.4 p.D774_K790delinsE 2593-2640 2321-2368 774-790 DSDGRINHGRIAYISSK/E gATTCTGATGGTAGAATTAACCATGGGCGAATTGCTTATATTTCTTCGAag/gag 1 deletion HGNC HGNC:8779 YES NM_000922.4 1 P2 CCDS7817.1 ENSP00000282096 Q13370.198 UPI000013DCB7 Q13370-1 PDB-ENSP_mappings:1so2.A&PDB-ENSP_mappings:1so2.B&PDB-ENSP_mappings:1so2.C&PDB-ENSP_mappings:1so2.D&PDB-ENSP_mappings:1soj.A&PDB-ENSP_mappings:1soj.B&PDB-ENSP_mappings:1soj.C&PDB-ENSP_mappings:1soj.D&PDB-ENSP_mappings:1soj.E&PDB-ENSP_mappings:1soj.F&PDB-ENSP_mappings:1soj.G&PDB-ENSP_mappings:1soj.H&PDB-ENSP_mappings:1soj.I&PDB-ENSP_mappings:1soj.J&PDB-ENSP_mappings:1soj.K&PDB-ENSP_mappings:1soj.L&PROSITE_profiles:PS51845&PANTHER:PTHR11347&Pfam:PF00233&Gene3D:1.10.1300.10&SMART:SM00471&Superfamily:SSF109604&AlphaFold_DB_import:AF-Q13370-F1 1 3 NA NA PASS SITE 157,100|40,19 NA NA 1 93 20,39 162,196 60,60 44 2.02 NA 31.11 NA FALSE 6.00 93 NA NA NA FALSE NA NA 233.87 3 14843826 HCC1395_HCC1395T 86 0.420 145 11,12 17,27 59,43 NA 0/1 NA NA NA NA 56,30,40,19 GATTCTGATGGTAGAATTAACCATGGGCGAATTGCTTATATTTCTTCGA/G PANCANCER NA FALSE PDE3B_p.D774_K790delinsE chr11:14843826:14843827:GATTCTGATGGTAGAATTAACCATGGGCGAATTGCTTATATTTCTTCGA:G indel 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 18707973 18707974 G T 91 187 0.486631016042781 MODIFIER TMEM86A ENSG00000151117 T downstream_gene_variant Transcript ENST00000280734 protein_coding NA 3188 1 SNV HGNC HGNC:26890 YES NM_153347.3 1 P1 CCDS7844.1 ENSP00000280734 Q8N2M4.119 UPI0000073C65 3 NA NA PASS SITE 147,193|33,58 NA NA 1 93 20,20 153,177 60,60 34 2.19 NA 46.01 NA FALSE 6.00 93 NA NA NA FALSE NA NA 240.61 3 18707973 HCC1395_HCC1395T 96 0.519 187 21,24 35,33 61,66 NA 0/1 NA NA NA NA 44,52,33,58 G/T PANCANCER NA FALSE TMEM86A chr11:18707973:18707974:G:T SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 20119412 20119413 C G 77 77 1 MODIFIER NAV2 ENSG00000166833 G 3_prime_UTR_variant Transcript ENST00000349880 protein_coding 38/38 ENST00000349880.9:c.*1154C>G NA 9303 1 SNV HGNC HGNC:15997 YES NM_145117.5 1 CCDS7850.1 ENSP00000309577 Q8IVL1.156 UPI00001E057F Q8IVL1-3 3 NA NA PASS SITE 52,35|42,35 NA NA 1 93 20,20 163,158 60,60 32 1.78 NA 17.71 NA FALSE 6.00 93 NA NA NA FALSE NA NA 229.80 3 20119412 HCC1395_HCC1395T 0 0.982 77 0,29 0,22 0,54 NA 0/1 NA NA NA NA 0,0,42,35 C/G PANCANCER NA FALSE NAV2 chr11:20119412:20119413:C:G SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 20638484 20638485 T A 54 130 0.415384615384615 MODIFIER SLC6A5 ENSG00000165970 A 3_prime_UTR_variant&NMD_transcript_variant Transcript ENST00000298923 nonsense_mediated_decay 12/15 ENST00000298923.11:c.*1192T>A NA 1835 COSV54233557 1 SNV HGNC HGNC:11051 1 ENSP00000298923 J3KNC4.47 UPI0001F7809F 1 1 1 3 NA NA PASS SITE 152,115|32,22 NA NA 1 93 20,20 157,163 60,60 31 2.09 NA 36.67 NA FALSE 6.00 93 NA NA NA FALSE NA NA 146.50 3 20638484 HCC1395_HCC1395T 76 0.454 130 15,13 33,25 48,40 NA 0/1 NA NA NA NA 42,34,32,22 T/A PANCANCER NA FALSE SLC6A5 chr11:20638484:20638485:T:A SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 31127523 31127524 T C 161 161 1 MODIFIER DCDC1 ENSG00000170959 C 3_prime_UTR_variant&NMD_transcript_variant Transcript ENST00000342355 nonsense_mediated_decay 11/22 ENST00000342355.8:c.*506A>G NA 1557 -1 SNV HGNC HGNC:20625 2 ENSP00000343496 M0R2J8.59 UPI00005A8061 M0R2J8-2 3 NA NA PASS SITE 93,73|88,73 NA NA 1 93 20,20 165,159 60,60 32 2.05 NA 33.11 NA FALSE 6.00 93 NA NA NA FALSE NA NA 491.35 3 31127523 HCC1395_HCC1395T 0 0.991 161 0,42 0,61 0,107 NA 0/1 NA NA NA NA 0,0,88,73 T/C PANCANCER NA FALSE DCDC1 chr11:31127523:31127524:T:C SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 32830061 32830062 G C 72 72 1 MODIFIER PRRG4 ENSG00000135378 C 5_prime_UTR_variant Transcript ENST00000257836 protein_coding 1/6 ENST00000257836.4:c.-135G>C NA 135 1 SNV HGNC HGNC:30799 YES NM_024081.6 1 P1 CCDS7881.1 ENSP00000257836 Q9BZD6.162 A0A0S2Z5N9.44 UPI000013707A 3 NA NA PASS SITE 62,50|39,33 NA NA 1 93 20,20 145,165 60,60 25 1.87 NA 22.18 NA FALSE 6.00 93 NA NA NA FALSE NA NA 228.79 3 32830061 HCC1395_HCC1395T 0 0.981 72 0,28 0,22 0,50 NA 0/1 NA NA NA NA 0,0,39,33 G/C PANCANCER NA FALSE PRRG4 chr11:32830061:32830062:G:C SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 45227439 45227440 A T 46 103 0.446601941747573 MODIFIER PRDM11 ENSG00000019485 T downstream_gene_variant Transcript ENST00000424263 protein_coding NA 2352 1 SNV HGNC HGNC:13996 2 CCDS58130.1 ENSP00000394314 Q9NQV5.144 UPI000013FA3F Q9NQV5-2 3 NA NA PASS SITE 102,100|29,17 NA NA 1 93 20,20 152,175 60,60 36 1.98 NA 28.29 NA FALSE 6.00 84 NA NA NA FALSE NA NA 119.45 3 45227439 HCC1395_HCC1395T 57 0.473 103 18,10 15,21 36,32 NA 0/1 NA NA NA NA 30,27,29,17 A/T PANCANCER NA FALSE PRDM11 chr11:45227439:45227440:A:T SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 47415410 47415411 C G 119 121 0.983471074380165 MODIFIER PSMC3 ENSG00000165916 G downstream_gene_variant Transcript ENST00000298852 protein_coding NA 3365 -1 SNV HGNC HGNC:9549 YES NM_002804.5 1 CCDS7935.1 ENSP00000298852 P17980.233 A0A140VK42.37 UPI0000132389 1 3 NA NA PASS SITE 77,100|54,65 NA NA 1 93 20,34 172,172 60,60 30 2.11 NA 37.62 NA FALSE 6.00 93 NA NA NA FALSE NA NA 403.79 3 47415410 HCC1395_HCC1395T 2 0.979 121 0,39 1,47 1,92 NA 0/1 NA NA NA NA 1,1,54,65 C/G PANCANCER NA FALSE PSMC3 chr11:47415410:47415411:C:G SNV 2:0 chr11:199891:50033053:2:0:1 TRUE NA 0.96 +chr11 55344370 55344371 C A 6 12 0.5 MODIFIER OR4A16 ENSG00000181961 A downstream_gene_variant Transcript ENST00000314721 protein_coding NA 183 1 SNV HGNC HGNC:15153 YES NM_001005274.1 P1 CCDS31499.1 ENSP00000325128 Q8NH70.151 A0A126GW87.42 UPI0000061EB2 3 NA NA PASS SITE 0,15|0,6 NA NA 1 39 40,37 237,223 60,60 12 1.03 NA 2.71 NA FALSE 6.00 34 NA NA NA FALSE NA NA 20.68 3 55344370 HCC1395_HCC1395T 6 0.507 12 3,5 2,1 6,6 NA 0/1 NA NA NA NA 0,6,0,6 C/A PANCANCER NA FALSE OR4A16 chr11:55344370:55344371:C:A SNV 2:1 chr11:54603280:58031899:2:1:1 TRUE NA 0.96 +chr11 56160039 56160040 G A 35 130 0.269230769230769 LOW OR8K5 ENSG00000181752 A synonymous_variant Transcript ENST00000313447 protein_coding 1/1 ENST00000313447.1:c.279C>T ENSP00000323853.1:p.S93= ENSP00000323853.1 p.S93= 279 279 93 S tcC/tcT rs777172595&COSV100537200&COSV57890037&COSV57890925 -1 SNV HGNC HGNC:15315 YES NM_001004058.2 P1 CCDS31521.1 ENSP00000323853 Q8NH50.157 UPI000004B231 Gene3D:1.20.1070.10&AlphaFold_DB_import:AF-Q8NH50-F1&Pfam:PF13853&Prints:PR00245&PROSITE_profiles:PS50262&PANTHER:PTHR48018&Superfamily:SSF81321&Transmembrane_helices:TMhelix&CDD:cd15413 7.965e-06 0 0 0 0 0 8.815e-06 0 3.267e-05 6.572e-06 0 0 0 0 0 0 0 0 0 0.0002072 0.0002072 gnomADg_SAS 0&1&1&1 0&1&1&1 3 NA NA PASS SITE 96,70|18,17 NA NA 1 93 20,20 174,166 60,60 31 1.71 NA 15.00 NA FALSE 6.00 85 NA NA NA FALSE NA NA 86.15 3 56160039 HCC1395_HCC1395T 95 0.260 130 27,13 37,9 70,24 NA 0/1 NA NA NA NA 56,39,18,17 G/A PANCANCER NA FALSE OR8K5_p.S93= chr11:56160039:56160040:G:A SNV 2:1 chr11:54603280:58031899:2:1:1 TRUE NA 0.96 +chr11 56542447 56542448 T C 69 293 0.235494880546075 MODERATE OR5M11 ENSG00000255223 C missense_variant Transcript ENST00000528616 protein_coding 1/1 ENST00000528616.5:c.811A>G ENSP00000432417.2:p.K271E ENSP00000432417.2 p.K271E 811 811 271 K/E Aaa/Gaa COSV73141937 -1 SNV HGNC HGNC:15291 YES NM_001005245.1 P1 CCDS53629.1 ENSP00000432417 Q96RB7.144 A0A126GVL9.41 UPI00000405CF deleterious(0.01) possibly_damaging(0.568) Gene3D:1.20.1070.10&AlphaFold_DB_import:AF-Q96RB7-F1&Pfam:PF13853&Prints:PR00237&PROSITE_profiles:PS50262&PANTHER:PTHR48018&Superfamily:SSF81321&CDD:cd15412 1 1 3 NA NA PASS SITE 155,205|27,42 NA NA 1 93 20,20 173,174 60,60 34 1.96 NA 27.09 NA FALSE 6.00 93 NA NA NA FALSE NA NA 172.35 3 56542447 HCC1395_HCC1395T 224 0.228 293 64,20 91,25 166,49 NA 0/1 NA NA NA NA 95,129,27,42 T/C PANCANCER NA FALSE OR5M11_p.K271E chr11:56542447:56542448:T:C SNV 2:1 chr11:54603280:58031899:2:1:1 TRUE NA 0.96 +chr11 57648341 57648342 G T 34 94 0.361702127659574 MODIFIER YPEL4 ENSG00000166793 T intron_variant Transcript ENST00000300022 protein_coding 1/4 ENST00000300022.8:c.-184-1050C>A NA -1 SNV HGNC HGNC:18328 YES NM_145008.3 1 P1 CCDS7963.1 ENSP00000300022 Q96NS1.140 A0A024R4Y8.56 UPI000013BE0B 3 NA NA PASS SITE 62,69|19,15 NA NA 1 93 20,20 167,160 60,60 28 1.67 NA 13.55 NA FALSE 6.00 55 NA NA NA FALSE NA NA 82.04 3 57648341 HCC1395_HCC1395T 60 0.353 94 18,5 21,17 43,23 NA 0/1 NA NA NA NA 31,29,19,15 G/T PANCANCER NA FALSE YPEL4 chr11:57648341:57648342:G:T SNV 2:1 chr11:54603280:58031899:2:1:1 TRUE NA 0.96 +chr11 58190517 58190518 G A 71 319 0.22257053291536 LOW OR9Q2 ENSG00000186513 A synonymous_variant Transcript ENST00000641291 protein_coding 2/2 ENST00000641291.1:c.27G>A ENSP00000492924.1:p.V9= ENSP00000492924.1 p.V9= 238 27 9 V gtG/gtA rs980204925 1 SNV HGNC HGNC:15328 YES NM_001005283.3 P1 CCDS31544.1 ENSP00000492924 Q8NGE9.145 A0A126GW85.46 UPI0000061ECB AlphaFold_DB_import:AF-Q8NGE9-F1&PANTHER:PTHR48018&Superfamily:SSF81321 6.569e-06 0 0 0 0 0 0 0 1.47e-05 0 0 1.47e-05 gnomADg_NFE 3 NA NA PASS SITE 216,185|42,29 NA NA 1 93 20,20 165,162 60,60 26 2.04 NA 32.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 166.56 3 58190517 HCC1395_HCC1395T 248 0.230 319 71,24 93,25 173,51 NA 0/1 NA NA NA NA 134,114,42,29 G/A PANCANCER NA FALSE OR9Q2_p.V9= chr11:58190517:58190518:G:A SNV 3:2 chr11:58179792:60334923:3:2:1 NA NA 0.96 +chr11 58190708 58190709 A T 132 270 0.488888888888889 MODERATE OR9Q2 ENSG00000186513 T missense_variant Transcript ENST00000641291 protein_coding 2/2 ENST00000641291.1:c.218A>T ENSP00000492924.1:p.Y73F ENSP00000492924.1 p.Y73F 429 218 73 Y/F tAc/tTc COSV61111758 1 SNV HGNC HGNC:15328 YES NM_001005283.3 P1 CCDS31544.1 ENSP00000492924 Q8NGE9.145 A0A126GW85.46 UPI0000061ECB deleterious(0.03) benign(0.075) Gene3D:1.20.1070.10&AlphaFold_DB_import:AF-Q8NGE9-F1&Pfam:PF13853&Prints:PR00237&PROSITE_profiles:PS50262&PANTHER:PTHR48018&Superfamily:SSF81321&Transmembrane_helices:TMhelix&CDD:cd15230 1 1 3 NA NA PASS SITE 149,151|59,73 NA NA 1 93 20,20 171,176 60,60 30 2.06 NA 33.96 NA FALSE 6.00 93 NA NA NA FALSE NA NA 367.53 3 58190708 HCC1395_HCC1395T 138 0.506 270 37,31 54,58 97,99 NA 0/1 NA NA NA NA 64,74,59,73 A/T PANCANCER NA FALSE OR9Q2_p.Y73F chr11:58190708:58190709:A:T SNV 3:2 chr11:58179792:60334923:3:2:1 NA NA 0.96 +chr11 59364559 59364560 T A 62 348 0.17816091954023 MODERATE OR5AN1 ENSG00000176495 A missense_variant Transcript ENST00000313940 protein_coding 1/1 ENST00000313940.2:c.101T>A ENSP00000320302.2:p.V34E ENSP00000320302.2 p.V34E 148 101 34 V/E gTg/gAg 1 SNV HGNC HGNC:15255 P1 CCDS31559.1 ENSP00000320302 Q8NGI8.156 A0A126GVP9.45 UPI000004B1FD tolerated(0.28) benign(0.115) Gene3D:1.20.1070.10&AlphaFold_DB_import:AF-Q8NGI8-F1&Pfam:PF13853&Prints:PR00237&PANTHER:PTHR48018&Superfamily:SSF81321&Transmembrane_helices:TMhelix&CDD:cd15417 3 NA NA PASS SITE 244,179|38,24 NA NA 1 93 20,20 167,179 60,60 32 1.99 NA 28.59 NA FALSE 6.00 93 NA NA NA FALSE NA NA 146.84 3 59364559 HCC1395_HCC1395T 286 0.187 348 71,15 118,27 195,44 NA 0/1 NA NA NA NA 165,121,38,24 T/A PANCANCER NA FALSE OR5AN1_p.V34E chr11:59364559:59364560:T:A SNV 3:2 chr11:58179792:60334923:3:2:1 NA NA 0.96 +chr11 60047594 60047595 C A 59 146 0.404109589041096 MODIFIER OOSP2 ENSG00000149507 A 3_prime_UTR_variant Transcript ENST00000278855 protein_coding 4/4 ENST00000278855.7:c.*521C>A NA 1049 1 SNV HGNC HGNC:26699 YES NM_173801.5 1 P2 CCDS7979.1 ENSP00000278855 Q86WS3.120 A0A140VJR6.39 UPI000000DC90 3 NA NA PASS SITE 138,30|56,3 NA NA 1 93 39,35 207,209 60,60 26 1.88 NA 21.07 NA FALSE 6.00 61 NA NA NA FALSE NA NA 175.67 3 60047594 HCC1395_HCC1395T 87 0.403 146 30,14 54,40 84,57 NA 0/1 NA NA NA NA 76,11,56,3 C/A PANCANCER NA FALSE OOSP2 chr11:60047594:60047595:C:A SNV 3:2 chr11:58179792:60334923:3:2:1 NA NA 0.96 +chr11 60708823 60708824 T C 121 228 0.530701754385965 MODIFIER MS4A8 ENSG00000166959 C intron_variant Transcript ENST00000300226 protein_coding 5/6 ENST00000300226.7:c.534+42T>C NA 1 SNV HGNC HGNC:13380 YES NM_031457.2 1 P1 CCDS7990.1 ENSP00000300226 Q9BY19.136 UPI0000047F97 3 NA NA PASS SITE 96,137|43,78 NA NA 1 93 20,20 167,171 60,60 30 1.92 NA 24.98 NA FALSE 6.00 93 NA NA NA FALSE NA NA 335.03 3 60708823 HCC1395_HCC1395T 107 0.535 228 24,32 43,44 73,84 NA 0/1 NA NA NA NA 41,66,43,78 T/C PANCANCER NA FALSE MS4A8 chr11:60708823:60708824:T:C SNV 3:2 chr11:60516154:62391414:3:2:1 NA NA 0.96 +chr11 61485250 61485251 G C 10 21 0.476190476190476 MODIFIER PPP1R32 ENSG00000162148 C intron_variant Transcript ENST00000338608 protein_coding 5/13 ENST00000338608.7:c.511-88G>C NA 1 SNV HGNC HGNC:28869 YES NM_145017.3 1 P1 CCDS8008.1 ENSP00000344140 Q7Z5V6.124 G3F4G3.72 UPI000013E13F Q7Z5V6-1 3 NA NA PASS SITE 17,3|9,1 NA NA 1 23 41,37 205,231 60,60 34 0.954 NA 2.41 NA FALSE 6.00 56 NA NA NA FALSE NA NA 31.47 3 61485250 HCC1395_HCC1395T 11 0.476 21 4,2 6,7 10,9 NA 0/1 NA NA NA NA 10,1,9,1 G/C PANCANCER NA FALSE PPP1R32 chr11:61485250:61485251:G:C SNV 3:2 chr11:60516154:62391414:3:2:1 NA NA 0.96 +chr11 61508413 61508414 G T 101 168 0.601190476190476 MODIFIER LRRC10B ENSG00000204950 T upstream_gene_variant Transcript ENST00000378075 protein_coding NA 336 1 SNV HGNC HGNC:37215 YES NM_001145077.2 P1 CCDS44621.1 ENSP00000367315 A6NIK2.101 UPI00006C114B 3 NA NA PASS SITE 119,35|84,17 NA NA 1 93 37,36 171,182 60,60 25 1.85 NA 20.47 NA FALSE 6.00 93 NA NA NA FALSE NA NA 317.52 3 61508413 HCC1395_HCC1395T 67 0.612 168 13,38 39,46 53,84 NA 0/1 NA NA NA NA 51,16,84,17 G/T PANCANCER NA FALSE LRRC10B chr11:61508413:61508414:G:T SNV 3:2 chr11:60516154:62391414:3:2:1 NA NA 0.96 +chr11 61955371 61955372 C G 114 245 0.46530612244898 MODIFIER BEST1 ENSG00000167995 G intron_variant Transcript ENST00000378043 protein_coding 3/10 ENST00000378043.9:c.247+170C>G NA 1 SNV HGNC HGNC:12703 YES NM_004183.4 1 P1 CCDS31580.1 ENSP00000367282 O76090.204 UPI0000138985 O76090-1 1 3 NA NA PASS SITE 137,133|54,60 NA NA 1 93 20,20 150,149 60,60 44 1.93 NA 24.68 NA FALSE 6.00 93 NA NA NA FALSE NA NA 286.51 3 61955371 HCC1395_HCC1395T 131 0.465 245 31,38 48,32 82,71 NA 0/1 NA NA NA NA 67,64,54,60 C/G PANCANCER NA FALSE BEST1 chr11:61955371:61955372:C:G SNV 3:2 chr11:60516154:62391414:3:2:1 NA NA 0.96 +chr11 62752451 62752452 G A 224 425 0.527058823529412 MODERATE ZBTB3 ENSG00000185670 A missense_variant Transcript ENST00000394807 protein_coding 2/2 ENST00000394807.5:c.1214C>T ENSP00000378286.4:p.S405F ENSP00000378286.4 p.S405F 1462 1214 405 S/F tCt/tTt COSV67361993 -1 SNV HGNC HGNC:22918 YES NM_001370809.1 1 P2 CCDS8034.2 ENSP00000378286 A0A6E1W9L1.9 UPI00004058EE deleterious(0.03) benign(0.284) AlphaFold_DB_import:AF-A0A6E1W9L1-F1 1 1 3 NA NA PASS SITE 218,212|110,114 NA NA 1 93 20,20 159,160 60,60 32 2.17 NA 43.95 NA FALSE 6.00 93 NA NA NA FALSE NA NA 575.36 3 62752451 HCC1395_HCC1395T 201 0.525 425 48,58 81,82 133,147 NA 0/1 NA NA NA NA 99,102,110,114 G/A PANCANCER NA FALSE ZBTB3_p.S405F chr11:62752451:62752452:G:A SNV 3:2 chr11:62671347:65043299:3:2:1 NA NA 0.96 +chr11 62827470 62827471 A C 46 109 0.422018348623853 MODIFIER STX5 ENSG00000162236 C intron_variant Transcript ENST00000294179 protein_coding 3/10 ENST00000294179.8:c.297-72T>G NA -1 SNV HGNC HGNC:11440 YES NM_003164.5 1 P1 CCDS8038.2 ENSP00000294179 Q13190.196 UPI00001FA9B0 Q13190-1 3 NA NA PASS SITE 60,44|22,24 NA NA 1 82 20,26 170,172 60,60 21 1.46 NA 8.43 NA FALSE 6.00 93 NA NA NA FALSE NA NA 128.50 3 62827470 HCC1395_HCC1395T 63 0.423 109 23,21 25,14 48,35 NA 0/1 NA NA NA NA 37,26,22,24 A/C PANCANCER NA FALSE STX5 chr11:62827470:62827471:A:C SNV 3:2 chr11:62671347:65043299:3:2:1 NA NA 0.96 +chr11 62910249 62910250 G T 10 590 0.0169491525423729 LOW CHRM1 ENSG00000168539 T synonymous_variant Transcript ENST00000306960 protein_coding 2/2 ENST00000306960.4:c.852C>A ENSP00000306490.3:p.S284= ENSP00000306490.3 p.S284= 1076 852 284 S tcC/tcA -1 SNV HGNC HGNC:1950 YES NM_000738.3 1 P1 CCDS8040.1 ENSP00000306490 P11229.217 Q53XZ3.153 UPI00001252AB P11229-1 1 Gene3D:1.20.1070.10&PDB-ENSP_mappings:6oij.R&AlphaFold_DB_import:AF-P11229-F1&Pfam:PF00001&Prints:PR00538&PROSITE_profiles:PS50262&PANTHER:PTHR24247&Superfamily:SSF81321&CDD:cd17790&MobiDB_lite:mobidb-lite 3 NA NA PASS SITE 317,603|3,7 NA NA 1 93 20,20 170,160 60,60 23 2.41 NA 76.36 NA FALSE 6.00 20 NA NA NA FALSE NA NA 13.01 3 62910249 HCC1395_HCC1395T 580 0.018 590 163,2 219,5 437,7 NA 0/1 NA NA NA NA 197,383,3,7 G/T PANCANCER NA FALSE CHRM1_p.S284= chr11:62910249:62910250:G:T SNV 3:2 chr11:62671347:65043299:3:2:1 NA NA 0.96 +chr11 62994723 62994724 A G 8 348 0.0229885057471264 LOW SLC22A8 ENSG00000149452 G synonymous_variant Transcript ENST00000311438 protein_coding 7/9 ENST00000311438.12:c.1035T>C ENSP00000311463.8:p.A345= ENSP00000311463.8 p.A345= 1035 1035 345 A gcT/gcC -1 SNV HGNC HGNC:10972 1 ENSP00000311463 H7BXN9.77 UPI0000EE47C2 PROSITE_profiles:PS50850&PANTHER:PTHR24064&Gene3D:1.20.1250.20&TIGRFAM:TIGR00898&Pfam:PF00083&Superfamily:SSF103473&Transmembrane_helices:TMhelix&AlphaFold_DB_import:AF-H7BXN9-F1 3 NA NA PASS SITE 248,273|3,5 NA NA 1 93 20,20 155,150 60,60 40 2.06 NA 33.97 NA FALSE 6.00 7 NA NA NA FALSE NA NA 11.63 3 62994723 HCC1395_HCC1395T 340 0.027 348 86,1 119,4 218,5 NA 0/1 NA NA NA NA 163,177,3,5 A/G PANCANCER NA FALSE SLC22A8_p.A345= chr11:62994723:62994724:A:G SNV 3:2 chr11:62671347:65043299:3:2:1 NA NA 0.96 +chr11 63290370 63290371 G A 272 504 0.53968253968254 MODERATE SLC22A10 ENSG00000184999 A missense_variant Transcript ENST00000332793 protein_coding 1/10 ENST00000332793.11:c.205G>A ENSP00000327569.6:p.E69K ENSP00000327569.6 p.E69K 468 205 69 E/K Gaa/Aaa 1 SNV HGNC HGNC:18057 YES NM_001039752.4 1 P1 CCDS41661.1 ENSP00000327569 Q63ZE4.131 UPI0000D62620 Q63ZE4-1 tolerated(0.21) benign(0.003) AlphaFold_DB_import:AF-Q63ZE4-F1&PANTHER:PTHR24064 3 NA NA PASS SITE 225,239|134,138 NA NA 1 93 20,20 159,167 60,60 30 2.19 NA 45.71 NA FALSE 6.00 93 NA NA NA FALSE NA NA 718.20 3 63290370 HCC1395_HCC1395T 232 0.531 504 49,75 104,102 165,187 NA 0/1 NA NA NA NA 112,120,134,138 G/A PANCANCER NA FALSE SLC22A10_p.E69K chr11:63290370:63290371:G:A SNV 3:2 chr11:62671347:65043299:3:2:1 NA NA 0.96 +chr11 63575069 63575070 TCACACTCTGTGTCAGGATC T 71 144 0.493055555555556 MODIFIER PLAAT3 ENSG00000176485 - intron_variant Transcript ENST00000323646 protein_coding 3/3 ENST00000323646.9:c.388-42_388-24del NA -1 deletion HGNC HGNC:17825 1 P1 CCDS8047.1 ENSP00000320337 P53816.172 A0A024R561.45 UPI000012CBE4 3 NA NA PASS SITE 27,110|14,57 NA NA 1 93 34,36 182,211 60,60 29 1.71 NA 14.23 NA FALSE 6.00 93 NA NA NA FALSE NA NA 283.46 3 63575069 HCC1395_HCC1395T 73 0.489 144 13,14 15,19 62,58 NA 0/1 NA NA NA NA 11,62,14,57 TCACACTCTGTGTCAGGATC/T PANCANCER NA FALSE PLAAT3 chr11:63575069:63575070:TCACACTCTGTGTCAGGATC:T indel 3:2 chr11:62671347:65043299:3:2:1 NA NA 0.96 +chr11 63813585 63813586 G T 8 18 0.444444444444444 MODIFIER SPINDOC ENSG00000168005 T 5_prime_UTR_variant Transcript ENST00000294244 protein_coding 1/6 ENST00000294244.9:c.-102G>T NA 130 1 SNV HGNC HGNC:25115 YES NM_138471.3 1 P1 CCDS31594.1 ENSP00000294244 Q9BUA3.153 UPI00001BDB3C 3 NA NA PASS SITE 40,13|7,1 NA NA 1 93 20,35 156,183 60,60 38 1.52 NA 9.33 NA FALSE 6.00 31 NA NA NA FALSE NA NA 23.28 3 63813585 HCC1395_HCC1395T 10 0.449 18 3,5 5,2 9,7 NA 0/1 NA NA NA NA 9,1,7,1 G/T PANCANCER NA FALSE SPINDOC chr11:63813585:63813586:G:T SNV 3:2 chr11:62671347:65043299:3:2:1 NA NA 0.96 +chr11 64320895 64320896 T C 201 449 0.447661469933185 MODIFIER ESRRA ENSG00000173153 C downstream_gene_variant Transcript ENST00000000442 protein_coding NA COSV50004583&COSV50008526 4152 1 SNV HGNC HGNC:3471 YES NM_004451.5 1 P4 CCDS41667.1 ENSP00000000442 P11474.233 Q569H8.166 UPI0000167B87 P11474-1 1&1 1&1 3 NA NA PASS SITE 262,228|106,95 NA NA 1 93 20,20 164,164 60,60 29 2.24 NA 50.81 NA FALSE 6.00 93 NA NA NA FALSE NA NA 506.59 3 64320895 HCC1395_HCC1395T 248 0.435 449 63,58 96,69 175,135 NA 0/1 NA NA NA NA 132,116,106,95 T/C PANCANCER NA FALSE ESRRA chr11:64320895:64320896:T:C SNV 3:2 chr11:62671347:65043299:3:2:1 NA NA 0.96 +chr11 64556481 64556482 G C 166 315 0.526984126984127 MODIFIER SLC22A11 ENSG00000168065 C intron_variant Transcript ENST00000301891 protein_coding 1/9 ENST00000301891.9:c.393+89G>C NA 1 SNV HGNC HGNC:18120 YES NM_018484.4 1 P1 CCDS8074.1 ENSP00000301891 Q9NSA0.159 UPI000003ED3F Q9NSA0-1 3 NA NA PASS SITE 139,211|64,102 NA NA 1 93 20,20 164,162 60,60 28 2.15 NA 41.84 NA FALSE 6.00 93 NA NA NA FALSE NA NA 420.39 3 64556481 HCC1395_HCC1395T 149 0.532 315 43,52 41,47 99,113 NA 0/1 NA NA NA NA 60,89,64,102 G/C PANCANCER NA FALSE SLC22A11 chr11:64556481:64556482:G:C SNV 3:2 chr11:62671347:65043299:3:2:1 NA NA 0.96 +chr11 65961566 65961567 C T 23 45 0.511111111111111 MODIFIER SART1 ENSG00000175467 T upstream_gene_variant Transcript ENST00000312397 protein_coding NA 168 1 SNV HGNC HGNC:10538 YES NM_005146.5 1 P1 CCDS31611.1 ENSP00000310448 O43290.184 UPI00000732D5 O43290-1 3 NA NA PASS SITE 50,4|20,3 NA NA 1 84 39,37 190,186 60,60 20 1.49 NA 8.73 NA FALSE 6.00 76 NA NA NA FALSE NA NA 76.67 3 65961566 HCC1395_HCC1395T 22 0.502 45 8,7 12,14 21,21 NA 0/1 NA NA NA NA 21,1,20,3 C/T PANCANCER NA FALSE SART1 chr11:65961566:65961567:C:T SNV 2:2 chr11:65180806:68348296:2:2:1 FALSE NA 0.96 +chr11 66474469 66474470 G T 66 110 0.6 MODIFIER PELI3 ENSG00000174516 T intron_variant Transcript ENST00000320740 protein_coding 7/7 ENST00000320740.12:c.840+544G>T NA 1 SNV HGNC HGNC:30010 YES NM_145065.3 1 CCDS31615.1 ENSP00000322532 Q8N2H9.155 A0A024R5B1.61 UPI00000707EF Q8N2H9-1 3 NA NA PASS SITE 48,70|21,45 NA NA 1 93 20,27 177,162 60,60 28 1.72 NA 15.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 190.09 3 66474469 HCC1395_HCC1395T 44 0.593 110 15,22 17,22 34,50 NA 0/1 NA NA NA NA 18,26,21,45 G/T PANCANCER NA FALSE PELI3 chr11:66474469:66474470:G:T SNV 2:2 chr11:65180806:68348296:2:2:1 FALSE NA 0.96 +chr11 68036604 68036605 G A 108 256 0.421875 MODIFIER TCIRG1 ENSG00000110719 A upstream_gene_variant Transcript ENST00000265686 protein_coding NA rs747618258&COSV99693652 2421 1 SNV HGNC HGNC:11647 YES NM_006019.4 1 P1 CCDS8177.1 ENSP00000265686 Q13488.204 A0A024R5E5.53 UPI000006EC9A Q13488-1 1 4e-06 0 2.895e-05 0 0 0 0 0 0 2.895e-05 gnomADe_AMR 0&1 0&1 3 NA NA PASS SITE 157,168|51,57 NA NA 1 93 20,20 163,163 60,60 26 2.05 NA 33.11 NA FALSE 6.00 93 NA NA NA FALSE NA NA 247.84 3 68036604 HCC1395_HCC1395T 148 0.399 256 42,26 52,36 101,67 NA 0/1 NA NA NA NA 69,79,51,57 G/A PANCANCER NA FALSE TCIRG1 chr11:68036604:68036605:G:A SNV 2:2 chr11:65180806:68348296:2:2:1 FALSE NA 0.96 +chr11 68174274 68174275 C G 13 35 0.371428571428571 MODIFIER KMT5B ENSG00000110066 G intron_variant Transcript ENST00000304363 protein_coding 5/10 ENST00000304363.9:c.544-361G>C NA -1 SNV HGNC HGNC:24283 YES NM_017635.5 5 P1 CCDS31623.1 ENSP00000305899 Q4FZB7.149 UPI00003FF22C Q4FZB7-1 1 3 NA NA PASS SITE 15,33|2,11 NA NA 1 62 40,40 198,210 60,60 24 1.32 NA 6.02 NA FALSE 6.00 91 NA NA NA FALSE NA NA 41.82 3 68174274 HCC1395_HCC1395T 22 0.371 35 6,6 12,5 21,12 NA 0/1 NA NA NA NA 6,16,2,11 C/G PANCANCER NA FALSE KMT5B chr11:68174274:68174275:C:G SNV 2:2 chr11:65180806:68348296:2:2:1 FALSE NA 0.96 +chr11 69698678 69698679 C A 48 96 0.5 MODIFIER FGF19 ENSG00000162344 A 3_prime_UTR_variant Transcript ENST00000294312 protein_coding 3/3 ENST00000294312.4:c.*584G>T NA 1381 -1 SNV HGNC HGNC:3675 YES NM_005117.3 1 P1 CCDS8193.1 ENSP00000294312 O95750.194 A0A7U3L4E7.7 UPI0000037216 3 NA NA PASS SITE 39,54|23,25 NA NA 1 93 20,20 164,160 60,60 31 1.52 NA 9.63 NA FALSE 6.00 87 NA NA NA FALSE NA NA 109.63 3 69698678 HCC1395_HCC1395T 48 0.460 96 18,11 13,15 34,29 NA 0/1 NA NA NA NA 22,26,23,25 C/A PANCANCER NA FALSE FGF19 chr11:69698678:69698679:C:A SNV 3:2 chr11:68403545:70124306:3:2:1 NA NA 0.96 +chr11 70087777 70087778 C T 78 409 0.190709046454768 MODERATE ANO1 ENSG00000131620 T missense_variant Transcript ENST00000316296 protein_coding 2/17 ENST00000316296.9:c.50C>T ENSP00000319477.5:p.P17L ENSP00000319477.5 p.P17L 155 50 17 P/L cCt/cTt rs905229830 1 SNV HGNC HGNC:21625 2 ENSP00000319477 Q5XXA6.145 UPI000006D029 Q5XXA6-3 1 deleterious_low_confidence(0) benign(0.034) AlphaFold_DB_import:AF-Q5XXA6-F1 3 NA NA PASS SITE 274,270|40,38 NA NA 1 93 20,20 155,163 60,60 28 2.14 NA 40.94 NA FALSE 6.00 93 NA NA NA FALSE NA NA 179.96 3 70087777 HCC1395_HCC1395T 331 0.193 409 105,20 107,30 224,53 NA 0/1 NA NA NA NA 163,168,40,38 C/T PANCANCER NA FALSE ANO1_p.P17L chr11:70087777:70087778:C:T SNV 3:2 chr11:68403545:70124306:3:2:1 NA NA 0.96 +chr11 71490986 71490987 C G 157 157 1 MODIFIER NADSYN1 ENSG00000172890 G intron_variant Transcript ENST00000319023 protein_coding 17/20 ENST00000319023.7:c.1694+10C>G NA 1 SNV HGNC HGNC:29832 YES NM_018161.5 1 P1 CCDS8201.1 ENSP00000326424 Q6IA69.150 UPI00001404C2 Q6IA69-1 1 3 NA NA PASS SITE 61,116|59,98 NA NA 1 93 20,20 161,169 60,60 29 2.10 NA 36.98 NA FALSE 6.00 93 NA NA NA FALSE NA NA 483.50 3 71490986 HCC1395_HCC1395T 0 0.991 157 0,40 0,58 0,108 NA 0/1 NA NA NA NA 0,0,59,98 C/G PANCANCER NA FALSE NADSYN1 chr11:71490986:71490987:C:G SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 72224782 72224783 G C 28 63 0.444444444444444 MODIFIER FOLR2 ENSG00000165457 C downstream_gene_variant Transcript ENST00000298223 protein_coding NA 2832 1 SNV HGNC HGNC:3793 YES NM_000803.5 1 P1 CCDS8212.1 ENSP00000298223 P14207.186 UPI000013E4AD 3 NA NA PASS SITE 73,60|15,14 NA NA 1 93 20,20 143,141 60,60 31 1.77 NA 17.67 NA FALSE 6.00 93 NA NA NA FALSE NA NA 69.79 3 72224782 HCC1395_HCC1395T 35 0.461 63 9,7 10,10 20,17 NA 0/1 NA NA NA NA 19,16,15,13 G/C PANCANCER NA FALSE FOLR2 chr11:72224782:72224783:G:C SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 72711404 72711405 C T 18 113 0.15929203539823 MODIFIER ARAP1 ENSG00000186635 T intron_variant Transcript ENST00000334211 protein_coding 6/32 ENST00000334211.12:c.357+26G>A NA rs1049695927 -1 SNV HGNC HGNC:16925 1 CCDS8217.2 ENSP00000335506 Q96P48.193 UPI00001678AE Q96P48-4 1.994e-05 0 0.0001159 0 0 0 8.831e-06 0 0 1.315e-05 0 0 0 0 0 0 0.006369 0 0 0 0.006369 gnomADg_MID 3 NA NA PASS SITE 147,83|13,5 NA NA 1 93 20,20 163,182 60,60 28 1.96 NA 26.79 NA FALSE 6.00 53 NA NA NA FALSE NA NA 42.18 3 72711404 HCC1395_HCC1395T 95 0.175 113 22,8 41,5 65,13 NA 0/1 NA NA NA NA 60,35,13,5 C/T PANCANCER NA FALSE ARAP1 chr11:72711404:72711405:C:T SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 72822508 72822509 G C 115 295 0.389830508474576 LOW ATG16L2 ENSG00000168010 C synonymous_variant Transcript ENST00000321297 protein_coding 6/18 ENST00000321297.10:c.675G>C ENSP00000326340.5:p.L225= ENSP00000326340.5 p.L225= 710 675 225 L ctG/ctC COSV58360831&COSV58361047 1 SNV HGNC HGNC:25464 YES NM_033388.2 1 P1 CCDS31634.1 ENSP00000326340 Q8NAA4.155 UPI0000140B06 Q8NAA4-1 AlphaFold_DB_import:AF-Q8NAA4-F1&PANTHER:PTHR19878 1&1 1&1 3 NA NA PASS SITE 297,342|51,64 NA NA 1 93 20,20 155,152 60,60 41 2.46 NA 84.88 NA FALSE 6.00 93 NA NA NA FALSE NA NA 284.24 3 72822508 HCC1395_HCC1395T 180 0.399 295 39,25 65,42 110,73 NA 0/1 NA NA NA NA 84,96,51,64 G/C PANCANCER NA FALSE ATG16L2_p.L225= chr11:72822508:72822509:G:C SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 77473516 77473517 G A 9 18 0.5 MODIFIER PAK1 ENSG00000149269 A intron_variant Transcript ENST00000278568 protein_coding 1/15 ENST00000278568.8:c.-22+36C>T NA -1 SNV HGNC HGNC:8590 2 CCDS44687.1 ENSP00000278568 Q13153.235 UPI000013DB7F Q13153-2 1 3 NA NA PASS SITE 23,12|6,3 NA NA 1 60 34,32 183,186 60,60 22 1.35 NA 6.27 NA FALSE 6.00 41 NA NA NA FALSE NA NA 24.04 3 77473516 HCC1395_HCC1395T 9 0.500 18 2,2 5,5 7,7 NA 0/1 NA NA NA NA 4,5,6,3 G/A PANCANCER NA FALSE PAK1 chr11:77473516:77473517:G:A SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 78109322 78109323 GGATTACAGGCATGAAATTTATCCTA G 13 51 0.254901960784314 MODIFIER ALG8 ENSG00000159063 - intron_variant Transcript ENST00000299626 protein_coding 9/12 ENST00000299626.10:c.1038+95_1038+119del NA -1 deletion HGNC HGNC:23161 YES NM_024079.5 1 P2 CCDS8258.1 ENSP00000299626 Q9BVK2.183 A0A024R5K5.54 UPI000013E5C8 Q9BVK2-1 1 3 NA NA PASS SITE 78,29|10,3 NA NA 2 93 39,41 170,187 60,60 29 1.43 NA 15.65 NA FALSE 6.00 93 NA NA NA FALSE NA NA 45.84 3 78109322 HCC1395_HCC1395T 38 0.275 51 8,1 7,8 28,10 NA 0|1 0|1 78109322_GGATTACAGGCATGAAATTTATCCTA_G NA 78109322 27,11,10,3 GGATTACAGGCATGAAATTTATCCTA|G PANCANCER NA FALSE ALG8 chr11:78109322:78109323:GGATTACAGGCATGAAATTTATCCTA:G indel 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 78109350 78109352 G GA 13 51 0.254901960784314 MODIFIER ALG8 ENSG00000159063 A intron_variant Transcript ENST00000299626 protein_coding 9/12 ENST00000299626.10:c.1038+91_1038+92insT NA -1 insertion HGNC HGNC:23161 YES NM_024079.5 1 P2 CCDS8258.1 ENSP00000299626 Q9BVK2.183 A0A024R5K5.54 UPI000013E5C8 Q9BVK2-1 1 3 NA NA PASS SITE 79,31|10,3 NA NA 2 93 20,40 167,187 60,60 32 1.45 NA 16.18 NA FALSE 6.00 93 NA NA NA FALSE NA NA 45.84 3 78109350 HCC1395_HCC1395T 38 0.275 51 11,1 15,9 28,10 NA 0|1 0|1 78109322_GGATTACAGGCATGAAATTTATCCTA_G NA 78109322 26,12,10,3 G|GA PANCANCER NA FALSE ALG8 chr11:78109350:78109352:G:GA indel 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 82934746 82934747 C G 6 14 0.428571428571429 MODIFIER DDIAS ENSG00000165490 G downstream_gene_variant Transcript ENST00000329143 protein_coding NA 91 1 SNV HGNC HGNC:26351 1 P2 CCDS8263.1 ENSP00000329930 Q8IXT1.136 UPI00001AF966 Q8IXT1-1 3 NA NA PASS SITE 4,15|1,5 NA NA 1 29 34,39 178,173 60,60 23 1.07 NA 3.01 NA FALSE 6.00 33 NA NA NA FALSE NA NA 18.99 3 82934746 HCC1395_HCC1395T 8 0.500 14 4,0 1,5 5,5 NA 0/1 NA NA NA NA 3,5,1,5 C/G PANCANCER NA FALSE DDIAS chr11:82934746:82934747:C:G SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 89420211 89420212 T C 10 14 0.714285714285714 MODIFIER NOX4 ENSG00000086991 C intron_variant Transcript ENST00000263317 protein_coding 8/17 ENST00000263317.9:c.629+1691A>G NA -1 SNV HGNC HGNC:7891 YES NM_016931.5 1 P1 CCDS8285.1 ENSP00000263317 Q9NPH5.167 UPI000045655B Q9NPH5-1 3 NA NA PASS SITE 7,11|4,6 NA NA 1 22 33,39 207,223 60,60 47 1.08 NA 3.31 NA FALSE 4.61 62 NA NA NA FALSE NA NA 33.15 3 89420211 HCC1395_HCC1395T 4 0.695 14 0,3 2,5 3,8 NA 0/1 NA NA NA NA 1,3,4,6 T/C PANCANCER NA FALSE NOX4 chr11:89420211:89420212:T:C SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 92982015 92982016 G T 93 183 0.508196721311475 MODERATE MTNR1B ENSG00000134640 T missense_variant Transcript ENST00000257068 protein_coding 2/2 ENST00000257068.3:c.792G>T ENSP00000257068.2:p.W264C ENSP00000257068.2 p.W264C 867 792 264 W/C tgG/tgT rs746103746 1 SNV HGNC HGNC:7464 YES NM_005959.5 1 P1 CCDS8290.1 ENSP00000257068 P49286.176 UPI0000050408 1 deleterious(0.01) probably_damaging(1) Gene3D:1.20.1070.10&PDB-ENSP_mappings:6me6.A&PDB-ENSP_mappings:6me6.B&PDB-ENSP_mappings:6me7.A&PDB-ENSP_mappings:6me7.B&PDB-ENSP_mappings:6me8.A&PDB-ENSP_mappings:6me8.B&PDB-ENSP_mappings:6me9.A&PDB-ENSP_mappings:6me9.B&PDB-ENSP_mappings:7vh0.A&AlphaFold_DB_import:AF-P49286-F1&Pfam:PF00001&Prints:PR00237&PROSITE_profiles:PS50262&PANTHER:PTHR24228&SMART:SM01381&Superfamily:SSF81321&Transmembrane_helices:TMhelix&CDD:cd15400 0 0 0 0 0 0 0 0 0 0 gnomADe_AFR&gnomADe_AMR&gnomADe_ASJ&gnomADe_EAS&gnomADe_FIN&gnomADe_NFE&gnomADe_OTH&gnomADe_SAS 3 NA NA PASS SITE 132,156|42,51 NA NA 1 93 20,20 176,170 60,60 27 2.19 NA 44.67 NA FALSE 6.00 93 NA NA NA FALSE NA NA 255.14 3 92982015 HCC1395_HCC1395T 90 0.504 183 20,18 37,46 66,67 NA 0/1 NA NA NA NA 42,48,42,51 G/T PANCANCER NA FALSE MTNR1B_p.W264C chr11:92982015:92982016:G:T SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 93699152 93699153 G A 27 111 0.243243243243243 MODERATE CEP295 ENSG00000166004 A missense_variant Transcript ENST00000325212 protein_coding 15/30 ENST00000325212.11:c.4240G>A ENSP00000316681.6:p.E1414K ENSP00000316681.6 p.E1414K 4359 4240 1414 E/K Gaa/Aaa 1 SNV HGNC HGNC:29366 YES NM_033395.2 2 P4 CCDS44708.1 ENSP00000316681 Q9C0D2.129 UPI0000251F0E Q9C0D2-1 tolerated(0.12) benign(0.014) AlphaFold_DB_import:AF-Q9C0D2-F1&PANTHER:PTHR21553 3 NA NA PASS SITE 91,110|13,14 NA NA 1 93 20,20 172,164 60,60 28 1.92 NA 24.64 NA FALSE 6.00 75 NA NA NA FALSE NA NA 57.68 3 93699152 HCC1395_HCC1395T 84 0.222 111 22,7 30,9 62,17 NA 0/1 NA NA NA NA 36,48,13,14 G/A PANCANCER NA FALSE CEP295_p.E1414K chr11:93699152:93699153:G:A SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 93721511 93721512 G A 7 33 0.212121212121212 MODIFIER CEP295 ENSG00000166004 A intron_variant Transcript ENST00000325212 protein_coding 19/29 ENST00000325212.11:c.5850+99G>A NA 1 SNV HGNC HGNC:29366 YES NM_033395.2 2 P4 CCDS44708.1 ENSP00000316681 Q9C0D2.129 UPI0000251F0E Q9C0D2-1 3 NA NA PASS SITE 14,38|2,5 NA NA 1 81 38,36 201,188 60,60 14 1.34 NA 6.32 NA FALSE 6.00 25 NA NA NA FALSE NA NA 22.75 3 93721511 HCC1395_HCC1395T 26 0.241 33 11,5 7,1 21,6 NA 0/1 NA NA NA NA 6,20,2,5 G/A PANCANCER NA FALSE CEP295 chr11:93721511:93721512:G:A SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 93814409 93814410 A G 36 79 0.455696202531646 MODIFIER MED17 ENSG00000042429 G 3_prime_UTR_variant Transcript ENST00000251871 protein_coding 12/12 ENST00000251871.9:c.*2345A>G NA 4533 1 SNV HGNC HGNC:2375 YES NM_004268.5 1 P1 CCDS8295.1 ENSP00000251871 Q9NVC6.174 UPI000013CD1D Q9NVC6-1 1 3 NA NA PASS SITE 35,84|8,28 NA NA 1 93 36,38 184,171 60,60 19 1.80 NA 18.36 NA FALSE 6.00 93 NA NA NA FALSE NA NA 110.31 3 93814409 HCC1395_HCC1395T 43 0.431 79 14,12 25,14 40,30 NA 0/1 NA NA NA NA 9,34,8,28 A/G PANCANCER NA FALSE MED17 chr11:93814409:93814410:A:G SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 108474713 108474714 C A 96 96 1 MODIFIER POGLUT3 ENSG00000178202 A 3_prime_UTR_variant Transcript ENST00000323468 protein_coding 8/8 ENST00000323468.10:c.*114G>T NA 1656 -1 SNV HGNC HGNC:28496 YES NM_153705.5 1 P1 CCDS41711.1 ENSP00000315386 Q7Z4H8.140 A0A024R3C4.61 UPI0000456580 Q7Z4H8-1 3 NA NA PASS SITE 91,64|62,34 NA NA 1 93 20,20 167,172 60,60 32 2.05 NA 31.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 285.53 3 108474713 HCC1395_HCC1395T 0 0.986 96 0,21 0,41 0,68 NA 0/1 NA NA NA NA 0,0,62,34 C/A PANCANCER NA FALSE POGLUT3 chr11:108474713:108474714:C:A SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 118531118 118531119 C A 79 79 1 MODIFIER TTC36 ENSG00000172425 A downstream_gene_variant Transcript ENST00000302783 protein_coding NA rs1205409460 125 1 SNV HGNC HGNC:33708 YES NM_001080441.4 1 P1 CCDS31687.1 ENSP00000307640 A6NLP5.119 UPI00001972C2 A6NLP5-1 1.315e-05 4.83e-05 0 0 0 0 0 0 0 0 0 4.83e-05 gnomADg_AFR 3 NA NA PASS SITE 46,57|36,43 NA NA 1 93 20,20 149,184 60,60 37 1.85 NA 20.46 NA FALSE 6.00 93 NA NA NA FALSE NA NA 241.87 3 118531118 HCC1395_HCC1395T 0 0.983 79 0,19 0,26 0,55 NA 0/1 NA NA NA NA 0,0,36,43 C/A PANCANCER NA FALSE TTC36 chr11:118531118:118531119:C:A SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 119663460 119663461 C T 48 97 0.494845360824742 MODIFIER NECTIN1 ENSG00000110400 T 3_prime_UTR_variant Transcript ENST00000264025 protein_coding 6/6 ENST00000264025.8:c.*1287G>A NA 3488 -1 SNV HGNC HGNC:9706 YES NM_002855.5 1 P1 CCDS8426.1 ENSP00000264025 Q15223.205 UPI000004A2BE Q15223-1 1 3 NA NA PASS SITE 117,81|31,17 NA NA 1 93 20,20 171,165 60,60 30 2.00 NA 29.45 NA FALSE 6.00 93 NA NA NA FALSE NA NA 124.86 3 119663460 HCC1395_HCC1395T 49 0.466 97 14,12 23,20 38,33 NA 0/1 NA NA NA NA 32,17,31,17 C/T PANCANCER NA FALSE NECTIN1 chr11:119663460:119663461:C:T SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 120299526 120299527 G C 56 56 1 MODIFIER POU2F3 ENSG00000137709 C intron_variant Transcript ENST00000260264 protein_coding 4/12 ENST00000260264.8:c.265-98G>C NA 1 SNV HGNC HGNC:19864 2 CCDS58190.1 ENSP00000260264 Q9UKI9.182 UPI0002064EE0 Q9UKI9-2 3 NA NA PASS SITE 48,23|37,19 NA NA 1 93 29,20 176,183 60,60 31 1.74 NA 16.21 NA FALSE 6.00 93 NA NA NA FALSE NA NA 185.21 3 120299526 HCC1395_HCC1395T 0 0.977 56 0,11 0,30 0,41 NA 0/1 NA NA NA NA 0,0,37,19 G/C PANCANCER NA FALSE POU2F3 chr11:120299526:120299527:G:C SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 122957249 122957250 C A 59 59 1 MODIFIER JHY ENSG00000109944 A intron_variant Transcript ENST00000227349 protein_coding 7/8 ENST00000227349.7:c.2011-114C>A NA 1 SNV HGNC HGNC:26288 YES NM_024806.4 1 P1 CCDS8438.1 ENSP00000227349 Q6NUN7.125 UPI00001FA5AB Q6NUN7-1 3 NA NA PASS SITE 45,35|27,32 NA NA 1 93 20,20 151,152 60,60 37 1.75 NA 16.21 NA FALSE 6.00 93 NA NA NA FALSE NA NA 173.01 3 122957249 HCC1395_HCC1395T 0 0.976 59 0,16 0,20 0,40 NA 0/1 NA NA NA NA 0,0,27,32 C/A PANCANCER NA FALSE JHY chr11:122957249:122957250:C:A SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 123730742 123730743 G A 82 183 0.448087431693989 LOW ZNF202 ENSG00000166261 A synonymous_variant Transcript ENST00000336139 protein_coding 3/8 ENST00000336139.8:c.147C>T ENSP00000337724.4:p.F49= ENSP00000337724.4 p.F49= 510 147 49 F ttC/ttT rs376917408 -1 SNV HGNC HGNC:12994 1 P1 CCDS8443.1 ENSP00000337724 O95125.203 A0A024R3M3.69 UPI000013E581 O95125-1 Gene3D:1.10.4020.10&AlphaFold_DB_import:AF-O95125-F1&Pfam:PF02023&PROSITE_profiles:PS50804&SMART:SM00431&Superfamily:SSF47353&CDD:cd07936 3.977e-06 6.152e-05 0 0 0 0 0 0 0 6.152e-05 gnomADe_AFR 3 NA NA PASS SITE 164,117|46,36 NA NA 1 93 20,20 166,171 60,60 26 2.14 NA 40.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 213.93 3 123730742 HCC1395_HCC1395T 101 0.443 183 29,19 42,36 77,61 NA 0/1 NA NA NA NA 60,41,46,36 G/A PANCANCER NA FALSE ZNF202_p.F49= chr11:123730742:123730743:G:A SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 123943667 123943668 G C 32 81 0.395061728395062 MODIFIER OR4D5 ENSG00000171014 C downstream_gene_variant Transcript ENST00000307033 protein_coding NA COSV100189974 3094 1 SNV HGNC HGNC:14852 YES NM_001001965.1 P1 CCDS31699.1 ENSP00000305970 Q8NGN0.147 A0A126GVD9.30 UPI000003F227 1 1 3 NA NA PASS SITE 82,98|14,18 NA NA 1 93 20,36 167,168 60,60 23 1.99 NA 28.29 NA FALSE 6.00 93 NA NA NA FALSE NA NA 95.81 3 123943667 HCC1395_HCC1395T 49 0.418 81 8,8 26,13 38,27 NA 0/1 NA NA NA NA 21,28,14,18 G/C PANCANCER NA FALSE OR4D5 chr11:123943667:123943668:G:C SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 124319974 124319975 G A 39 39 1 MODIFIER OR8B7P ENSG00000254976 A downstream_gene_variant Transcript ENST00000526868 unprocessed_pseudogene NA COSV62488367 4897 -1 SNV HGNC HGNC:8476 YES 1 1 3 NA NA PASS SITE 35,21|25,14 NA NA 1 93 36,38 183,211 60,60 25 1.67 NA 13.50 NA FALSE 6.00 93 NA NA NA FALSE NA NA 149.96 3 124319974 HCC1395_HCC1395T 0 0.974 39 0,11 0,22 0,35 NA 0/1 NA NA NA NA 0,0,25,14 G/A PANCANCER NA FALSE OR8B7P chr11:124319974:124319975:G:A SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 125003781 125003782 G A 16 29 0.551724137931034 MODIFIER CCDC15 ENSG00000149548 A intron_variant Transcript ENST00000344762 protein_coding 11/15 ENST00000344762.6:c.2215-86G>A NA 1 SNV HGNC HGNC:25798 YES NM_025004.3 5 A2 CCDS44756.1 ENSP00000341684 Q0P6D6.102 UPI0000EE3BEA 3 NA NA PASS SITE 34,8|13,3 NA NA 1 71 35,37 188,208 60,60 29 1.42 NA 7.48 NA FALSE 6.00 60 NA NA NA FALSE NA NA 47.51 3 125003781 HCC1395_HCC1395T 13 0.589 29 2,4 5,8 9,13 NA 0/1 NA NA NA NA 9,4,13,3 G/A PANCANCER NA FALSE CCDC15 chr11:125003781:125003782:G:A SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 126256472 126256473 C T 94 94 1 MODIFIER FAM118B ENSG00000197798 T intron_variant Transcript ENST00000360194 protein_coding 5/7 ENST00000360194.8:c.697-95C>T NA 1 SNV HGNC HGNC:26110 5 A1 CCDS81647.1 ENSP00000353321 J3KP39.69 UPI0000D4ED4C 3 NA NA PASS SITE 51,34|51,43 NA NA 1 93 20,20 163,173 60,60 34 1.79 NA 18.36 NA FALSE 6.00 93 NA NA NA FALSE NA NA 283.17 3 126256472 HCC1395_HCC1395T 0 0.985 94 0,22 0,41 0,64 NA 0/1 NA NA NA NA 0,0,51,43 C/T PANCANCER NA FALSE FAM118B chr11:126256472:126256473:C:T SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 128968555 128968556 A C 11 29 0.379310344827586 MODIFIER ARHGAP32 ENSG00000134909 C 3_prime_UTR_variant Transcript ENST00000310343 protein_coding 22/22 ENST00000310343.13:c.*352T>G NA 6616 -1 SNV HGNC HGNC:17399 1 A1 CCDS44769.1 ENSP00000310561 A7KAX9.139 UPI000159C61F A7KAX9-1 3 NA NA PASS SITE 32,21|5,6 NA NA 1 85 35,20 203,178 60,60 41 1.46 NA 8.38 NA FALSE 6.00 59 NA NA NA FALSE NA NA 29.95 3 128968555 HCC1395_HCC1395T 18 0.346 29 5,6 9,2 16,8 NA 0/1 NA NA NA NA 13,5,5,6 A/C PANCANCER NA FALSE ARHGAP32 chr11:128968555:128968556:A:C SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 130123667 130123668 G C 25 199 0.125628140703518 MODERATE APLP2 ENSG00000084234 C missense_variant Transcript ENST00000263574 protein_coding 7/18 ENST00000263574.9:c.978G>C ENSP00000263574.5:p.W326C ENSP00000263574.5 p.W326C 1050 978 326 W/C tgG/tgC COSV53843629 1 SNV HGNC HGNC:598 1 P4 CCDS8486.1 ENSP00000263574 Q06481.217 UPI0000125CAE Q06481-1 deleterious_low_confidence(0) PDB-ENSP_mappings:5jbt.Y&CDD:cd22607&Gene3D:4.10.410.10&Pfam:PF00014&SMART:SM00131&Superfamily:SSF57362&PROSITE_profiles:PS50279&PANTHER:PTHR23103&AlphaFold_DB_import:AF-Q06481-F1 1 1 3 NA NA PASS SITE 252,120|15,10 NA NA 1 93 20,20 156,153 60,60 28 2.17 NA 42.91 NA FALSE 6.00 50 NA NA NA FALSE NA NA 48.79 3 130123667 HCC1395_HCC1395T 174 0.117 199 51,4 65,11 120,15 NA 0/1 NA NA NA NA 114,60,15,10 G/C PANCANCER NA FALSE APLP2_p.W326C chr11:130123667:130123668:G:C SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 132436786 132436787 G A 22 61 0.360655737704918 LOW OPCML ENSG00000183715 A splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000331898 protein_coding 4/6 ENST00000331898.11:c.665-7C>T NA rs1389448867 -1 SNV HGNC HGNC:8143 1 P2 CCDS8492.1 ENSP00000330862 Q14982.190 A8K0Y0.121 UPI0000055AE0 Q14982-1 1 6.574e-06 0 0 6.548e-05 0 0 0 0 0 0 0 6.548e-05 gnomADg_AMR 3 NA NA PASS SITE 39,92|3,19 NA NA 1 93 20,36 174,185 60,60 38 1.84 NA 19.88 NA FALSE 6.00 6 NA NA NA FALSE NA NA 48.78 3 132436786 HCC1395_HCC1395T 39 0.382 61 9,6 9,0 31,19 NA 0/1 NA NA NA NA 10,29,3,19 G/A PANCANCER NA FALSE OPCML chr11:132436786:132436787:G:A SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr11 134985917 134985918 C G 4 4 1 MODIFIER ENSG00000279046 G non_coding_transcript_exon_variant Transcript ENST00000624288 TEC 1/1 ENST00000624288.1:n.235C>G NA 235 rs10894924 1 SNV YES 0.04397 0.1455 0.04791 0.01648 0.1133 0.009892 0.03767 0.04858 0.02406 0.01087 0.01907 0 0.0107 0.02564 0 0.01095 0 0.008451 0.01786 0.01923 0.1455 gnomADe_AFR 3 NA NA PASS SITE 15,19|0,5 NA NA 1 26 37,37 176,167 27,42 2 -3.150e-02 NA 5.75 NA FALSE 1.68 69 NA NA NA FALSE NA NA 15.71 3 134985917 HCC1395_HCC1395T 0 0.841 4 0,1 0,3 0,4 NA 0/1 NA NA NA NA 0,0,0,4 C/G PANCANCER NA FALSE chr11:134985917:134985918:C:G SNV 2:0 chr11:70698816:134986767:2:0:1 TRUE NA 0.96 +chr12 889170 889171 C G 202 297 0.68013468013468 MODERATE WNK1 ENSG00000060237 G missense_variant Transcript ENST00000315939 protein_coding 21/28 ENST00000315939.11:c.5395C>G ENSP00000313059.6:p.Q1799E ENSP00000313059.6 p.Q1799E 6382 5395 1799 Q/E Caa/Gaa COSV60047841 1 SNV HGNC HGNC:14540 YES NM_018979.4 1 P2 CCDS8506.1 ENSP00000313059 Q9H4A3.216 UPI000013CD65 Q9H4A3-1 1 deleterious_low_confidence(0) AlphaFold_DB_import:AF-Q9H4A3-F1 1 1 4 NA NA PASS SITE 121,144|96,106 NA NA 1 93 20,20 156,160 60,60 35 2.03 NA 32.12 NA FALSE 6.00 93 NA NA NA FALSE NA NA 543.19 4 889170 HCC1395_HCC1395T 95 0.694 297 11,49 41,71 56,128 NA 0/1 NA NA NA NA 48,47,96,106 C/G PANCANCER NA FALSE WNK1_p.Q1799E chr12:889170:889171:C:G SNV 3:0 chr12:140964:6731043:3:0:1 NA NA 0.96 +chr12 1970848 1970849 G C 49 188 0.26063829787234 MODIFIER DCP1B ENSG00000151065 C intron_variant Transcript ENST00000280665 protein_coding 3/8 ENST00000280665.11:c.320-2938C>G NA -1 SNV HGNC HGNC:24451 YES NM_152640.5 1 P1 CCDS31727.1 ENSP00000280665 Q8IZD4.160 UPI000013DC30 Q8IZD4-1 4 NA NA PASS SITE 192,68|40,9 NA NA 1 93 34,37 174,163 60,60 20 1.95 NA 26.10 NA FALSE 6.00 93 NA NA NA FALSE NA NA 136.75 4 1970848 HCC1395_HCC1395T 139 0.274 188 37,14 71,27 110,41 NA 0/1 NA NA NA NA 106,33,40,9 G/C PANCANCER NA FALSE DCP1B chr12:1970848:1970849:G:C SNV 3:0 chr12:140964:6731043:3:0:1 NA NA 0.96 +chr12 4489659 4489660 G C 116 116 1 MODIFIER C12orf4 ENSG00000047621 C 3_prime_UTR_variant Transcript ENST00000261250 protein_coding 14/14 ENST00000261250.8:c.*148C>G NA 1893 -1 SNV HGNC HGNC:1184 YES NM_020374.4 1 P1 CCDS8528.1 ENSP00000261250 Q9NQ89.135 UPI0000038C60 1 4 NA NA PASS SITE 29,29|57,59 NA NA 1 93 39,37 206,203 60,60 26 1.69 NA 14.45 NA FALSE 6.00 93 NA NA NA FALSE NA NA 401.90 4 4489659 HCC1395_HCC1395T 0 0.990 116 0,37 0,50 0,93 NA 0/1 NA NA NA NA 0,0,57,59 G/C PANCANCER NA FALSE C12orf4 chr12:4489659:4489660:G:C SNV 3:0 chr12:140964:6731043:3:0:1 NA NA 0.96 +chr12 6600860 6600861 G C 108 135 0.8 MODIFIER CHD4 ENSG00000111642 C intron_variant Transcript ENST00000357008 protein_coding 7/39 ENST00000357008.7:c.927+66C>G NA rs1324327890 -1 SNV HGNC HGNC:1919 1 CCDS86267.1 ENSP00000349508 A0A2U3TZM0.28 UPI0003EAE9C7 1 1.315e-05 4.832e-05 0 0 0 0 0 0 0 0 0 4.832e-05 gnomADg_AFR 4 NA NA PASS SITE 75,42|74,34 NA NA 1 93 20,20 170,166 60,60 25 1.78 NA 17.76 NA FALSE 6.00 93 NA NA NA FALSE NA NA 327.32 4 6600860 HCC1395_HCC1395T 27 0.774 135 9,29 12,47 22,78 NA 0/1 NA NA NA NA 19,8,74,34 G/C PANCANCER TRUE FALSE CHD4 chr12:6600860:6600861:G:C SNV 3:0 chr12:140964:6731043:3:0:1 NA NA 0.96 +chr12 6850642 6850643 C G 21 69 0.304347826086957 MODIFIER GNB3 ENSG00000111664 G downstream_gene_variant Transcript ENST00000229264 protein_coding NA 3249 1 SNV HGNC HGNC:4400 YES NM_002075.4 5 P1 CCDS8564.1 ENSP00000229264 P16520.220 F1T0G5.86 UPI0000030A36 P16520-1 1 4 NA NA PASS SITE 48,49|12,9 NA NA 1 93 20,20 165,176 60,60 32 1.57 NA 10.83 NA FALSE 6.00 93 NA NA NA FALSE NA NA 48.82 4 6850642 HCC1395_HCC1395T 48 0.292 69 15,7 15,6 33,13 NA 0/1 NA NA NA NA 26,22,12,9 C/G PANCANCER NA FALSE GNB3 chr12:6850642:6850643:C:G SNV 4:0 chr12:6731205:8867893:4:0:1 NA NA 0.96 +chr12 6867653 6867654 G C 311 490 0.63469387755102 MODIFIER USP5 ENSG00000111667 C downstream_gene_variant Transcript ENST00000229268 protein_coding NA 1021 1 SNV HGNC HGNC:12628 YES NM_001098536.2 1 A1 CCDS41743.1 ENSP00000229268 P45974.216 A0A140VJZ1.43 UPI00001379E1 P45974-1 4 NA NA PASS SITE 275,359|129,182 NA NA 1 93 20,20 158,160 60,60 39 2.46 NA 85.79 NA FALSE 6.00 93 NA NA NA FALSE NA NA 829.65 4 6867653 HCC1395_HCC1395T 179 0.633 490 42,85 50,70 115,199 NA 0/1 NA NA NA NA 73,106,129,182 G/C PANCANCER NA FALSE USP5 chr12:6867653:6867654:G:C SNV 4:0 chr12:6731205:8867893:4:0:1 NA NA 0.96 +chr12 6938930 6938931 C T 110 403 0.272952853598015 LOW ATN1 ENSG00000111676 T synonymous_variant Transcript ENST00000356654 protein_coding 7/10 ENST00000356654.8:c.2967C>T ENSP00000349076.3:p.F989= ENSP00000349076.3 p.F989= 3204 2967 989 F ttC/ttT rs782274469 1 SNV HGNC HGNC:3033 1 P1 CCDS31734.1 ENSP00000349076 P54259.197 UPI000006F554 1 AlphaFold_DB_import:AF-P54259-F1&Pfam:PF03154&PANTHER:PTHR13859&Low_complexity_(Seg):seg 7.985e-06 0 0 0 0 0 1.765e-05 0 0 1.765e-05 gnomADe_NFE 4 NA NA PASS SITE 290,340|49,61 NA NA 1 93 20,20 166,175 60,60 30 2.39 NA 71.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 254.34 4 6938930 HCC1395_HCC1395T 293 0.266 403 95,33 109,39 214,77 NA 0/1 NA NA NA NA 142,151,49,61 C/T PANCANCER NA FALSE ATN1_p.F989= chr12:6938930:6938931:C:T SNV 4:0 chr12:6731205:8867893:4:0:1 NA NA 0.96 +chr12 6977354 6977355 G T 25 175 0.142857142857143 MODIFIER LPCAT3 ENSG00000111684 T intron_variant Transcript ENST00000261407 protein_coding 11/12 ENST00000261407.9:c.1347+13C>A NA -1 SNV HGNC HGNC:30244 YES NM_005768.6 1 P1 CCDS8572.1 ENSP00000261407 Q6P1A2.152 UPI0000034DFC Q6P1A2-1 4 NA NA PASS SITE 109,139|10,15 NA NA 1 93 20,35 164,161 60,60 37 1.85 NA 20.72 NA FALSE 6.00 59 NA NA NA FALSE NA NA 60.57 4 6977354 HCC1395_HCC1395T 150 0.165 175 30,6 61,13 100,19 NA 0/1 NA NA NA NA 62,88,10,15 G/T PANCANCER NA FALSE LPCAT3 chr12:6977354:6977355:G:T SNV 4:0 chr12:6731205:8867893:4:0:1 NA NA 0.96 +chr12 7101769 7101770 G A 125 204 0.612745098039216 MODIFIER C1RL ENSG00000139178 A intron_variant Transcript ENST00000266542 protein_coding 3/5 ENST00000266542.9:c.490+129C>T NA -1 SNV HGNC HGNC:21265 YES NM_016546.4 1 P1 CCDS8573.1 ENSP00000266542 Q9NZP8.166 UPI0000EE67FA 4 NA NA PASS SITE 82,124|46,79 NA NA 1 93 20,20 171,175 60,60 27 1.98 NA 27.99 NA FALSE 6.00 93 NA NA NA FALSE NA NA 347.86 4 7101769 HCC1395_HCC1395T 79 0.601 204 23,31 30,47 59,89 NA 0/1 NA NA NA NA 26,53,46,79 G/A PANCANCER NA FALSE C1RL chr12:7101769:7101770:G:A SNV 4:0 chr12:6731205:8867893:4:0:1 NA NA 0.96 +chr12 8853974 8853975 G A 4 17 0.235294117647059 MODIFIER A2ML1 ENSG00000166535 A intron_variant Transcript ENST00000299698 protein_coding 20/35 ENST00000299698.12:c.2591-154G>A NA 1 SNV HGNC HGNC:23336 YES NM_144670.6 1 P1 CCDS8596.2 ENSP00000299698 A8K2U0.118 UPI000022904E A8K2U0-1 1 4 NA NA PASS SITE 22,0|4,0 NA NA 1 26 42,34 223,167 60,60 11 1.000 NA 2.71 NA FALSE 6.00 16 NA NA NA FALSE NA NA 10.67 4 8853974 HCC1395_HCC1395T 13 0.264 17 7,1 5,3 13,4 NA 0/1 NA NA NA NA 13,0,4,0 G/A PANCANCER NA FALSE A2ML1 chr12:8853974:8853975:G:A SNV 4:0 chr12:6731205:8867893:4:0:1 NA NA 0.96 +chr12 8933295 8933296 C G 211 287 0.735191637630662 HIGH PHC1 ENSG00000111752 G stop_gained Transcript ENST00000433083 protein_coding 7/14 ENST00000433083.6:c.1703C>G ENSP00000399194.2:p.S568* ENSP00000399194.2 p.S568* 1848 1703 568 S/* tCa/tGa COSV70418845 1 SNV HGNC HGNC:3182 1 ENSP00000399194 J3KQH6.75 UPI000204AA8A 1 PANTHER:PTHR12247&AlphaFold_DB_import:AF-J3KQH6-F1 1 1 4 NA NA PASS SITE 153,136|114,97 NA NA 1 93 20,20 160,159 60,60 32 2.12 NA 39.08 NA FALSE 6.00 93 NA NA NA FALSE NA NA 581.19 4 8933295 HCC1395_HCC1395T 76 0.743 287 18,58 26,72 45,132 NA 0/1 NA NA NA NA 42,34,114,97 C/G PANCANCER NA FALSE PHC1_p.S568* chr12:8933295:8933296:C:G SNV 3:0 chr12:8868316:9164177:3:0:1 NA NA 0.96 +chr12 9068692 9068693 C A 32 151 0.211920529801325 MODIFIER A2M ENSG00000175899 A intron_variant Transcript ENST00000318602 protein_coding 34/35 ENST00000318602.12:c.4366+48G>T NA -1 SNV HGNC HGNC:7 YES NM_000014.6 1 P1 CCDS44827.1 ENSP00000323929 P01023.236 UPI000014038F 4 NA NA PASS SITE 146,40|27,5 NA NA 1 93 37,34 183,181 60,60 24 1.73 NA 15.61 NA FALSE 6.00 71 NA NA NA FALSE NA NA 81.15 4 9068692 HCC1395_HCC1395T 119 0.220 151 33,10 64,17 98,27 NA 0/1 NA NA NA NA 95,24,27,5 C/A PANCANCER NA FALSE A2M chr12:9068692:9068693:C:A SNV 3:0 chr12:8868316:9164177:3:0:1 NA NA 0.96 +chr12 10191484 10191485 G C 18 29 0.620689655172414 MODIFIER TMEM52B ENSG00000165685 C 3_prime_UTR_variant Transcript ENST00000298530 protein_coding 4/4 ENST00000298530.7:c.*1344G>C NA 2414 1 SNV HGNC HGNC:26438 1 CCDS8619.1 ENSP00000298530 Q4KMG9.111 UPI000006D360 Q4KMG9-2 4 NA NA PASS SITE 21,4|17,1 NA NA 1 43 38,39 195,201 60,60 21 1.08 NA 3.31 NA FALSE 6.00 79 NA NA NA FALSE NA NA 65.94 4 10191484 HCC1395_HCC1395T 11 0.600 29 7,5 4,12 11,17 NA 0/1 NA NA NA NA 10,1,17,1 G/C PANCANCER NA FALSE TMEM52B chr12:10191484:10191485:G:C SNV 4:0 chr12:9164311:21474738:4:0:1 NA NA 0.96 +chr12 10213914 10213915 G C 37 229 0.161572052401747 MODIFIER GABARAPL1 ENSG00000139112 C intron_variant Transcript ENST00000266458 protein_coding 1/3 ENST00000266458.10:c.90+695G>C NA 1 SNV HGNC HGNC:4068 YES NM_031412.4 1 P1 CCDS8620.1 ENSP00000266458 Q9H0R8.190 A0A024RAP5.50 UPI00000233F0 Q9H0R8-1 4 NA NA PASS SITE 179,180|15,22 NA NA 1 93 20,20 159,157 60,60 32 2.01 NA 30.40 NA FALSE 6.00 60 NA NA NA FALSE NA NA 81.70 4 10213914 HCC1395_HCC1395T 192 0.166 229 46,5 74,17 125,24 NA 0/1 NA NA NA NA 95,97,15,22 G/C PANCANCER NA FALSE GABARAPL1 chr12:10213914:10213915:G:C SNV 4:0 chr12:9164311:21474738:4:0:1 NA NA 0.96 +chr12 12119339 12119340 G A 43 243 0.176954732510288 MODIFIER LRP6 ENSG00000070018 A 3_prime_UTR_variant Transcript ENST00000261349 protein_coding 23/23 ENST00000261349.9:c.*1787C>T NA 6938 rs749857104 -1 SNV HGNC HGNC:6698 YES NM_002336.3 1 P1 CCDS8647.1 ENSP00000261349 O75581.195 UPI00001FB66C 1 0 0 0 0 0 0 0 0 0 0 0 0 gnomADg_AFR&gnomADg_AMI&gnomADg_AMR&gnomADg_ASJ&gnomADg_EAS&gnomADg_FIN&gnomADg_MID&gnomADg_NFE&gnomADg_OTH&gnomADg_SAS 4 NA NA PASS SITE 152,189|16,29 NA NA 1 93 20,34 175,194 60,60 28 2.03 NA 31.04 NA FALSE 6.00 38 NA NA NA FALSE NA NA 106.32 4 12119339 HCC1395_HCC1395T 200 0.186 243 36,5 68,16 152,34 NA 0/1 NA NA NA NA 85,115,16,27 G/A PANCANCER NA FALSE LRP6 chr12:12119339:12119340:G:A SNV 4:0 chr12:9164311:21474738:4:0:1 NA NA 0.96 +chr12 12562148 12562149 G C 21 70 0.3 MODIFIER DUSP16 ENSG00000111266 C 5_prime_UTR_variant Transcript ENST00000228862 protein_coding 1/6 ENST00000228862.3:c.-397C>G NA 236 -1 SNV HGNC HGNC:17909 5 ENSP00000228862 Q9BY84.180 UPI000006F54D Q9BY84-2 4 NA NA PASS SITE 61,41|13,8 NA NA 1 93 20,20 157,159 60,60 36 1.56 NA 10.54 NA FALSE 6.00 73 NA NA NA FALSE NA NA 49.01 4 12562148 HCC1395_HCC1395T 49 0.320 70 11,9 17,5 31,14 NA 0/1 NA NA NA NA 28,21,13,8 G/C PANCANCER NA FALSE DUSP16 chr12:12562148:12562149:G:C SNV 4:0 chr12:9164311:21474738:4:0:1 NA NA 0.96 +chr12 12562343 12562344 G C 8 33 0.242424242424242 MODIFIER DUSP16 ENSG00000111266 C 5_prime_UTR_variant Transcript ENST00000228862 protein_coding 1/6 ENST00000228862.3:c.-592C>G NA 41 rs1000135766 -1 SNV HGNC HGNC:17909 5 ENSP00000228862 Q9BY84.180 UPI000006F54D Q9BY84-2 1.977e-05 7.267e-05 0 0 0 0 0 0 0 0 0 7.267e-05 gnomADg_AFR 4 NA NA PASS SITE 14,27|2,6 NA NA 1 34 20,29 171,185 60,60 21 1.11 NA 3.61 NA FALSE 6.00 18 NA NA NA FALSE NA NA 19.58 4 12562343 HCC1395_HCC1395T 25 0.269 33 5,4 10,0 18,6 NA 0/1 NA NA NA NA 9,16,2,6 G/C PANCANCER NA FALSE DUSP16 chr12:12562343:12562344:G:C SNV 4:0 chr12:9164311:21474738:4:0:1 NA NA 0.96 +chr12 12612221 12612222 C G 102 437 0.233409610983982 MODIFIER CREBL2 ENSG00000111269 G intron_variant Transcript ENST00000228865 protein_coding 1/3 ENST00000228865.3:c.15+34C>G NA 1 SNV HGNC HGNC:2350 YES NM_001310.4 1 P1 CCDS8651.1 ENSP00000228865 O60519.152 UPI0000070749 4 NA NA PASS SITE 300,383|45,57 NA NA 1 93 20,20 156,158 60,60 32 2.35 NA 66.82 NA FALSE 6.00 93 NA NA NA FALSE NA NA 231.50 4 12612221 HCC1395_HCC1395T 335 0.222 437 86,22 124,41 227,64 NA 0/1 NA NA NA NA 148,187,45,57 C/G PANCANCER NA FALSE CREBL2 chr12:12612221:12612222:C:G SNV 4:0 chr12:9164311:21474738:4:0:1 NA NA 0.96 +chr12 18563498 18563499 A G 6 478 0.0125523012552301 MODERATE PIK3C2G ENSG00000139144 G missense_variant&splice_region_variant Transcript ENST00000433979 protein_coding 27/32 ENST00000433979.6:c.3779A>G ENSP00000404845.1:p.E1260G ENSP00000404845.1 p.E1260G 3895 3779 1260 E/G gAg/gGg rs761512887 1 SNV HGNC HGNC:8973 5 CCDS44839.1 ENSP00000404845 O75747.196 UPI000013D6EF deleterious(0) probably_damaging(0.965) PDB-ENSP_mappings:2wwe.A&Gene3D:3.30.1520.10&AlphaFold_DB_import:AF-O75747-F1&Pfam:PF00787&PROSITE_profiles:PS50195&SMART:SM00312&Superfamily:SSF64268&CDD:cd06896 8.036e-06 0 0 0 0 0 1.773e-05 0 0 1.773e-05 gnomADe_NFE 4 NA NA PASS SITE 295,365|3,3 NA NA 1 93 20,38 157,193 60,60 49 2.09 NA 36.33 NA FALSE 6.00 18 NA NA NA FALSE NA NA 9.63 4 18563498 HCC1395_HCC1395T 472 0.019 478 100,2 186,3 302,5 NA 0/1 NA NA NA NA 207,265,3,3 A/G PANCANCER NA FALSE PIK3C2G_p.E1260G chr12:18563498:18563499:A:G SNV 4:0 chr12:9164311:21474738:4:0:1 NA NA 0.96 +chr12 21267942 21267943 C T 10 662 0.0151057401812689 MODIFIER SLCO1A2 ENSG00000084453 T 3_prime_UTR_variant Transcript ENST00000307378 protein_coding 16/16 ENST00000307378.10:c.*1606G>A NA 4340 -1 SNV HGNC HGNC:10956 1 P1 CCDS8686.1 ENSP00000305974 P46721.192 A0A024RAT5.56 UPI0000037575 P46721-1 4 NA NA PASS SITE 602,388|5,5 NA NA 1 93 20,20 169,194 60,60 44 2.37 NA 69.74 NA FALSE 6.00 31 NA NA NA FALSE NA NA 14.64 4 21267942 HCC1395_HCC1395T 652 0.017 662 155,4 285,3 450,7 NA 0/1 NA NA NA NA 403,249,5,5 C/T PANCANCER NA FALSE SLCO1A2 chr12:21267942:21267943:C:T SNV 4:0 chr12:9164311:21474738:4:0:1 NA NA 0.96 +chr12 21654542 21654543 C A 128 152 0.842105263157895 HIGH LDHB ENSG00000111716 A splice_donor_variant Transcript ENST00000350669 protein_coding 2/7 ENST00000350669.5:c.129+1G>T NA COSV63365641 -1 SNV HGNC HGNC:6541 YES NM_002300.8 1 P1 CCDS8691.1 ENSP00000229319 P07195.247 Q5U077.170 UPI000013C8F6 1 1 1 4 NA NA PASS SITE 69,34|97,31 NA NA 1 93 20,36 167,173 60,60 25 1.75 NA 16.25 NA FALSE 6.00 93 NA NA NA FALSE NA NA 417.71 4 21654542 HCC1395_HCC1395T 24 0.839 152 5,35 12,64 19,101 NA 0/1 NA NA NA NA 18,6,97,31 C/A PANCANCER NA FALSE LDHB chr12:21654542:21654543:C:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 22449571 22449572 C G 39 189 0.206349206349206 MODIFIER C2CD5 ENSG00000111731 G 3_prime_UTR_variant Transcript ENST00000333957 protein_coding 25/25 ENST00000333957.8:c.*189G>C NA 3448 -1 SNV HGNC HGNC:29062 1 CCDS31758.1 ENSP00000334229 Q86YS7.160 UPI000000D850 Q86YS7-1 4 NA NA PASS SITE 102,123|18,21 NA NA 1 93 20,20 166,176 60,60 35 1.76 NA 16.86 NA FALSE 6.00 49 NA NA NA FALSE NA NA 89.82 4 22449571 HCC1395_HCC1395T 150 0.210 189 36,5 58,19 97,25 NA 0/1 NA NA NA NA 66,84,18,21 C/G PANCANCER NA FALSE C2CD5 chr12:22449571:22449572:C:G SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 27962641 27962642 T C 40 122 0.327868852459016 MODIFIER PTHLH ENSG00000087494 C 3_prime_UTR_variant Transcript ENST00000201015 protein_coding 4/4 ENST00000201015.8:c.*703A>G NA 1553 -1 SNV HGNC HGNC:9607 3 A1 CCDS8715.1 ENSP00000201015 P12272.224 Q53XY9.128 UPI000002B1CC P12272-2 1 4 NA NA PASS SITE 34,150|9,31 NA NA 1 93 37,33 184,193 60,60 16 1.93 NA 24.89 NA FALSE 6.00 50 NA NA NA FALSE NA NA 106.47 4 27962641 HCC1395_HCC1395T 82 0.309 122 26,7 39,20 70,31 NA 0/1 NA NA NA NA 13,69,9,31 T/C PANCANCER NA FALSE PTHLH chr12:27962641:27962642:T:C SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 31116248 31116249 G C 7 18 0.388888888888889 MODIFIER ENSG00000291250 C intron_variant&non_coding_transcript_variant Transcript ENST00000391394 lncRNA 3/6 ENST00000391394.4:n.322+109C>G NA -1 SNV 1 4 NA NA PASS SITE 22,0|7,0 NA NA 1 34 41,38 202,215 60,60 8 1.08 NA 3.31 NA FALSE 6.00 54 NA NA NA FALSE NA NA 23.74 4 31116248 HCC1395_HCC1395T 11 0.400 18 3,5 7,2 11,7 NA 0/1 NA NA NA NA 11,0,7,0 G/C PANCANCER NA FALSE chr12:31116248:31116249:G:C SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 31697922 31697923 G T 64 213 0.300469483568075 MODERATE AMN1 ENSG00000151743 T missense_variant Transcript ENST00000281471 protein_coding 4/7 ENST00000281471.11:c.352C>A ENSP00000281471.6:p.H118N ENSP00000281471.6 p.H118N 365 352 118 H/N Cac/Aac COSV55671696 -1 SNV HGNC HGNC:27281 YES NM_001113402.2 1 P1 CCDS44858.1 ENSP00000281471 Q8IY45.127 UPI000013DC7A Q8IY45-1 tolerated(0.09) benign(0.024) Gene3D:3.80.10.10&AlphaFold_DB_import:AF-Q8IY45-F1&PANTHER:PTHR13318&SMART:SM00367&Superfamily:SSF52047&CDD:cd09293 1 1 4 NA NA PASS SITE 104,194|16,48 NA NA 1 93 20,34 173,169 60,60 31 2.05 NA 32.80 NA FALSE 6.00 93 NA NA NA FALSE NA NA 178.06 4 31697922 HCC1395_HCC1395T 149 0.323 213 35,12 45,20 103,49 NA 0/1 NA NA NA NA 53,96,16,48 G/T PANCANCER NA FALSE AMN1_p.H118N chr12:31697922:31697923:G:T SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 32108541 32108542 C G 54 74 0.72972972972973 MODIFIER BICD1 ENSG00000151746 G intron_variant&NMD_transcript_variant Transcript ENST00000395758 nonsense_mediated_decay 1/9 ENST00000395758.3:c.213+997C>G NA 1 SNV HGNC HGNC:1049 1 CCDS86290.1 ENSP00000379107 A8MVZ6.122 UPI0000E00509 4 NA NA PASS SITE 13,78|3,51 NA NA 1 93 39,39 189,226 60,60 29 1.79 NA 18.06 NA FALSE 6.00 93 NA NA NA FALSE NA NA 204.41 4 32108541 HCC1395_HCC1395T 20 0.716 74 8,19 12,32 20,52 NA 0/1 NA NA NA NA 0,20,3,51 C/G PANCANCER NA FALSE BICD1 chr12:32108541:32108542:C:G SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 40446404 40446405 A G 7 11 0.636363636363636 MODIFIER MUC19 ENSG00000205592 G intron_variant Transcript ENST00000454784 protein_coding_LoF 37/172 ENST00000454784.10:c.4736-84A>G NA 1 SNV HGNC HGNC:14362 YES 5 P1 ENSP00000508949 4 NA NA PASS SITE 13,0|7,0 NA NA 1 27 37,34 196,189 60,60 21 1.000 NA 2.71 NA FALSE 6.00 44 NA NA NA FALSE NA NA 22.44 4 40446404 HCC1395_HCC1395T 4 0.615 11 1,2 3,5 4,7 NA 0/1 NA NA NA NA 4,0,7,0 A/G PANCANCER NA FALSE MUC19 chr12:40446404:40446405:A:G SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 40943965 40943966 G C 32 32 1 MODIFIER CNTN1 ENSG00000018236 C intron_variant Transcript ENST00000347616 protein_coding 12/22 ENST00000347616.5:c.1508-30G>C NA 1 SNV HGNC HGNC:2171 1 P2 CCDS8737.1 ENSP00000325660 Q12860.203 A0A024R104.67 UPI0000127EBA Q12860-1 1 4 NA NA PASS SITE 16,5|28,4 NA NA 1 70 38,37 164,177 60,60 19 1.28 NA 5.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 118.90 4 40943965 HCC1395_HCC1395T 0 0.967 32 0,9 0,18 0,28 NA 0/1 NA NA NA NA 0,0,28,4 G/C PANCANCER NA FALSE CNTN1 chr12:40943965:40943966:G:C SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 47795780 47795781 C T 160 160 1 LOW HDAC7 ENSG00000061273 T splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000080059 protein_coding 9/25 ENST00000080059.12:c.907-13G>A NA rs755042409 -1 SNV HGNC HGNC:14067 YES NM_015401.5 1 CCDS8756.2 ENSP00000080059 Q8WUI4.206 UPI00001D9A86 Q8WUI4-5 7.852e-06 0 0 0 0 0 2.098e-05 0 0 1.326e-05 0 0 0 0 0 0 0 2.945e-05 0 0 2.945e-05 gnomADg_NFE 4 NA NA PASS SITE 141,142|82,79 NA NA 1 93 20,20 160,159 60,60 37 2.30 NA 57.48 NA FALSE 6.00 93 NA NA NA FALSE NA NA 454.95 4 47795780 HCC1395_HCC1395T 0 0.990 160 0,46 0,50 0,103 NA 0/1 NA NA NA NA 0,0,81,79 C/T PANCANCER NA FALSE HDAC7 chr12:47795780:47795781:C:T SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 48693120 48693121 G C 120 120 1 MODERATE CCNT1 ENSG00000129315 C missense_variant Transcript ENST00000261900 protein_coding 9/9 ENST00000261900.8:c.2094C>G ENSP00000261900.3:p.I698M ENSP00000261900.3 p.I698M 2126 2094 698 I/M atC/atG COSV56066635 -1 SNV HGNC HGNC:1599 YES NM_001240.4 1 P1 CCDS8766.1 ENSP00000261900 O60563.217 UPI0000044259 O60563-1 tolerated_low_confidence(0.4) benign(0.001) PDB-ENSP_mappings:6gzh.B&MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-O60563-F1 1 1 4 NA NA PASS SITE 78,60|69,51 NA NA 1 93 20,20 149,159 60,60 31 1.97 NA 27.39 NA FALSE 6.00 93 NA NA NA FALSE NA NA 356.94 4 48693120 HCC1395_HCC1395T 0 0.987 120 0,34 0,41 0,78 NA 0/1 NA NA NA NA 0,0,69,51 G/C PANCANCER NA FALSE CCNT1_p.I698M chr12:48693120:48693121:G:C SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 48782540 48782542 GC AT 15 15 1 MODIFIER ADCY6 ENSG00000174233 AT intron_variant Transcript ENST00000307885 protein_coding 1/20 ENST00000307885.4:c.864+30_864+31delinsAT NA -1 substitution HGNC HGNC:237 1 P1 CCDS8767.1 ENSP00000311405 O43306.206 UPI000003EC29 O43306-1 1 4 NA NA PASS SITE 12,0|14,1 NA NA 1 45 39,35 193,206 60,60 16 1.17 NA 3.61 NA FALSE 6.00 93 NA NA NA FALSE NA NA 66.29 4 48782540 HCC1395_HCC1395T 0 0.942 15 0,6 0,8 0,14 NA 0/1 NA NA NA NA 0,0,14,1 GC/AT PANCANCER NA FALSE ADCY6 chr12:48782540:48782542:GC:AT indel 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 49069827 49069828 G A 197 197 1 MODIFIER RHEBL1 ENSG00000167550 A 5_prime_UTR_variant Transcript ENST00000301068 protein_coding 1/8 ENST00000301068.11:c.-42C>T NA 153 rs1269212115 -1 SNV HGNC HGNC:21166 YES NM_144593.3 1 P1 CCDS8778.1 ENSP00000301068 Q8TAI7.180 UPI00000412A8 Q8TAI7-1 4.095e-06 0 0 0 0 0 0 0.0001666 0 0.0001666 gnomADe_OTH 4 NA NA PASS SITE 92,150|75,122 NA NA 1 93 20,20 161,170 60,60 26 2.24 NA 50.82 NA FALSE 6.00 93 NA NA NA FALSE NA NA 595.84 4 49069827 HCC1395_HCC1395T 0 0.993 197 0,62 0,61 0,135 NA 0/1 NA NA NA NA 0,0,75,122 G/A PANCANCER NA FALSE RHEBL1 chr12:49069827:49069828:G:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 49463428 49463429 A G 15 51 0.294117647058824 MODIFIER SPATS2 ENSG00000123352 G intron_variant Transcript ENST00000321898 protein_coding 2/12 ENST00000321898.10:c.25+2391A>G NA 1 SNV HGNC HGNC:18650 1 P1 CCDS31794.1 ENSP00000326841 Q86XZ4.145 A0A024R101.62 UPI0000171C5F 4 NA NA PASS SITE 62,48|10,5 NA NA 1 93 36,33 188,168 60,60 19 1.79 NA 17.63 NA FALSE 6.00 59 NA NA NA FALSE NA NA 27.93 4 49463428 HCC1395_HCC1395T 36 0.290 51 7,5 14,4 30,12 NA 0/1 NA NA NA NA 19,17,10,5 A/G PANCANCER NA FALSE SPATS2 chr12:49463428:49463429:A:G SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 49526215 49526216 G A 75 75 1 MODERATE SPATS2 ENSG00000123352 A missense_variant Transcript ENST00000321898 protein_coding 13/13 ENST00000321898.10:c.1598G>A ENSP00000326841.6:p.R533H ENSP00000326841.6 p.R533H 1954 1598 533 R/H cGc/cAc rs775186083&COSV58918125 1 SNV HGNC HGNC:18650 1 P1 CCDS31794.1 ENSP00000326841 Q86XZ4.145 A0A024R101.62 UPI0000171C5F deleterious(0.02) possibly_damaging(0.788) PANTHER:PTHR15623&MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-Q86XZ4-F1 3.186e-05 6.155e-05 2.895e-05 0 0 0 2.642e-05 0 9.805e-05 8.544e-05 0.0002172 0 0 0 0 0 0 4.41e-05 0 0.000207 0.0002172 gnomADg_AFR 0&1 0&1 4 NA NA PASS SITE 77,56|46,29 NA NA 1 93 20,35 159,186 60,60 27 2.00 NA 28.89 NA FALSE 3.91 93 NA NA NA FALSE NA NA 259.54 4 49526215 HCC1395_HCC1395T 0 0.984 75 0,25 0,36 0,61 NA 0/1 NA NA NA NA 0,0,46,29 G/A PANCANCER NA FALSE SPATS2_p.R533H chr12:49526215:49526216:G:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 49649096 49649097 C T 194 194 1 MODIFIER PRPF40B ENSG00000110844 T downstream_gene_variant Transcript ENST00000261897 protein_coding NA COSV53300658 4430 1 SNV HGNC HGNC:25031 1 ENSP00000261897 Q6NWY9.145 UPI000006CEE9 Q6NWY9-2 1 1 1 4 NA NA PASS SITE 131,125|99,95 NA NA 1 93 20,20 152,157 60,60 32 2.21 NA 48.15 NA FALSE 6.00 93 NA NA NA FALSE NA NA 559.57 4 49649096 HCC1395_HCC1395T 0 0.992 194 0,49 0,73 0,127 NA 0/1 NA NA NA NA 0,0,99,95 C/T PANCANCER NA FALSE PRPF40B chr12:49649096:49649097:C:T SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 51495109 51495110 C T 16 56 0.285714285714286 MODIFIER SLC4A8 ENSG00000050438 T non_coding_transcript_exon_variant Transcript ENST00000319957 retained_intron 21/22 ENST00000319957.10:n.2949C>T NA 2949 COSV60656568 1 SNV HGNC HGNC:11034 2 1 1 4 NA NA PASS SITE 33,75|4,12 NA NA 1 93 28,35 165,181 60,60 18 1.73 NA 15.35 NA FALSE 6.00 56 NA NA NA FALSE NA NA 42.41 4 51495109 HCC1395_HCC1395T 40 0.304 56 11,4 19,7 31,13 NA 0/1 NA NA NA NA 11,29,4,12 C/T PANCANCER NA FALSE SLC4A8 chr12:51495109:51495110:C:T SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 52771163 52771164 G C 94 94 1 LOW KRT76 ENSG00000185069 C synonymous_variant Transcript ENST00000332411 protein_coding 7/9 ENST00000332411.2:c.1320C>G ENSP00000330101.2:p.L440= ENSP00000330101.2 p.L440= 1374 1320 440 L ctC/ctG -1 SNV HGNC HGNC:24430 YES NM_015848.4 1 P1 CCDS8838.1 ENSP00000330101 Q01546.178 UPI000019B3C1 PROSITE_profiles:PS51842&PANTHER:PTHR45616&Gene3D:1.20.5.170&Pfam:PF00038&SMART:SM01391&Superfamily:SSF64593&Prints:PR01276&Coiled-coils_(Ncoils):Coil&AlphaFold_DB_import:AF-Q01546-F1 4 NA NA PASS SITE 80,81|49,45 NA NA 1 93 20,20 149,168 60,60 36 2.01 NA 30.40 NA FALSE 6.00 93 NA NA NA FALSE NA NA 284.08 4 52771163 HCC1395_HCC1395T 0 0.984 94 0,23 0,35 0,62 NA 0/1 NA NA NA NA 0,0,49,45 G/C PANCANCER NA FALSE KRT76_p.L440= chr12:52771163:52771164:G:C SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 54584153 54584154 C T 10 10 1 MODIFIER PDE1B ENSG00000123360 T downstream_gene_variant Transcript ENST00000243052 protein_coding NA 4914 1 SNV HGNC HGNC:8775 YES NM_000924.4 1 CCDS8882.1 ENSP00000243052 Q01064.197 A0A024RB59.65 UPI0000001607 Q01064-1 4 NA NA PASS SITE 21,3|10,0 NA NA 1 73 38,38 188,187 60,60 13 1.37 NA 6.62 NA FALSE 6.00 90 NA NA NA FALSE NA NA 37.50 4 54584153 HCC1395_HCC1395T 0 0.916 10 0,3 0,6 0,10 NA 0/1 NA NA NA NA 0,0,10,0 C/T PANCANCER NA FALSE PDE1B chr12:54584153:54584154:C:T SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 57571935 57571936 A T 21 35 0.6 MODIFIER KIF5A ENSG00000155980 T intron_variant Transcript ENST00000286452 protein_coding 10/25 ENST00000286452.5:c.1096-126A>T NA 1 SNV HGNC HGNC:6323 2 CCDS86312.1 ENSP00000286452 J3KNA1.80 UPI000206534A 1 4 NA NA PASS SITE 30,13|13,8 NA NA 1 93 34,20 193,151 60,60 33 1.41 NA 7.52 NA FALSE 6.00 73 NA NA NA FALSE NA NA 51.25 4 57571935 HCC1395_HCC1395T 14 0.565 35 3,4 5,9 10,13 NA 0/1 NA NA NA NA 9,5,13,8 A/T PANCANCER NA FALSE KIF5A chr12:57571935:57571936:A:T SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 67318946 67318947 A G 38 263 0.144486692015209 MODIFIER CAND1 ENSG00000111530 G downstream_gene_variant Transcript ENST00000544619 protein_coding NA 4338 1 cds_start_NF SNV HGNC HGNC:30688 1 ENSP00000444089 A0A0C4DGH5.43 UPI0000070F2D 4 NA NA PASS SITE 213,283|15,23 NA NA 1 93 20,20 162,168 60,60 35 2.23 NA 50.22 NA FALSE 6.00 79 NA NA NA FALSE NA NA 83.22 4 67318946 HCC1395_HCC1395T 225 0.155 263 52,9 78,13 141,25 NA 0/1 NA NA NA NA 97,128,15,23 A/G PANCANCER NA FALSE CAND1 chr12:67318946:67318947:A:G SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 67649776 67649777 C A 108 108 1 MODIFIER DYRK2 ENSG00000127334 A 5_prime_UTR_variant Transcript ENST00000319833 protein_coding 1/2 ENST00000319833.6:c.-191C>A NA 95 1 cds_end_NF SNV HGNC HGNC:3093 3 ENSP00000324733 A0A0A0MR56.41 UPI0003F481B2 4 NA NA PASS SITE 90,77|60,48 NA NA 1 93 20,20 155,161 60,60 37 2.03 NA 31.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 299.79 4 67649776 HCC1395_HCC1395T 0 0.986 108 0,25 0,39 0,68 NA 0/1 NA NA NA NA 0,0,60,48 C/A PANCANCER NA FALSE DYRK2 chr12:67649776:67649777:C:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 70336611 70336612 C G 54 54 1 MODIFIER CNOT2 ENSG00000111596 G intron_variant Transcript ENST00000229195 protein_coding 8/15 ENST00000229195.8:c.776-778C>G NA 1 SNV HGNC HGNC:7878 YES NM_014515.7 1 CCDS31857.1 ENSP00000229195 Q9NZN8.185 A0A024RBD8.64 UPI0000052E12 Q9NZN8-1 1 4 NA NA PASS SITE 64,27|47,7 NA NA 1 93 20,40 179,189 60,60 27 1.85 NA 20.14 NA FALSE 6.00 93 NA NA NA FALSE NA NA 209.68 4 70336611 HCC1395_HCC1395T 0 0.981 54 0,19 0,29 0,48 NA 0/1 NA NA NA NA 0,0,47,7 C/G PANCANCER NA FALSE CNOT2 chr12:70336611:70336612:C:G SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 71704186 71704187 G C 16 31 0.516129032258065 MODIFIER TMEM19 ENSG00000139291 C 3_prime_UTR_variant Transcript ENST00000266673 protein_coding 6/6 ENST00000266673.10:c.*3191G>C NA 4801 1 SNV HGNC HGNC:25605 YES NM_018279.4 1 P1 CCDS9002.1 ENSP00000266673 Q96HH6.132 A0A024RBA1.41 UPI000006EFAF Q96HH6-1 4 NA NA PASS SITE 3,25|3,13 NA NA 1 93 38,40 213,202 60,60 30 1.16 NA 3.91 NA FALSE 6.00 93 NA NA NA FALSE NA NA 53.27 4 71704186 HCC1395_HCC1395T 15 0.536 31 4,7 7,6 12,14 NA 0/1 NA NA NA NA 3,12,3,13 G/C PANCANCER NA FALSE TMEM19 chr12:71704186:71704187:G:C SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 72575519 72575520 C T 14 58 0.241379310344828 LOW TRHDE ENSG00000072657 T synonymous_variant Transcript ENST00000261180 protein_coding 12/19 ENST00000261180.10:c.2298C>T ENSP00000261180.5:p.I766= ENSP00000261180.5 p.I766= 2572 2298 766 I atC/atT rs771321069&COSV53857323 1 SNV HGNC HGNC:30748 YES NM_013381.3 1 P1 CCDS9004.2 ENSP00000261180 Q9UKU6.179 UPI0000577D58 PANTHER:PTHR11533&Pfam:PF11838&Gene3D:1.25.50.20&AlphaFold_DB_import:AF-Q9UKU6-F1 4.777e-05 0.0001231 0 0 0.0004898 0 8.802e-06 0 0 5.917e-05 0.0001449 0 6.553e-05 0 0.0001926 0 0 1.47e-05 0 0 0.0004898 gnomADe_EAS 0&1 0&1 4 NA NA PASS SITE 56,77|6,8 NA NA 1 93 20,20 155,159 60,60 46 1.74 NA 16.21 NA FALSE 4.31 46 NA NA NA FALSE NA NA 32.18 4 72575519 HCC1395_HCC1395T 44 0.263 58 6,3 19,6 27,9 NA 0/1 NA NA NA NA 19,25,6,8 C/T PANCANCER NA FALSE TRHDE_p.I766= chr12:72575519:72575520:C:T SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 76050689 76050690 G A 139 139 1 MODIFIER NAP1L1 ENSG00000187109 A intron_variant Transcript ENST00000393263 protein_coding 11/15 ENST00000393263.7:c.937-36C>T NA -1 SNV HGNC HGNC:7637 1 P1 CCDS9013.1 ENSP00000376947 P55209.203 A0A024RBB7.58 UPI0000052A55 P55209-1 4 NA NA PASS SITE 78,78|68,71 NA NA 1 93 20,20 158,164 60,60 38 1.96 NA 26.79 NA FALSE 6.00 93 NA NA NA FALSE NA NA 389.15 4 76050689 HCC1395_HCC1395T 0 0.989 139 0,30 0,51 0,86 NA 0/1 NA NA NA NA 0,0,68,71 G/A PANCANCER NA FALSE NAP1L1 chr12:76050689:76050690:G:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 80495234 80495235 C A 2 2 1 MODERATE PTPRQ ENSG00000139304 A missense_variant Transcript ENST00000616559 protein_coding 13/45 ENST00000616559.4:c.1871C>A ENSP00000483259.1:p.S624Y ENSP00000483259.1 p.S624Y 1871 1871 624 S/Y tCt/tAt COSV57047978&COSV57056511 1 SNV HGNC HGNC:9679 5 A2 ENSP00000483259 A0A087X0B9.57 UPI0004E4CCEC 1 deleterious(0) possibly_damaging(0.553) Low_complexity_(Seg):seg&CDD:cd00063&Gene3D:2.60.40.10&Pfam:PF00041&SMART:SM00060&Superfamily:SSF49265&PROSITE_profiles:PS50853&PANTHER:PTHR46957 1&1 1&1 4 NA NA PASS SITE 8,5|0,0 NA NA 1 41 39,33 221,249 60,60 25 1.11 NA 3.61 NA FALSE 6.00 36 NA NA NA FALSE NA NA 7.07 4 80495234 HCC1395_HCC1395T 0 0.750 2 0,1 0,1 0,2 NA 0/1 NA NA NA NA 0,0,1,1 C/A PANCANCER NA FALSE PTPRQ_p.S624Y chr12:80495234:80495235:C:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 81312084 81312085 G T 38 38 1 MODIFIER PPFIA2 ENSG00000139220 T intron_variant Transcript ENST00000333447 protein_coding 18/28 ENST00000333447.11:c.2346-12702C>A NA -1 SNV HGNC HGNC:9246 5 CCDS55852.1 ENSP00000327416 O75334.171 UPI0002065590 O75334-6 4 NA NA PASS SITE 30,25|23,15 NA NA 1 93 20,20 139,156 60,60 29 1.54 NA 10.23 NA FALSE 6.00 93 NA NA NA FALSE NA NA 113.51 4 81312084 HCC1395_HCC1395T 0 0.965 38 0,8 0,18 0,26 NA 0/1 NA NA NA NA 0,0,23,15 G/T PANCANCER NA FALSE PPFIA2 chr12:81312084:81312085:G:T SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 85979205 85979206 A G 32 32 1 MODIFIER MGAT4C ENSG00000182050 G downstream_gene_variant Transcript ENST00000547225 protein_coding NA 328 -1 cds_end_NF SNV HGNC HGNC:30871 1 ENSP00000449172 F8VWY2.64 UPI0003F47B56 4 NA NA PASS SITE 17,11|20,12 NA NA 1 76 20,20 171,172 60,60 32 1.32 NA 6.02 NA FALSE 6.00 93 NA NA NA FALSE NA NA 85.66 4 85979205 HCC1395_HCC1395T 0 0.955 32 0,8 0,12 0,20 NA 0/1 NA NA NA NA 0,0,20,12 A/G PANCANCER NA FALSE MGAT4C chr12:85979205:85979206:A:G SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 88153291 88153292 G T 31 31 1 HIGH TMTC3 ENSG00000139324 T stop_gained&splice_region_variant Transcript ENST00000266712 protein_coding 3/14 ENST00000266712.11:c.190G>T ENSP00000266712.6:p.E64* ENSP00000266712.6 p.E64* 399 190 64 E/* Gag/Tag 1 SNV HGNC HGNC:26899 YES NM_181783.4 1 P1 CCDS9032.1 ENSP00000266712 Q6ZXV5.148 UPI000004D255 Q6ZXV5-2 1 AlphaFold_DB_import:AF-Q6ZXV5-F1&PANTHER:PTHR44395 4 NA NA PASS SITE 15,9|21,10 NA NA 1 61 20,20 179,176 60,60 39 1.20 NA 4.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 92.66 4 88153291 HCC1395_HCC1395T 0 0.958 31 0,8 0,14 0,22 NA 0/1 NA NA NA NA 0,0,21,10 G/T PANCANCER NA FALSE TMTC3_p.E64* chr12:88153291:88153292:G:T SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 91178613 91178614 G A 150 307 0.488599348534202 MODIFIER DCN ENSG00000011465 A intron_variant Transcript ENST00000052754 protein_coding 1/7 ENST00000052754.10:c.-33-28C>T NA -1 SNV HGNC HGNC:2705 YES NM_001920.5 1 P1 CCDS9039.1 ENSP00000052754 P07585.230 Q6FH10.160 UPI000013187E P07585-1 1 4 NA NA PASS SITE 197,248|68,82 NA NA 1 93 20,20 152,154 60,60 34 2.28 NA 57.18 NA FALSE 6.00 93 NA NA NA FALSE NA NA 369.01 4 91178613 HCC1395_HCC1395T 157 0.487 307 37,27 59,62 100,95 NA 0/1 NA NA NA NA 70,87,68,82 G/A PANCANCER NA FALSE DCN chr12:91178613:91178614:G:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 105066420 105066421 C T 2 8 0.25 MODIFIER ALDH1L2 ENSG00000136010 T intron_variant Transcript ENST00000258494 protein_coding 5/22 ENST00000258494.14:c.696+148G>A NA -1 SNV HGNC HGNC:26777 YES NM_001034173.4 1 P1 CCDS31891.1 ENSP00000258494 Q3SY69.153 UPI00000477A9 Q3SY69-1 4 NA NA PASS SITE 18,7|1,1 NA NA 1 45 35,40 174,118 60,60 37 1.18 NA 4.21 NA FALSE 6.00 14 NA NA NA FALSE NA NA 7.23 4 105066420 HCC1395_HCC1395T 6 0.250 8 0,0 5,1 5,1 NA 0/1 NA NA NA NA 4,2,1,1 C/T PANCANCER NA FALSE ALDH1L2 chr12:105066420:105066421:C:T SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 106066126 106066127 G C 39 39 1 MODIFIER NUAK1 ENSG00000074590 C 3_prime_UTR_variant Transcript ENST00000261402 protein_coding 7/7 ENST00000261402.7:c.*676C>G NA 2963 -1 SNV HGNC HGNC:14311 YES NM_014840.3 1 P1 CCDS31892.1 ENSP00000261402 O60285.196 A0A024RBL3.56 UPI00000403BC O60285-1 4 NA NA PASS SITE 33,19|21,18 NA NA 1 93 20,20 169,156 60,60 35 1.58 NA 11.09 NA FALSE 6.00 93 NA NA NA FALSE NA NA 115.31 4 106066126 HCC1395_HCC1395T 0 0.964 39 0,9 0,15 0,25 NA 0/1 NA NA NA NA 0,0,21,18 G/C PANCANCER NA FALSE NUAK1 chr12:106066126:106066127:G:C SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 107746274 107746275 C T 204 205 0.995121951219512 HIGH PRDM4 ENSG00000110851 T splice_donor_variant Transcript ENST00000228437 protein_coding 6/11 ENST00000228437.10:c.1276+1G>A NA rs752524838&COSV57308076 -1 SNV HGNC HGNC:9348 YES NM_012406.4 2 P1 CCDS9115.1 ENSP00000228437 Q9UKN5.190 A0A024RBM7.63 UPI000013217D 3.986e-06 0 0 0 0 0 0 0.0001636 0 0.0001636 gnomADe_OTH 0&1 0&1 4 NA NA PASS SITE 113,74|124,80 NA NA 1 93 20,20 159,165 60,60 37 2.10 NA 37.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 596.72 4 107746274 HCC1395_HCC1395T 1 0.985 205 1,60 0,66 1,132 NA 0/1 NA NA NA NA 1,0,124,80 C/T PANCANCER NA FALSE PRDM4 chr12:107746274:107746275:C:T SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 108912017 108912018 C A 20 47 0.425531914893617 MODIFIER SVOP ENSG00000166111 A 3_prime_UTR_variant Transcript ENST00000610966 protein_coding 16/16 ENST00000610966.5:c.*518G>T NA 2365 rs1162802063 -1 SNV HGNC HGNC:25417 YES NM_018711.5 1 P1 CCDS73520.1 ENSP00000479104 Q8N4V2.151 UPI000006E50F 6.573e-06 0 0 0 0 0 0 0 1.47e-05 0 0 1.47e-05 gnomADg_NFE 4 NA NA PASS SITE 36,49|8,12 NA NA 1 93 20,27 167,178 60,60 32 1.60 NA 11.74 NA FALSE 6.00 83 NA NA NA FALSE NA NA 52.83 4 108912017 HCC1395_HCC1395T 27 0.444 47 7,8 11,6 19,15 NA 0/1 NA NA NA NA 11,16,8,12 C/A PANCANCER NA FALSE SVOP chr12:108912017:108912018:C:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 109447417 109447418 C A 25 39 0.641025641025641 MODIFIER KCTD10 ENSG00000110906 A downstream_gene_variant Transcript ENST00000228495 protein_coding NA 1238 -1 SNV HGNC HGNC:23236 YES NM_031954.5 1 P1 CCDS9128.1 ENSP00000228495 Q9H3F6.154 A0A024RBJ2.62 UPI000004DAE1 Q9H3F6-1 4 NA NA PASS SITE 24,33|9,16 NA NA 1 93 20,20 159,174 60,60 23 1.50 NA 9.03 NA FALSE 6.00 81 NA NA NA FALSE NA NA 65.04 4 109447417 HCC1395_HCC1395T 14 0.626 39 4,7 3,10 10,17 NA 0/1 NA NA NA NA 5,9,9,16 C/A PANCANCER NA FALSE KCTD10 chr12:109447417:109447418:C:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 109786790 109786791 C A 160 160 1 LOW TRPV4 ENSG00000111199 A synonymous_variant Transcript ENST00000261740 protein_coding 14/16 ENST00000261740.7:c.2256G>T ENSP00000261740.2:p.L752= ENSP00000261740.2 p.L752= 2336 2256 752 L ctG/ctT -1 SNV HGNC HGNC:18083 YES NM_021625.5 1 P1 CCDS9134.1 ENSP00000261740 Q9HBA0.185 UPI000003BB44 Q9HBA0-1 1 PDB-ENSP_mappings:7aa5.A&PDB-ENSP_mappings:7aa5.B&PDB-ENSP_mappings:7aa5.C&PDB-ENSP_mappings:7aa5.D&AlphaFold_DB_import:AF-Q9HBA0-F1&PANTHER:PTHR10582&TIGRFAM:TIGR00870&CDD:cd22195 4 NA NA PASS SITE 140,140|78,82 NA NA 1 93 20,20 157,155 60,60 34 2.25 NA 52.93 NA FALSE 6.00 93 NA NA NA FALSE NA NA 458.48 4 109786790 HCC1395_HCC1395T 0 0.991 160 0,42 0,54 0,103 NA 0/1 NA NA NA NA 0,0,78,82 C/A PANCANCER NA FALSE TRPV4_p.L752= chr12:109786790:109786791:C:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 110028429 110028430 C A 114 114 1 MODIFIER ANKRD13A ENSG00000076513 A intron_variant Transcript ENST00000261739 protein_coding 9/14 ENST00000261739.9:c.946-83C>A NA 1 SNV HGNC HGNC:21268 YES NM_033121.2 1 P1 CCDS9140.1 ENSP00000261739 Q8IZ07.165 Q3ZTS7.128 UPI000004472C 4 NA NA PASS SITE 51,58|53,61 NA NA 1 93 20,20 160,179 60,60 27 1.88 NA 21.97 NA FALSE 6.00 93 NA NA NA FALSE NA NA 348.66 4 110028429 HCC1395_HCC1395T 0 0.988 114 0,40 0,33 0,82 NA 0/1 NA NA NA NA 0,0,53,61 C/A PANCANCER NA FALSE ANKRD13A chr12:110028429:110028430:C:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 110899112 110899113 T G 23 88 0.261363636363636 LOW CCDC63 ENSG00000173093 G synonymous_variant Transcript ENST00000308208 protein_coding 10/12 ENST00000308208.10:c.1329T>G ENSP00000312399.5:p.L443= ENSP00000312399.5 p.L443= 1544 1329 443 L ctT/ctG 1 SNV HGNC HGNC:26669 YES NM_152591.3 2 P2 CCDS9151.1 ENSP00000312399 Q8NA47.127 UPI000006F794 Q8NA47-1 AlphaFold_DB_import:AF-Q8NA47-F1&PANTHER:PTHR21694 4 NA NA PASS SITE 61,94|9,15 NA NA 1 93 20,20 170,157 60,60 30 1.78 NA 17.71 NA FALSE 6.00 46 NA NA NA FALSE NA NA 46.07 4 110899112 HCC1395_HCC1395T 65 0.242 88 15,2 26,10 45,14 NA 0/1 NA NA NA NA 23,42,9,14 T/G PANCANCER NA FALSE CCDC63_p.L443= chr12:110899112:110899113:T:G SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 112043095 112043096 A C 35 35 1 MODERATE NAA25 ENSG00000111300 C missense_variant Transcript ENST00000261745 protein_coding 19/24 ENST00000261745.9:c.2367T>G ENSP00000261745.4:p.S789R ENSP00000261745.4 p.S789R 2377 2367 789 S/R agT/agG COSV55709939 -1 SNV HGNC HGNC:25783 YES NM_024953.4 1 P1 CCDS9159.1 ENSP00000261745 Q14CX7.136 UPI00001FBB50 Q14CX7-1 tolerated(0.53) benign(0.015) PDB-ENSP_mappings:6vp9.B&PDB-ENSP_mappings:7stx.B&AlphaFold_DB_import:AF-Q14CX7-F1&PANTHER:PTHR22767 1 1 4 NA NA PASS SITE 26,11|23,12 NA NA 1 93 20,20 165,171 60,60 31 1.44 NA 7.78 NA FALSE 6.00 93 NA NA NA FALSE NA NA 104.74 4 112043095 HCC1395_HCC1395T 0 0.961 35 0,11 0,12 0,23 NA 0/1 NA NA NA NA 0,0,23,12 A/C PANCANCER NA FALSE NAA25_p.S789R chr12:112043095:112043096:A:C SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 112966053 112966054 G C 76 76 1 MODIFIER OAS3 ENSG00000111331 C intron_variant Transcript ENST00000228928 protein_coding 12/15 ENST00000228928.12:c.2689+24G>C NA 1 SNV HGNC HGNC:8088 YES NM_006187.4 1 P2 CCDS44981.1 ENSP00000228928 Q9Y6K5.174 UPI000034ECD3 4 NA NA PASS SITE 55,67|28,48 NA NA 1 93 20,20 156,170 60,60 30 1.92 NA 24.08 NA FALSE 6.00 93 NA NA NA FALSE NA NA 234.87 4 112966053 HCC1395_HCC1395T 0 0.982 76 0,20 0,25 0,52 NA 0/1 NA NA NA NA 0,0,28,48 G/C PANCANCER NA FALSE OAS3 chr12:112966053:112966054:G:C SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 120184837 120184838 G A 32 124 0.258064516129032 LOW GCN1 ENSG00000089154 A synonymous_variant Transcript ENST00000300648 protein_coding 3/58 ENST00000300648.7:c.172C>T ENSP00000300648.6:p.L58= ENSP00000300648.6 p.L58= 190 172 58 L Ctg/Ttg COSV56106751 -1 SNV HGNC HGNC:4199 YES NM_006836.2 1 P1 CCDS41847.1 ENSP00000300648 Q92616.193 UPI0000451CA7 AlphaFold_DB_import:AF-Q92616-F1 1 1 4 NA NA PASS SITE 104,98|15,17 NA NA 2 93 20,20 153,153 60,60 43 1.84 NA 20.16 NA FALSE 6.00 60 NA NA NA FALSE NA NA 75.26 4 120184837 HCC1395_HCC1395T 92 0.268 124 17,6 33,11 59,21 NA 0/1 NA NA NA NA 47,45,15,17 G/A PANCANCER NA FALSE GCN1_p.L58= chr12:120184837:120184838:G:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 120351300 120351301 C T 53 53 1 MODIFIER MSI1 ENSG00000135097 T intron_variant Transcript ENST00000257552 protein_coding 11/14 ENST00000257552.7:c.790+44G>A NA -1 SNV HGNC HGNC:7330 YES NM_002442.4 1 P1 CCDS9196.1 ENSP00000257552 O43347.169 UPI0000073DD8 1 4 NA NA PASS SITE 52,17|36,17 NA NA 1 93 26,26 161,193 60,60 28 1.72 NA 15.65 NA FALSE 6.00 93 NA NA NA FALSE NA NA 171.00 4 120351300 HCC1395_HCC1395T 0 0.976 53 0,17 0,21 0,39 NA 0/1 NA NA NA NA 0,0,36,17 C/T PANCANCER NA FALSE MSI1 chr12:120351300:120351301:C:T SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 120784750 120784751 G A 93 93 1 MODIFIER SPPL3 ENSG00000157837 A intron_variant Transcript ENST00000353487 protein_coding 3/10 ENST00000353487.7:c.191-157C>T NA rs535730912 -1 SNV HGNC HGNC:30424 YES NM_139015.5 1 P1 CCDS9208.1 ENSP00000288680 Q8TCT6.166 UPI0000013590 Q8TCT6-2 0.0008 0.003 0 0 0 0 0.001295 0.00459 0 0.0003273 0 0 0 0 0 0.0009569 0 0.00459 gnomADg_AFR 4 NA NA PASS SITE 50,52|41,52 NA NA 1 93 20,20 158,161 60,60 35 1.85 NA 20.46 NA FALSE 2.97 93 NA NA NA FALSE NA NA 281.09 4 120784750 HCC1395_HCC1395T 0 0.984 93 0,22 0,35 0,61 NA 0/1 NA NA NA NA 0,0,41,52 G/A PANCANCER NA FALSE SPPL3 chr12:120784750:120784751:G:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 121863392 121863394 CA TG 2 5 0.4 MODIFIER HPD ENSG00000158104 TG upstream_gene_variant Transcript ENST00000289004 protein_coding NA 4533 -1 substitution HGNC HGNC:5147 YES NM_002150.3 1 P1 CCDS9224.1 ENSP00000289004 A0A0B4J1R4.45 UPI0000366920 1 4 NA NA PASS SITE 9,4|1,1 NA NA 1 35 36,37 168,121 60,60 13 1.05 NA 2.71 NA FALSE 6.00 9 NA NA NA FALSE NA NA 6.86 4 121863392 HCC1395_HCC1395T 3 0.323 5 2,0 0,1 3,1 NA 0/1 NA NA NA NA 2,1,1,1 CA/TG PANCANCER NA FALSE HPD chr12:121863392:121863394:CA:TG indel 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 122591322 122591323 C T 59 131 0.450381679389313 LOW KNTC1 ENSG00000184445 T splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000333479 protein_coding 41/63 ENST00000333479.12:c.4129-15C>T NA 1 SNV HGNC HGNC:17255 YES NM_014708.6 1 P1 CCDS45002.1 ENSP00000328236 P50748.176 UPI0000047FD6 P50748-1 4 NA NA PASS SITE 129,68|41,18 NA NA 1 93 20,20 169,172 60,60 30 1.97 NA 27.34 NA FALSE 6.00 79 NA NA NA FALSE NA NA 158.53 4 122591322 HCC1395_HCC1395T 72 0.483 131 15,11 30,30 45,42 NA 0/1 NA NA NA NA 41,31,41,18 C/T PANCANCER NA FALSE KNTC1 chr12:122591322:122591323:C:T SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 130806849 130806850 C G 26 50 0.52 MODIFIER STX2 ENSG00000111450 G intron_variant Transcript ENST00000261653 protein_coding 6/9 ENST00000261653.11:c.463+133G>C NA -1 SNV HGNC HGNC:3403 1 CCDS9269.1 ENSP00000261653 P32856.197 UPI000000DBFE P32856-2 4 NA NA PASS SITE 36,24|16,10 NA NA 1 93 20,20 161,178 60,60 36 1.41 NA 7.22 NA FALSE 6.00 85 NA NA NA FALSE NA NA 64.96 4 130806849 HCC1395_HCC1395T 24 0.486 50 9,5 7,11 17,16 NA 0/1 NA NA NA NA 13,11,16,10 C/G PANCANCER NA FALSE STX2 chr12:130806849:130806850:C:G SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 131844177 131844178 G C 66 66 1 MODIFIER MMP17 ENSG00000198598 C intron_variant Transcript ENST00000360564 protein_coding 6/9 ENST00000360564.5:c.968+96G>C NA 1 SNV HGNC HGNC:7163 YES NM_016155.7 1 P1 CCDS31927.1 ENSP00000353767 Q9ULZ9.203 UPI00001AF305 Q9ULZ9-1 4 NA NA PASS SITE 72,74|31,35 NA NA 1 93 20,20 161,160 60,60 34 2.01 NA 30.40 NA FALSE 6.00 93 NA NA NA FALSE NA NA 186.70 4 131844177 HCC1395_HCC1395T 0 0.978 66 0,17 0,22 0,42 NA 0/1 NA NA NA NA 0,0,31,35 G/C PANCANCER NA FALSE MMP17 chr12:131844177:131844178:G:C SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 132053416 132053417 C A 10 17 0.588235294117647 MODERATE EP400 ENSG00000183495 A missense_variant Transcript ENST00000389561 protein_coding 43/53 ENST00000389561.7:c.7547C>A ENSP00000374212.2:p.P2516Q ENSP00000374212.2 p.P2516Q 7677 7547 2516 P/Q cCa/cAa 1 SNV HGNC HGNC:11958 YES NM_015409.5 5 P1 CCDS31929.2 ENSP00000374212 Q96L91.197 UPI00004566BC Q96L91-2 tolerated_low_confidence(0.19) unknown(0) Low_complexity_(Seg):seg&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite 4 NA NA PASS SITE 7,10|3,7 NA NA 1 28 36,37 167,190 60,60 34 1.04 NA 3.01 NA FALSE 6.00 46 NA NA NA FALSE NA NA 28.87 4 132053416 HCC1395_HCC1395T 7 0.601 17 3,3 2,5 5,8 NA 0/1 NA NA NA NA 3,4,3,7 C/A PANCANCER NA FALSE EP400_p.P2516Q chr12:132053416:132053417:C:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr12 132066878 132066879 G A 51 116 0.439655172413793 LOW EP400 ENSG00000183495 A synonymous_variant Transcript ENST00000330386 protein_coding 3/7 ENST00000330386.7:c.411G>A ENSP00000330620.7:p.P137= ENSP00000330620.7 p.P137= 410 411 137 P ccG/ccA rs756853270&COSV57769568 1 cds_start_NF SNV HGNC HGNC:11958 2 ENSP00000330620 A0A0A0MR70.52 UPI0004620ABC Low_complexity_(Seg):seg&PANTHER:PTHR46459 3.992e-06 0 0 0 0 0 8.835e-06 0 0 1.972e-05 2.414e-05 0 6.547e-05 0 0 0 0 0 0 0.0002072 0.0002072 gnomADg_SAS 0&1 0&1 4 NA NA PASS SITE 67,149|13,38 NA NA 1 93 20,38 175,176 60,60 32 2.04 NA 32.16 NA FALSE 4.61 93 NA NA NA FALSE NA NA 151.28 4 132066878 HCC1395_HCC1395T 65 0.436 116 21,15 28,20 52,40 NA 0/1 NA NA NA NA 15,50,13,38 G/A PANCANCER NA FALSE EP400_p.P137= chr12:132066878:132066879:G:A SNV 2:0 chr12:21474811:133219598:2:0:1 TRUE NA 0.96 +chr13 24690373 24690374 C G 16 126 0.126984126984127 LOW ATP12A ENSG00000075673 G synonymous_variant Transcript ENST00000218548 protein_coding 6/23 ENST00000218548.10:c.582C>G ENSP00000218548.6:p.T194= ENSP00000218548.6 p.T194= 915 582 194 T acC/acG 1 SNV HGNC HGNC:13816 1 A1 CCDS53858.1 ENSP00000218548 P54707.211 UPI000006D1DE P54707-2 Gene3D:1.20.1110.10&Gene3D:2.70.150.10&AlphaFold_DB_import:AF-P54707-F1&Pfam:PF00122&PANTHER:PTHR43294&Superfamily:SSF81653&Superfamily:SSF81665&TIGRFAM:TIGR01106&TIGRFAM:TIGR01494&CDD:cd02608 5 NA NA PASS SITE 117,97|9,7 NA NA 1 93 20,20 162,153 60,60 37 1.82 NA 18.96 NA FALSE 6.00 80 NA NA NA FALSE NA NA 29.24 5 24690373 HCC1395_HCC1395T 110 0.134 126 20,5 47,5 70,10 NA 0/1 NA NA NA NA 59,51,9,7 C/G PANCANCER NA FALSE ATP12A_p.T194= chr13:24690373:24690374:C:G SNV 2:1 chr13:19025793:32267482:2:1:1 TRUE NA 0.96 +chr13 25169964 25169965 C T 70 234 0.299145299145299 LOW AMER2 ENSG00000165566 T synonymous_variant Transcript ENST00000357816 protein_coding 3/3 ENST00000357816.2:c.1299G>A ENSP00000350469.2:p.G433= ENSP00000350469.2 p.G433= 1775 1299 433 G ggG/ggA -1 SNV HGNC HGNC:26360 2 CCDS9312.1 ENSP00000350469 Q8N7J2.125 UPI000013E4CB Q8N7J2-2 AlphaFold_DB_import:AF-Q8N7J2-F1&Pfam:PF09422&MobiDB_lite:mobidb-lite 5 NA NA PASS SITE 213,167|37,33 NA NA 1 93 20,20 158,165 60,60 28 2.17 NA 43.34 NA FALSE 6.00 93 NA NA NA FALSE NA NA 167.57 5 25169964 HCC1395_HCC1395T 164 0.305 234 47,24 56,23 111,48 NA 0/1 NA NA NA NA 93,71,37,33 C/T PANCANCER NA FALSE AMER2_p.G433= chr13:25169964:25169965:C:T SNV 2:1 chr13:19025793:32267482:2:1:1 TRUE NA 0.96 +chr13 25541937 25541939 GA CT 64 227 0.281938325991189 MODIFIER ATP8A2 ENSG00000132932 CT 3_prime_UTR_variant&NMD_transcript_variant Transcript ENST00000281620 nonsense_mediated_decay 9/38 ENST00000281620.11:c.*297_*298delinsCT NA 660-661 1 substitution HGNC HGNC:13533 1 ENSP00000281620 F8W9B3.78 UPI001B89A405 1 5 NA NA PASS SITE 166,149|33,31 NA NA 1 93 20,20 157,159 60,60 33 1.99 NA 29.20 NA FALSE 6.00 93 NA NA NA FALSE NA NA 248.61 5 25541937 HCC1395_HCC1395T 163 0.294 227 34,14 58,23 100,41 NA 0/1 NA NA NA NA 89,74,33,31 GA/CT PANCANCER NA FALSE ATP8A2 chr13:25541937:25541939:GA:CT indel 2:1 chr13:19025793:32267482:2:1:1 TRUE NA 0.96 +chr13 32339132 32339133 G T 63 163 0.386503067484663 HIGH BRCA2 ENSG00000139618 T stop_gained Transcript ENST00000380152 protein_coding 11/27 ENST00000380152.8:c.4777G>T ENSP00000369497.3:p.E1593* ENSP00000369497.3 p.E1593* 4976 4777 1593 E/* Gaa/Taa COSV66463787 1 SNV HGNC HGNC:1101 YES NM_000059.4 5 P2 CCDS9344.1 ENSP00000369497 P51587.235 UPI00001FCBCC 1 PIRSF:PIRSF002397&PANTHER:PTHR11289 1 1 5 NA NA PASS SITE 79,101|21,43 NA NA 1 93 20,20 175,169 60,60 34 -3.662e-01 NA 13.27 NA FALSE 6.00 93 NA NA NA FALSE NA NA 158.86 5 32339132 HCC1395_HCC1395T 100 0.394 163 29,19 38,21 71,46 NA 0/1 NA NA NA NA 42,58,21,42 G/T PANCANCER TRUE TRUE BRCA2_p.E1593* chr13:32339132:32339133:G:T SNV 4:1 chr13:32310516:36365621:4:1:1 NA NA 0.96 +chr13 33016643 33016644 C T 17 570 0.0298245614035088 MODERATE KL ENSG00000133116 T missense_variant Transcript ENST00000380099 protein_coding 1/5 ENST00000380099.4:c.203C>T ENSP00000369442.3:p.A68V ENSP00000369442.3 p.A68V 221 203 68 A/V gCc/gTc 1 SNV HGNC HGNC:6344 YES NM_004795.4 1 P1 CCDS9347.1 ENSP00000369442 Q9UEF7.176 UPI000013CEBA Q9UEF7-1 1 deleterious(0) possibly_damaging(0.816) PDB-ENSP_mappings:5w21.A&PANTHER:PTHR10353&PROSITE_patterns:PS00653&Gene3D:3.20.20.80&Pfam:PF00232&Superfamily:SSF51445&AlphaFold_DB_import:AF-Q9UEF7-F1 5 NA NA PASS SITE 502,425|9,8 NA NA 1 93 20,20 156,152 60,60 43 2.37 NA 68.28 NA FALSE 6.00 41 NA NA NA FALSE NA NA 24.88 5 33016643 HCC1395_HCC1395T 553 0.030 570 159,5 174,5 350,10 NA 0/1 NA NA NA NA 307,246,9,8 C/T PANCANCER NA FALSE KL_p.A68V chr13:33016643:33016644:C:T SNV 4:1 chr13:32310516:36365621:4:1:1 NA NA 0.96 +chr13 37746422 37746423 C T 41 83 0.493975903614458 MODIFIER TRPC4 ENSG00000133107 T intron_variant Transcript ENST00000338947 protein_coding 2/9 ENST00000338947.9:c.378+36534G>A NA COSV59022928 -1 SNV HGNC HGNC:12336 5 CCDS45035.1 ENSP00000342580 Q9UBN4.205 UPI00000715A3 Q9UBN4-6 1 1 5 NA NA PASS SITE 38,70|11,30 NA NA 1 93 20,20 179,170 60,60 21 1.68 NA 13.84 NA FALSE 6.00 93 NA NA NA FALSE NA NA 108.06 5 37746422 HCC1395_HCC1395T 42 0.519 83 8,10 12,11 28,30 NA 0/1 NA NA NA NA 15,27,11,30 C/T PANCANCER NA FALSE TRPC4 chr13:37746422:37746423:C:T SNV 2:2 chr13:36370137:48709351:2:2:1 FALSE NA 0.96 +chr13 43891611 43891612 T A 6 24 0.25 MODIFIER LACC1 ENSG00000179630 A 3_prime_UTR_variant Transcript ENST00000325686 protein_coding 7/7 ENST00000325686.7:c.*164T>A NA 1707 1 SNV HGNC HGNC:26789 YES NM_153218.4 1 P1 CCDS9391.1 ENSP00000317619 Q8IV20.129 UPI00000746BB 1 5 NA NA PASS SITE 14,20|0,6 NA NA 1 45 34,38 230,139 60,60 21 1.24 NA 4.47 NA FALSE 6.00 9 NA NA NA FALSE NA NA 19.02 5 43891611 HCC1395_HCC1395T 18 0.269 24 7,6 11,0 18,6 NA 0/1 NA NA NA NA 8,10,0,6 T/A PANCANCER NA FALSE LACC1 chr13:43891611:43891612:T:A SNV 2:2 chr13:36370137:48709351:2:2:1 FALSE NA 0.96 +chr13 45399009 45399010 C T 59 131 0.450381679389313 MODIFIER SLC25A30 ENSG00000174032 T 3_prime_UTR_variant&NMD_transcript_variant Transcript ENST00000310862 nonsense_mediated_decay 8/10 ENST00000310862.11:c.*422G>A NA 876 COSV60433641 -1 SNV HGNC HGNC:27371 1 ENSP00000311856 D6RJI0.70 UPI0001D3B057 1 1 5 NA NA PASS SITE 70,70|28,31 NA NA 1 93 20,20 160,158 60,60 38 1.69 NA 14.14 NA FALSE 6.00 80 NA NA NA FALSE NA NA 137.11 5 45399009 HCC1395_HCC1395T 72 0.442 131 19,10 26,22 47,37 NA 0/1 NA NA NA NA 37,35,28,31 C/T PANCANCER NA FALSE SLC25A30 chr13:45399009:45399010:C:T SNV 2:2 chr13:36370137:48709351:2:2:1 FALSE NA 0.96 +chr13 46834690 46834691 T C 17 88 0.193181818181818 MODIFIER HTR2A ENSG00000102468 C 3_prime_UTR_variant Transcript ENST00000542664 protein_coding 4/4 ENST00000542664.4:c.*147A>G NA 2271 -1 SNV HGNC HGNC:5293 YES NM_000621.5 1 P1 CCDS9405.1 ENSP00000437737 P28223.218 UPI000000126E P28223-1 1 5 NA NA PASS SITE 52,63|7,10 NA NA 1 88 20,20 169,155 60,60 43 1.44 NA 7.83 NA FALSE 6.00 33 NA NA NA FALSE NA NA 41.19 5 46834690 HCC1395_HCC1395T 71 0.200 88 22,3 24,9 51,12 NA 0/1 NA NA NA NA 32,39,7,10 T/C PANCANCER NA FALSE HTR2A chr13:46834690:46834691:T:C SNV 2:2 chr13:36370137:48709351:2:2:1 FALSE NA 0.96 +chr13 48040820 48040821 C A 2 3 0.666666666666667 MODIFIER NUDT15 ENSG00000136159 A intron_variant Transcript ENST00000258662 protein_coding 1/2 ENST00000258662.3:c.159-100C>A NA 1 SNV HGNC HGNC:23063 YES NM_018283.4 1 P1 CCDS9407.1 ENSP00000258662 Q9NV35.157 UPI000006EA15 1 5 NA NA PASS SITE 9,0|1,1 NA NA 1 26 39,38 221,0 60,60 50 0.951 NA 2.36 NA FALSE 6.00 21 NA NA NA FALSE NA NA 7.41 5 48040820 HCC1395_HCC1395T 1 0.500 3 1,1 0,0 1,1 NA 0/1 NA NA NA NA 1,0,1,1 C/A PANCANCER NA FALSE NUDT15 chr13:48040820:48040821:C:A SNV 2:2 chr13:36370137:48709351:2:2:1 FALSE NA 0.96 +chr13 75594962 75594963 T A 2 8 0.25 LOW UCHL3 ENSG00000118939 A synonymous_variant Transcript ENST00000377595 protein_coding 7/9 ENST00000377595.8:c.522T>A ENSP00000366819.3:p.V174= ENSP00000366819.3 p.V174= 552 522 174 V gtT/gtA 1 SNV HGNC HGNC:12515 YES NM_006002.5 1 P1 CCDS9453.1 ENSP00000366819 P15374.207 A0A140VJZ4.35 UPI000004D00E PDB-ENSP_mappings:1uch.A&PDB-ENSP_mappings:1xd3.A&PDB-ENSP_mappings:1xd3.C&PDB-ENSP_mappings:6isu.A&PDB-ENSP_mappings:6qml.A&PDB-ENSP_mappings:6qml.D&CDD:cd09616&PANTHER:PTHR10589&Gene3D:3.40.532.10&Pfam:PF01088&Superfamily:SSF54001&Prints:PR00707&AlphaFold_DB_import:AF-P15374-F1 5 NA NA PASS SITE 24,20|1,1 NA NA 1 68 20,35 172,122 60,60 43 1.36 NA 6.58 NA FALSE 6.00 17 NA NA NA FALSE NA NA 6.38 5 75594962 HCC1395_HCC1395T 6 0.286 8 1,0 3,1 4,1 NA 0/1 NA NA NA NA 3,3,1,1 T/A PANCANCER NA FALSE UCHL3_p.V174= chr13:75594962:75594963:T:A SNV 2:0 chr13:49188820:114324544:2:0:1 TRUE NA 0.96 +chr13 91398955 91398956 T C 44 110 0.4 MODIFIER GPC5 ENSG00000179399 C 5_prime_UTR_variant Transcript ENST00000377067 protein_coding 1/8 ENST00000377067.9:c.-92T>C NA 335 1 SNV HGNC HGNC:4453 YES NM_004466.6 1 P1 CCDS9468.1 ENSP00000366267 P78333.175 UPI0000001C85 1 5 NA NA PASS SITE 121,145|20,24 NA NA 1 93 20,31 173,166 60,60 26 2.15 NA 40.89 NA FALSE 6.00 93 NA NA NA FALSE NA NA 123.39 5 91398955 HCC1395_HCC1395T 66 0.425 110 19,12 17,12 46,34 NA 0/1 NA NA NA NA 27,39,20,24 T/C PANCANCER NA FALSE GPC5 chr13:91398955:91398956:T:C SNV 2:0 chr13:49188820:114324544:2:0:1 TRUE NA 0.96 +chr13 98431278 98431279 G T 6 6 1 MODERATE FARP1 ENSG00000152767 T missense_variant&splice_region_variant Transcript ENST00000319562 protein_coding 18/27 ENST00000319562.11:c.2141G>T ENSP00000322926.6:p.R714L ENSP00000322926.6 p.R714L 2563 2141 714 R/L cGa/cTa rs1458028855&COSV60350700 1 SNV HGNC HGNC:3591 YES NM_005766.4 1 P1 CCDS9487.1 ENSP00000322926 Q9Y4F1.181 A0A2X0TVY0.24 UPI000007052C Q9Y4F1-1 deleterious_low_confidence(0) benign(0.179) PDB-ENSP_mappings:4h6y.A&PDB-ENSP_mappings:4h6y.B&CDD:cd00160&Pfam:PF00621&Gene3D:1.20.900.10&SMART:SM00325&Superfamily:SSF48065&PROSITE_profiles:PS50010&PANTHER:PTHR45858&AlphaFold_DB_import:AF-Q9Y4F1-F1 5.179e-06 0 0 0 0 0 1.23e-05 0 0 1.23e-05 gnomADe_NFE 0&1 0&1 5 NA NA PASS SITE 6,13|0,6 NA NA 1 56 20,35 155,179 60,60 15 1.16 NA 3.91 NA FALSE 6.00 77 NA NA NA FALSE NA NA 22.36 5 98431278 HCC1395_HCC1395T 0 0.880 6 0,3 0,3 0,6 NA 0/1 NA NA NA NA 0,0,0,6 G/T PANCANCER NA FALSE FARP1_p.R714L chr13:98431278:98431279:G:T SNV 2:0 chr13:49188820:114324544:2:0:1 TRUE NA 0.96 +chr13 98829823 98829824 G A 45 45 1 MODIFIER DOCK9 ENSG00000088387 A intron_variant&NMD_transcript_variant Transcript ENST00000339416 nonsense_mediated_decay 42/48 ENST00000339416.7:c.*458-67C>T NA rs528608246 -1 SNV HGNC HGNC:14132 2 ENSP00000341086 Q6ZSL5.122 UPI00001C0DFE 0.0002 0 0 0.001 0 0 0.0001117 0 0 0 0 0.002701 0 0 4.41e-05 0 0 0.002701 gnomADg_EAS 5 NA NA PASS SITE 11,35|12,33 NA NA 1 93 34,20 167,172 60,60 23 1.58 NA 10.84 NA FALSE 3.65 93 NA NA NA FALSE NA NA 143.09 5 98829823 HCC1395_HCC1395T 0 0.972 45 0,13 0,17 0,33 NA 0/1 NA NA NA NA 0,0,12,33 G/A PANCANCER NA FALSE DOCK9 chr13:98829823:98829824:G:A SNV 2:0 chr13:49188820:114324544:2:0:1 TRUE NA 0.96 +chr13 99963377 99963378 A T 4 12 0.333333333333333 MODIFIER ZIC5 ENSG00000139800 T 3_prime_UTR_variant Transcript ENST00000267294 protein_coding 2/2 ENST00000267294.5:c.*2000T>A NA 4084 -1 SNV HGNC HGNC:20322 YES NM_033132.5 1 P1 CCDS9494.3 ENSP00000267294 Q96T25.157 UPI00000727B2 5 NA NA PASS SITE 20,3|2,2 NA NA 1 43 38,36 201,67 60,60 34 1.19 NA 4.21 NA FALSE 6.00 28 NA NA NA FALSE NA NA 13.73 5 99963377 HCC1395_HCC1395T 8 0.271 12 2,2 5,0 7,2 NA 0/1 NA NA NA NA 7,1,2,2 A/T PANCANCER NA FALSE ZIC5 chr13:99963377:99963378:A:T SNV 2:0 chr13:49188820:114324544:2:0:1 TRUE NA 0.96 +chr13 106567754 106567755 ACCGCGACTC A 57 247 0.230769230769231 MODIFIER ARGLU1 ENSG00000134884 - upstream_gene_variant Transcript ENST00000360629 protein_coding_CDS_not_defined NA 132 -1 deletion HGNC HGNC:25482 2 5 NA NA PASS SITE 327,209|34,23 NA NA 1 93 20,35 164,187 60,60 36 2.41 NA 74.04 NA FALSE 6.00 93 NA NA NA FALSE NA NA 210.15 5 106567754 HCC1395_HCC1395T 190 0.236 247 49,13 57,24 145,44 NA 0/1 NA NA NA NA 124,66,34,23 ACCGCGACTC/A PANCANCER NA FALSE ARGLU1 chr13:106567754:106567755:ACCGCGACTC:A indel 2:0 chr13:49188820:114324544:2:0:1 TRUE NA 0.96 +chr13 113425168 113425169 G T 33 67 0.492537313432836 MODERATE ADPRHL1 ENSG00000153531 T missense_variant Transcript ENST00000356501 protein_coding 5/7 ENST00000356501.8:c.412C>A ENSP00000348894.4:p.H138N ENSP00000348894.4 p.H138N 588 412 138 H/N Cac/Aac -1 SNV HGNC HGNC:21303 1 CCDS9536.1 ENSP00000348894 Q8NDY3.133 UPI0000070D32 Q8NDY3-2 tolerated(0.53) benign(0.023) Gene3D:1.10.4080.10&AlphaFold_DB_import:AF-Q8NDY3-F1&Pfam:PF03747&PANTHER:PTHR16222&Superfamily:SSF101478 5 NA NA PASS SITE 38,62|10,23 NA NA 1 93 20,20 158,171 60,60 33 1.65 NA 12.89 NA FALSE 6.00 93 NA NA NA FALSE NA NA 86.50 5 113425168 HCC1395_HCC1395T 34 0.509 67 5,9 14,12 22,23 NA 0/1 NA NA NA NA 13,21,10,23 G/T PANCANCER NA FALSE ADPRHL1_p.H138N chr13:113425168:113425169:G:T SNV 2:0 chr13:49188820:114324544:2:0:1 TRUE NA 0.96 +chr13 114015135 114015136 C G 36 36 1 MODIFIER RASA3 ENSG00000185989 G intron_variant Transcript ENST00000334062 protein_coding 14/23 ENST00000334062.8:c.1405+74G>C NA -1 SNV HGNC HGNC:20331 YES NM_007368.4 1 P1 CCDS32016.1 ENSP00000335029 Q14644.195 UPI000000DBC1 Q14644-1 5 NA NA PASS SITE 44,16|27,9 NA NA 1 93 26,26 167,175 60,60 26 1.68 NA 13.85 NA FALSE 6.00 93 NA NA NA FALSE NA NA 121.20 5 114015135 HCC1395_HCC1395T 0 0.966 36 0,9 0,18 0,27 NA 0/1 NA NA NA NA 0,0,27,9 C/G PANCANCER NA FALSE RASA3 chr13:114015135:114015136:C:G SNV 2:0 chr13:49188820:114324544:2:0:1 TRUE NA 0.96 +chr14 20557431 20557432 G A 10 66 0.151515151515152 MODIFIER RNASE9 ENSG00000188655 A intron_variant Transcript ENST00000338904 protein_coding 1/1 ENST00000338904.7:c.-14-348C>T NA rs1227494836 -1 SNV HGNC HGNC:20673 1 P2 CCDS32036.1 ENSP00000340162 P60153.141 W0UV99.52 UPI000016087B P60153-1 6 NA NA PASS SITE 10,74|2,8 NA NA 1 93 40,39 221,262 60,60 42 1.42 NA 7.52 NA FALSE 6.00 42 NA NA NA FALSE NA NA 27.19 6 20557431 HCC1395_HCC1395T 56 0.154 66 19,5 32,3 54,9 NA 0/1 NA NA NA NA 5,51,2,8 G/A PANCANCER NA FALSE RNASE9 chr14:20557431:20557432:G:A SNV 2:2 chr14:19921447:24379075:2:2:1 FALSE NA 0.96 +chr14 21324542 21324543 C G 121 228 0.530701754385965 MODIFIER RPGRIP1 ENSG00000092200 G intron_variant Transcript ENST00000382933 protein_coding 4/11 ENST00000382933.8:c.688+2538C>G NA 1 SNV HGNC HGNC:13436 1 CCDS91848.1 ENSP00000372391 Q96KN7.180 UPI00015DFD47 Q96KN7-4 1 6 NA NA PASS SITE 129,70|79,42 NA NA 1 93 20,20 171,166 60,60 35 1.82 NA 19.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 341.78 6 21324542 HCC1395_HCC1395T 107 0.532 228 27,32 46,48 75,85 NA 0/1 NA NA NA NA 69,38,79,42 C/G PANCANCER NA FALSE RPGRIP1 chr14:21324542:21324543:C:G SNV 2:2 chr14:19921447:24379075:2:2:1 FALSE NA 0.96 +chr14 22982724 22982725 A T 7 16 0.4375 MODIFIER AJUBA ENSG00000129474 T upstream_gene_variant Transcript ENST00000262713 protein_coding NA rs149530987 173 -1 SNV HGNC HGNC:20250 YES NM_032876.6 1 P1 CCDS9581.1 ENSP00000262713 Q96IF1.176 UPI0000040AEC Q96IF1-1 6.572e-06 2.414e-05 0 0 0 0 0 0 0 0 0 2.414e-05 gnomADg_AFR 6 NA NA PASS SITE 2,18|0,7 NA NA 1 29 36,34 211,219 60,60 19 1.04 NA 3.01 NA FALSE 6.00 33 NA NA NA FALSE NA NA 21.43 6 22982724 HCC1395_HCC1395T 9 0.444 16 3,1 5,5 9,7 NA 0/1 NA NA NA NA 0,9,0,7 A/T PANCANCER NA FALSE AJUBA chr14:22982724:22982725:A:T SNV 2:2 chr14:19921447:24379075:2:2:1 FALSE NA 0.96 +chr14 23273393 23273394 C G 33 66 0.5 MODIFIER HOMEZ ENSG00000290292 G 3_prime_UTR_variant Transcript ENST00000357460 protein_coding 2/2 ENST00000357460.7:c.*2182G>C NA 4015 -1 SNV HGNC HGNC:20164 YES NM_020834.3 1 P2 CCDS45085.1 ENSP00000350049 Q8IX15.178 UPI0000EE4A53 Q8IX15-1 6 NA NA PASS SITE 67,11|31,2 NA NA 1 93 38,41 197,219 60,60 30 1.65 NA 12.64 NA FALSE 6.00 93 NA NA NA FALSE NA NA 126.13 6 23273393 HCC1395_HCC1395T 33 0.515 66 11,10 20,22 31,33 NA 0/1 NA NA NA NA 30,3,31,2 C/G PANCANCER NA FALSE HOMEZ chr14:23273393:23273394:C:G SNV 2:2 chr14:19921447:24379075:2:2:1 FALSE NA 0.96 +chr14 24060744 24060745 G A 93 191 0.486910994764398 LOW CARMIL3 ENSG00000186648 A synonymous_variant Transcript ENST00000342740 protein_coding 25/40 ENST00000342740.6:c.2178G>A ENSP00000340467.5:p.K726= ENSP00000340467.5 p.K726= 2323 2178 726 K aaG/aaA COSV57725941 1 SNV HGNC HGNC:20272 YES NM_138360.4 5 P1 CCDS32054.1 ENSP00000340467 Q8ND23.133 UPI0000DBEF11 Q8ND23-1 AlphaFold_DB_import:AF-Q8ND23-F1&PANTHER:PTHR24112 1 1 6 NA NA PASS SITE 108,137|41,52 NA NA 1 93 20,20 150,160 60,60 28 1.99 NA 28.29 NA FALSE 6.00 93 NA NA NA FALSE NA NA 239.81 6 24060744 HCC1395_HCC1395T 98 0.488 191 29,22 32,36 65,62 NA 0/1 NA NA NA NA 41,57,41,52 G/A PANCANCER NA FALSE CARMIL3_p.K726= chr14:24060744:24060745:G:A SNV 2:2 chr14:19921447:24379075:2:2:1 FALSE NA 0.96 +chr14 24118216 24118217 G T 125 206 0.606796116504854 MODIFIER DCAF11 ENSG00000100897 T intron_variant&NMD_transcript_variant Transcript ENST00000326009 nonsense_mediated_decay 6/14 ENST00000326009.9:c.*338+61G>T NA 1 SNV HGNC HGNC:20258 1 ENSP00000323680 H0YN03.62 UPI00022F8664 6 NA NA PASS SITE 69,133|40,85 NA NA 1 93 30,26 169,171 60,60 27 1.97 NA 27.39 NA FALSE 6.00 93 NA NA NA FALSE NA NA 349.35 6 24118216 HCC1395_HCC1395T 81 0.597 206 14,35 38,44 61,91 NA 0/1 NA NA NA NA 25,56,40,85 G/T PANCANCER NA FALSE DCAF11 chr14:24118216:24118217:G:T SNV 2:2 chr14:19921447:24379075:2:2:1 FALSE NA 0.96 +chr14 26447828 26447829 A T 27 63 0.428571428571429 MODIFIER NOVA1 ENSG00000139910 T downstream_gene_variant Transcript ENST00000347476 protein_coding NA 890 -1 cds_end_NF SNV HGNC HGNC:7886 4 ENSP00000299472 G8JLA5.57 UPI00020CDFD4 6 NA NA PASS SITE 68,12|24,3 NA NA 1 93 36,38 207,201 60,60 24 1.62 NA 12.04 NA FALSE 6.00 62 NA NA NA FALSE NA NA 94.57 6 26447828 HCC1395_HCC1395T 36 0.431 63 10,6 26,21 36,27 NA 0/1 NA NA NA NA 33,3,24,3 A/T PANCANCER NA FALSE NOVA1 chr14:26447828:26447829:A:T SNV 2:1 chr14:24413106:35831689:2:1:1 TRUE NA 0.96 +chr14 26448938 26448939 G C 35 92 0.380434782608696 MODERATE NOVA1 ENSG00000139910 C missense_variant Transcript ENST00000347476 protein_coding 4/4 ENST00000347476.10:c.107C>G ENSP00000299472.8:p.T36R ENSP00000299472.8 p.T36R 329 107 36 T/R aCa/aGa COSV57490852 -1 cds_end_NF SNV HGNC HGNC:7886 4 ENSP00000299472 G8JLA5.57 UPI00020CDFD4 deleterious(0) possibly_damaging(0.809) PROSITE_profiles:PS50084&CDD:cd22436&PANTHER:PTHR10288&Gene3D:3.30.1370.10&Pfam:PF00013&SMART:SM00322&Superfamily:SSF54791&AlphaFold_DB_import:AF-G8JLA5-F1 1 1 6 NA NA PASS SITE 20,80|9,26 NA NA 1 93 37,20 179,179 60,60 29 1.56 NA 10.49 NA FALSE 6.00 93 NA NA NA FALSE NA NA 98.51 6 26448938 HCC1395_HCC1395T 57 0.360 92 20,10 26,11 47,26 NA 0/1 NA NA NA NA 11,46,9,26 G/C PANCANCER NA FALSE NOVA1_p.T36R chr14:26448938:26448939:G:C SNV 2:1 chr14:24413106:35831689:2:1:1 TRUE NA 0.96 +chr14 28769266 28769267 G C 101 169 0.597633136094675 MODIFIER FOXG1 ENSG00000176165 C 3_prime_UTR_variant Transcript ENST00000313071 protein_coding 1/1 ENST00000313071.7:c.*517G>C NA 2480 1 SNV HGNC HGNC:3811 YES NM_005249.5 P1 CCDS9636.1 ENSP00000339004 P55316.182 UPI00001AE46C 1 6 NA NA PASS SITE 126,54|79,22 NA NA 1 93 34,36 197,201 60,60 16 1.98 NA 28.10 NA FALSE 6.00 93 NA NA NA FALSE NA NA 319.19 6 28769266 HCC1395_HCC1395T 68 0.611 169 10,32 35,45 55,87 NA 0/1 NA NA NA NA 47,21,79,22 G/C PANCANCER NA FALSE FOXG1 chr14:28769266:28769267:G:C SNV 2:1 chr14:24413106:35831689:2:1:1 TRUE NA 0.96 +chr14 30877397 30877398 C T 11 16 0.6875 MODIFIER COCH ENSG00000100473 T intron_variant Transcript ENST00000216361 protein_coding 2/10 ENST00000216361.9:c.278-175C>T NA 1 SNV HGNC HGNC:2180 1 CCDS86382.1 ENSP00000216361 A0A2U3TZE7.24 UPI0007DC528F 1 6 NA NA PASS SITE 16,0|11,0 NA NA 1 34 38,37 244,236 60,60 29 1.08 NA 3.26 NA FALSE 6.00 41 NA NA NA FALSE NA NA 40.38 6 30877397 HCC1395_HCC1395T 5 0.668 16 2,2 3,9 5,11 NA 0/1 NA NA NA NA 5,0,11,0 C/T PANCANCER NA FALSE COCH chr14:30877397:30877398:C:T SNV 2:1 chr14:24413106:35831689:2:1:1 TRUE NA 0.96 +chr14 32600791 32600792 A T 42 66 0.636363636363636 MODERATE AKAP6 ENSG00000151320 T missense_variant&splice_region_variant Transcript ENST00000280979 protein_coding 7/14 ENST00000280979.9:c.2729A>T ENSP00000280979.4:p.K910M ENSP00000280979.4 p.K910M 2874 2729 910 K/M aAg/aTg COSV55237106 1 SNV HGNC HGNC:376 YES NM_004274.5 1 P1 CCDS9644.1 ENSP00000280979 Q13023.181 UPI000013DC48 Q13023-1 deleterious(0) probably_damaging(0.911) AlphaFold_DB_import:AF-Q13023-F1 1 1 6 NA NA PASS SITE 18,45|13,30 NA NA 1 50 20,20 162,187 60,60 33 -1.096e+00 NA 4.95 NA FALSE 6.00 93 NA NA NA FALSE NA NA 124.13 6 32600791 HCC1395_HCC1395T 24 0.653 66 7,11 6,19 16,31 NA 0/1 NA NA NA NA 8,16,13,29 A/T PANCANCER NA FALSE AKAP6_p.K910M chr14:32600791:32600792:A:T SNV 2:1 chr14:24413106:35831689:2:1:1 TRUE NA 0.96 +chr14 32773881 32773882 G T 194 368 0.527173913043478 MODERATE AKAP6 ENSG00000151320 T missense_variant Transcript ENST00000280979 protein_coding 12/14 ENST00000280979.9:c.3576G>T ENSP00000280979.4:p.M1192I ENSP00000280979.4 p.M1192I 3721 3576 1192 M/I atG/atT COSV55229969&COSV55237121 1 SNV HGNC HGNC:376 YES NM_004274.5 1 P1 CCDS9644.1 ENSP00000280979 Q13023.181 UPI000013DC48 Q13023-1 deleterious(0) benign(0.003) Gene3D:1.20.58.60&AlphaFold_DB_import:AF-Q13023-F1&PANTHER:PTHR14514 1&1 1&1 6 NA NA PASS SITE 212,215|103,91 NA NA 1 93 20,20 166,176 60,60 34 2.24 NA 51.98 NA FALSE 6.00 93 NA NA NA FALSE NA NA 527.55 6 32773881 HCC1395_HCC1395T 174 0.533 368 36,48 79,84 121,138 NA 0/1 NA NA NA NA 91,83,103,91 G/T PANCANCER NA FALSE AKAP6_p.M1192I chr14:32773881:32773882:G:T SNV 2:1 chr14:24413106:35831689:2:1:1 TRUE NA 0.96 +chr14 39247883 39247884 G C 30 30 1 MODERATE MIA2 ENSG00000150527 C missense_variant Transcript ENST00000280082 protein_coding 4/6 ENST00000280082.4:c.1309G>C ENSP00000280082.3:p.D437H ENSP00000280082.3 p.D437H 1508 1309 437 D/H Gat/Cat COSV54487111 1 SNV HGNC HGNC:18432 1 CCDS9672.1 ENSP00000280082 Q96PC5.160 UPI0000351D6B Q96PC5-2 tolerated(0.05) possibly_damaging(0.852) Low_complexity_(Seg):seg&PANTHER:PTHR23158&AlphaFold_DB_import:AF-Q96PC5-F1 1 1 6 NA NA PASS SITE 19,23|15,15 NA NA 1 93 33,37 181,190 60,60 27 1.53 NA 9.93 NA FALSE 6.00 93 NA NA NA FALSE NA NA 106.79 6 39247883 HCC1395_HCC1395T 0 0.963 30 0,4 0,15 0,25 NA 0/1 NA NA NA NA 0,0,15,15 G/C PANCANCER NA FALSE MIA2_p.D437H chr14:39247883:39247884:G:C SNV 2:0 chr14:36299070:46845735:2:0:1 TRUE NA 0.96 +chr14 49602531 49602532 G C 7 33 0.212121212121212 MODIFIER LRR1 ENSG00000165501 C intron_variant Transcript ENST00000298288 protein_coding 2/3 ENST00000298288.11:c.282+63G>C NA 1 SNV HGNC HGNC:19742 YES NM_152329.4 1 P1 CCDS9686.1 ENSP00000298288 Q96L50.164 UPI000013E4BC Q96L50-1 6 NA NA PASS SITE 4,35|0,7 NA NA 1 52 40,42 204,232 60,60 28 1.16 NA 3.91 NA FALSE 6.00 42 NA NA NA FALSE NA NA 22.68 6 49602531 HCC1395_HCC1395T 26 0.229 33 5,1 10,5 26,7 NA 0/1 NA NA NA NA 2,24,0,7 G/C PANCANCER NA FALSE LRR1 chr14:49602531:49602532:G:C SNV 2:2 chr14:46845924:58648052:2:2:1 FALSE NA 0.96 +chr14 49840710 49840711 C G 27 209 0.129186602870813 LOW NEMF ENSG00000165525 G splice_region_variant&intron_variant Transcript ENST00000298310 protein_coding 5/32 ENST00000298310.10:c.506+8G>C NA -1 SNV HGNC HGNC:10663 YES NM_004713.6 5 P1 CCDS9694.1 ENSP00000298310 O60524.168 UPI0000246D16 O60524-1 1 6 NA NA PASS SITE 177,93|16,11 NA NA 1 93 20,20 167,155 60,60 24 1.81 NA 18.96 NA FALSE 6.00 61 NA NA NA FALSE NA NA 56.51 6 49840710 HCC1395_HCC1395T 182 0.124 209 43,5 81,11 126,17 NA 0/1 NA NA NA NA 121,61,16,11 C/G PANCANCER NA FALSE NEMF chr14:49840710:49840711:C:G SNV 2:2 chr14:46845924:58648052:2:2:1 FALSE NA 0.96 +chr14 50886809 50886810 C T 140 303 0.462046204620462 MODIFIER ABHD12B ENSG00000131969 T intron_variant Transcript ENST00000337334 protein_coding 8/12 ENST00000337334.7:c.700+125C>T NA 1 SNV HGNC HGNC:19837 YES NM_001206673.2 1 P1 CCDS55916.1 ENSP00000336693 Q7Z5M8.143 UPI00001ADDF5 Q7Z5M8-1 6 NA NA PASS SITE 179,194|63,77 NA NA 1 93 20,20 163,155 60,60 34 2.14 NA 40.94 NA FALSE 6.00 93 NA NA NA FALSE NA NA 365.18 6 50886809 HCC1395_HCC1395T 163 0.470 303 27,30 60,40 105,93 NA 0/1 NA NA NA NA 79,84,63,77 C/T PANCANCER NA FALSE ABHD12B chr14:50886809:50886810:C:T SNV 2:2 chr14:46845924:58648052:2:2:1 FALSE NA 0.96 +chr14 50944813 50944814 C T 15 36 0.416666666666667 MODIFIER PYGL ENSG00000100504 T upstream_gene_variant Transcript ENST00000216392 protein_coding NA 330 -1 SNV HGNC HGNC:9725 YES NM_002863.5 1 P1 CCDS32080.1 ENSP00000216392 P06737.241 UPI000011136E P06737-1 1 6 NA NA PASS SITE 3,27|3,12 NA NA 1 26 40,34 207,172 60,60 37 1.02 NA 2.66 NA FALSE 6.00 10 NA NA NA FALSE NA NA 40.70 6 50944813 HCC1395_HCC1395T 21 0.408 36 3,1 11,8 18,12 NA 0/1 NA NA NA NA 3,18,3,12 C/T PANCANCER NA FALSE PYGL chr14:50944813:50944814:C:T SNV 2:2 chr14:46845924:58648052:2:2:1 FALSE NA 0.96 +chr14 51968123 51968124 A G 162 619 0.261712439418417 MODIFIER GNG2 ENSG00000186469 G 3_prime_UTR_variant Transcript ENST00000335281 protein_coding 3/3 ENST00000335281.8:c.*1436A>G NA 2058 1 SNV HGNC HGNC:4404 2 P1 CCDS32082.1 ENSP00000334448 P59768.182 UPI0000001245 6 NA NA PASS SITE 403,386|81,81 NA NA 1 93 20,20 159,153 60,60 40 2.34 NA 64.41 NA FALSE 6.00 93 NA NA NA FALSE NA NA 368.77 6 51968123 HCC1395_HCC1395T 457 0.258 619 98,39 175,55 292,101 NA 0/1 NA NA NA NA 233,224,81,81 A/G PANCANCER NA FALSE GNG2 chr14:51968123:51968124:A:G SNV 2:2 chr14:46845924:58648052:2:2:1 FALSE NA 0.96 +chr14 54776354 54776355 C T 30 133 0.225563909774436 MODIFIER SAMD4A ENSG00000020577 T intron_variant Transcript ENST00000251091 protein_coding 8/10 ENST00000251091.9:c.1654-60C>T NA 1 SNV HGNC HGNC:23023 1 A1 CCDS55917.2 ENSP00000251091 Q9UPU9.167 UPI0001AE4F37 Q9UPU9-3 6 NA NA PASS SITE 107,82|16,14 NA NA 1 93 20,20 161,168 60,60 44 1.78 NA 17.75 NA FALSE 6.00 45 NA NA NA FALSE NA NA 65.77 6 54776354 HCC1395_HCC1395T 103 0.220 133 33,5 31,14 70,19 NA 0/1 NA NA NA NA 58,45,16,14 C/T PANCANCER NA FALSE SAMD4A chr14:54776354:54776355:C:T SNV 2:2 chr14:46845924:58648052:2:2:1 FALSE NA 0.96 +chr14 55411452 55411453 C G 11 21 0.523809523809524 MODIFIER ATG14 ENSG00000126775 G intron_variant Transcript ENST00000247178 protein_coding 1/9 ENST00000247178.6:c.221+150G>C NA -1 SNV HGNC HGNC:19962 YES NM_014924.5 1 P1 CCDS32087.1 ENSP00000247178 Q6ZNE5.148 UPI00001FD5B2 Q6ZNE5-1 6 NA NA PASS SITE 25,0|11,0 NA NA 1 42 39,42 227,228 60,60 29 1.23 NA 4.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 41.43 6 55411452 HCC1395_HCC1395T 10 0.522 21 5,6 5,5 10,11 NA 0/1 NA NA NA NA 10,0,11,0 C/G PANCANCER NA FALSE ATG14 chr14:55411452:55411453:C:G SNV 2:2 chr14:46845924:58648052:2:2:1 FALSE NA 0.96 +chr14 60286594 60286595 T A 52 458 0.11353711790393 MODIFIER PPM1A ENSG00000100614 A intron_variant Transcript ENST00000325642 protein_coding 3/5 ENST00000325642.7:c.1171+853T>A NA 1 SNV HGNC HGNC:9275 2 CCDS45120.1 ENSP00000327255 P35813.214 UPI0000E01530 P35813-3 6 NA NA PASS SITE 375,301|29,23 NA NA 1 93 20,24 165,167 60,60 37 2.30 NA 58.35 NA FALSE 6.00 60 NA NA NA FALSE NA NA 121.43 6 60286594 HCC1395_HCC1395T 406 0.125 458 90,9 173,28 279,39 NA 0/1 NA NA NA NA 229,177,29,23 T/A PANCANCER NA FALSE PPM1A chr14:60286594:60286595:T:A SNV 2:1 chr14:59323009:60296211:2:1:1 TRUE NA 0.96 +chr14 60724008 60724009 C G 255 257 0.992217898832685 MODERATE SIX4 ENSG00000100625 G missense_variant Transcript ENST00000216513 protein_coding 1/3 ENST00000216513.5:c.67G>C ENSP00000216513.4:p.E23Q ENSP00000216513.4 p.E23Q 344 67 23 E/Q Gaa/Caa COSV53670433&COSV53671889 -1 SNV HGNC HGNC:10890 YES NM_017420.5 1 P1 CCDS9749.2 ENSP00000216513 Q9UIU6.167 UPI000066D924 deleterious(0.01) benign(0.413) AlphaFold_DB_import:AF-Q9UIU6-F1&MobiDB_lite:mobidb-lite 1&1 1&1 6 NA NA PASS SITE 142,147|140,116 NA NA 1 93 20,20 154,162 60,60 35 2.26 NA 53.69 NA FALSE 6.00 93 NA NA NA FALSE NA NA 771.85 6 60724008 HCC1395_HCC1395T 2 0.988 257 1,70 0,88 1,168 NA 0/1 NA NA NA NA 1,1,140,115 C/G PANCANCER NA FALSE SIX4_p.E23Q chr14:60724008:60724009:C:G SNV 2:0 chr14:60297381:64952575:2:0:1 TRUE NA 0.96 +chr14 63543468 63543469 T A 9 21 0.428571428571429 MODIFIER PPP2R5E ENSG00000154001 A upstream_gene_variant Transcript ENST00000337537 protein_coding NA rs1359889941 91 -1 SNV HGNC HGNC:9313 YES NM_006246.5 1 P1 CCDS9758.1 ENSP00000337641 Q16537.181 UPI0000124E94 Q16537-1 6.573e-06 2.413e-05 0 0 0 0 0 0 0 0 0 2.413e-05 gnomADg_AFR 6 NA NA PASS SITE 8,22|4,5 NA NA 1 39 36,20 209,191 60,60 26 1.25 NA 5.07 NA FALSE 4.61 60 NA NA NA FALSE NA NA 21.65 6 63543468 HCC1395_HCC1395T 12 0.368 21 6,3 5,3 11,6 NA 0/1 NA NA NA NA 6,6,4,5 T/A PANCANCER NA FALSE PPP2R5E chr14:63543468:63543469:T:A SNV 2:0 chr14:60297381:64952575:2:0:1 TRUE NA 0.96 +chr14 64232449 64232450 C G 34 34 1 MODIFIER ESR2 ENSG00000140009 G downstream_gene_variant Transcript ENST00000267525 protein_coding NA 580 -1 SNV HGNC HGNC:3468 1 CCDS61469.1 ENSP00000267525 Q92731.240 UPI000002A91C Q92731-7 1 6 NA NA PASS SITE 23,23|15,19 NA NA 1 93 20,20 162,176 60,60 37 1.51 NA 9.33 NA FALSE 6.00 93 NA NA NA FALSE NA NA 98.54 6 64232449 HCC1395_HCC1395T 0 0.961 34 0,10 0,12 0,23 NA 0/1 NA NA NA NA 0,0,15,19 C/G PANCANCER NA FALSE ESR2 chr14:64232449:64232450:C:G SNV 2:0 chr14:60297381:64952575:2:0:1 TRUE NA 0.96 +chr14 70047519 70047520 T A 10 67 0.149253731343284 MODIFIER SLC8A3 ENSG00000100678 A intron_variant Transcript ENST00000216568 protein_coding 5/5 ENST00000216568.11:c.521-1196A>T NA -1 SNV HGNC HGNC:11070 1 CCDS45131.1 ENSP00000216568 P57103.175 UPI00004B2BCC P57103-5 6 NA NA PASS SITE 54,93|4,6 NA NA 1 93 20,20 172,161 60,60 28 1.82 NA 19.22 NA FALSE 6.00 40 NA NA NA FALSE NA NA 21.07 6 70047519 HCC1395_HCC1395T 57 0.154 67 18,5 19,2 43,7 NA 0/1 NA NA NA NA 19,38,4,6 T/A PANCANCER NA FALSE SLC8A3 chr14:70047519:70047520:T:A SNV 2:0 chr14:69570894:74894474:2:0:1 TRUE NA 0.96 +chr14 70060890 70060891 C G 164 164 1 MODIFIER SLC8A3 ENSG00000100678 G 5_prime_UTR_variant Transcript ENST00000216568 protein_coding 2/6 ENST00000216568.11:c.-36G>C NA 292 COSV53689852&COSV53693405 -1 SNV HGNC HGNC:11070 1 CCDS45131.1 ENSP00000216568 P57103.175 UPI00004B2BCC P57103-5 1&1 1&1 6 NA NA PASS SITE 70,80|85,79 NA NA 1 93 20,20 163,150 60,60 41 2.00 NA 29.80 NA FALSE 6.00 93 NA NA NA FALSE NA NA 478.98 6 70060890 HCC1395_HCC1395T 0 0.991 164 0,33 0,65 0,104 NA 0/1 NA NA NA NA 0,0,85,79 C/G PANCANCER NA FALSE SLC8A3 chr14:70060890:70060891:C:G SNV 2:0 chr14:69570894:74894474:2:0:1 TRUE NA 0.96 +chr14 75292133 75292134 C T 142 628 0.226114649681529 MODIFIER LINC01220 ENSG00000259687 T upstream_gene_variant Transcript ENST00000558575 lncRNA NA 2274 1 SNV HGNC HGNC:49664 1 6 NA NA PASS SITE 436,405|77,65 NA NA 1 93 20,20 153,163 60,60 32 2.37 NA 69.18 NA FALSE 6.00 93 NA NA NA FALSE NA NA 321.37 6 75292133 HCC1395_HCC1395T 486 0.239 628 111,33 183,56 307,96 NA 0/1 NA NA NA NA 258,228,77,65 C/T PANCANCER NA FALSE LINC01220 chr14:75292133:75292134:C:T SNV 4:0 chr14:74906308:85529264:4:0:1 NA NA 0.96 +chr14 76763118 76763119 A T 115 115 1 LOW VASH1 ENSG00000071246 T synonymous_variant Transcript ENST00000167106 protein_coding 1/7 ENST00000167106.9:c.297A>T ENSP00000167106.4:p.T99= ENSP00000167106.4 p.T99= 1651 297 99 T acA/acT 1 SNV HGNC HGNC:19964 YES NM_014909.5 1 P1 CCDS9851.1 ENSP00000167106 Q7L8A9.135 UPI0000073F7C Q7L8A9-1 PDB-ENSP_mappings:6j4u.A&PDB-ENSP_mappings:6j7b.A&PDB-ENSP_mappings:6j8f.B&PDB-ENSP_mappings:6j8n.B&PDB-ENSP_mappings:6j8n.D&PDB-ENSP_mappings:6j8o.B&PDB-ENSP_mappings:6j91.B&PDB-ENSP_mappings:6j9h.B&PDB-ENSP_mappings:6j9h.D&PDB-ENSP_mappings:6k81.A&PDB-ENSP_mappings:6lpg.A&PDB-ENSP_mappings:6nvq.C&PDB-ENSP_mappings:6ocf.A&PDB-ENSP_mappings:6ocg.A&PDB-ENSP_mappings:6och.A&PDB-ENSP_mappings:6och.C&PDB-ENSP_mappings:6wsl.C&PDB-ENSP_mappings:6wsl.G&AlphaFold_DB_import:AF-Q7L8A9-F1&Pfam:PF14822&PANTHER:PTHR15750 6 NA NA PASS SITE 50,51|48,67 NA NA 1 93 20,20 160,172 60,60 36 1.82 NA 19.26 NA FALSE 6.00 93 NA NA NA FALSE NA NA 358.44 6 76763118 HCC1395_HCC1395T 0 0.988 115 0,33 0,42 0,81 NA 0/1 NA NA NA NA 0,0,48,67 A/T PANCANCER NA FALSE VASH1_p.T99= chr14:76763118:76763119:A:T SNV 4:0 chr14:74906308:85529264:4:0:1 NA NA 0.96 +chr14 76857485 76857486 C G 186 186 1 MODIFIER LRRC74A ENSG00000100565 G intron_variant&NMD_transcript_variant Transcript ENST00000216450 nonsense_mediated_decay 9/12 ENST00000216450.7:c.*404+10C>G NA 1 SNV HGNC HGNC:23346 2 ENSP00000216450 H7BXD0.50 UPI000155D521 6 NA NA PASS SITE 60,87|66,120 NA NA 1 93 20,20 153,155 60,60 30 1.99 NA 28.90 NA FALSE 6.00 93 NA NA NA FALSE NA NA 592.52 6 76857485 HCC1395_HCC1395T 0 0.992 186 0,51 0,63 0,129 NA 0/1 NA NA NA NA 0,0,66,120 C/G PANCANCER NA FALSE LRRC74A chr14:76857485:76857486:C:G SNV 4:0 chr14:74906308:85529264:4:0:1 NA NA 0.96 +chr14 88615631 88615632 G T 114 136 0.838235294117647 MODIFIER ZC3H14 ENSG00000100722 T 3_prime_UTR_variant Transcript ENST00000251038 protein_coding 17/17 ENST00000251038.10:c.*3880G>T NA 6188 rs946882440&COSV99192933 1 SNV HGNC HGNC:20509 YES NM_024824.5 1 P3 CCDS32133.1 ENSP00000251038 Q6PJT7.168 UPI00001BDB9B Q6PJT7-1 1 0&1 0&1 6 NA NA PASS SITE 45,32|61,53 NA NA 1 93 20,31 169,171 60,60 30 1.61 NA 11.44 NA FALSE 6.00 93 NA NA NA FALSE NA NA 362.89 6 88615631 HCC1395_HCC1395T 22 0.830 136 6,26 10,53 17,87 NA 0/1 NA NA NA NA 12,10,61,53 G/T PANCANCER NA FALSE ZC3H14 chr14:88615631:88615632:G:T SNV 5:1 chr14:85529270:97751535:5:1:1 NA NA 0.96 +chr14 88687042 88687043 T A 22 41 0.536585365853659 MODIFIER EML5 ENSG00000165521 A intron_variant Transcript ENST00000380664 protein_coding 19/41 ENST00000380664.9:c.2854+174A>T NA -1 SNV HGNC HGNC:18197 5 P4 CCDS91916.1 ENSP00000370039 Q05BV3.141 UPI000183882B Q05BV3-1 6 NA NA PASS SITE 34,1|21,1 NA NA 1 84 38,37 219,202 60,60 17 1.25 NA 4.82 NA FALSE 6.00 65 NA NA NA FALSE NA NA 72.62 6 88687042 HCC1395_HCC1395T 19 0.535 41 7,5 11,15 18,21 NA 0/1 NA NA NA NA 18,1,21,1 T/A PANCANCER NA FALSE EML5 chr14:88687042:88687043:T:A SNV 5:1 chr14:85529270:97751535:5:1:1 NA NA 0.96 +chr14 91783160 91783161 T A 67 310 0.216129032258065 MODERATE TC2N ENSG00000165929 A missense_variant Transcript ENST00000340892 protein_coding 12/12 ENST00000340892.9:c.1413A>T ENSP00000343199.5:p.K471N ENSP00000343199.5 p.K471N 1727 1413 471 K/N aaA/aaT COSV100563212 -1 SNV HGNC HGNC:19859 1 P1 CCDS9897.1 ENSP00000343199 Q8N9U0.145 UPI000013E531 Q8N9U0-1 deleterious(0.02) possibly_damaging(0.473) Gene3D:2.60.40.150&AlphaFold_DB_import:AF-Q8N9U0-F1&PROSITE_profiles:PS50004&PANTHER:PTHR46887&SMART:SM00239&Superfamily:SSF49562&CDD:cd08692 1 1 6 NA NA PASS SITE 156,232|27,40 NA NA 1 93 20,20 170,172 60,60 35 1.98 NA 27.99 NA FALSE 6.00 93 NA NA NA FALSE NA NA 149.47 6 91783160 HCC1395_HCC1395T 243 0.216 310 44,14 106,26 162,44 NA 0/1 NA NA NA NA 95,148,27,40 T/A PANCANCER NA FALSE TC2N_p.K471N chr14:91783160:91783161:T:A SNV 5:1 chr14:85529270:97751535:5:1:1 NA NA 0.96 +chr14 92515490 92515491 A G 303 360 0.841666666666667 MODIFIER RIN3 ENSG00000100599 G intron_variant Transcript ENST00000216487 protein_coding 1/9 ENST00000216487.12:c.44+1514A>G NA 1 SNV HGNC HGNC:18751 YES NM_024832.5 1 P2 CCDS32144.1 ENSP00000216487 Q8TB24.169 UPI00001C1C97 Q8TB24-1 6 NA NA PASS SITE 63,124|104,199 NA NA 1 93 20,20 186,180 60,60 30 1.99 NA 28.80 NA FALSE 6.00 93 NA NA NA FALSE NA NA 924.44 6 92515490 HCC1395_HCC1395T 57 0.831 360 5,64 31,126 43,216 NA 0/1 NA NA NA NA 15,42,104,199 A/G PANCANCER NA FALSE RIN3 chr14:92515490:92515491:A:G SNV 5:1 chr14:85529270:97751535:5:1:1 NA NA 0.96 +chr14 93621382 93621384 CC TT 4 20 0.2 MODIFIER UNC79 ENSG00000133958 TT intron_variant Transcript ENST00000256339 protein_coding 29/49 ENST00000256339.8:c.3857-239_3857-238delinsTT NA 1 substitution HGNC HGNC:19966 5 CCDS9911.2 ENSP00000256339 Q9P2D8.125 UPI0000D62441 Q9P2D8-2 6 NA NA PASS SITE 24,1|4,0 NA NA 1 24 39,34 194,168 60,60 4 1.03 NA 2.71 NA FALSE 6.00 24 NA NA NA FALSE NA NA 13.11 6 93621382 HCC1395_HCC1395T 16 0.238 20 8,1 6,3 15,4 NA 0/1 NA NA NA NA 15,1,4,0 CC/TT PANCANCER NA FALSE UNC79 chr14:93621382:93621384:CC:TT indel 5:1 chr14:85529270:97751535:5:1:1 NA NA 0.96 +chr14 93692019 93692020 C T 14 98 0.142857142857143 MODIFIER UNC79 ENSG00000133958 T intron_variant Transcript ENST00000256339 protein_coding 47/49 ENST00000256339.8:c.7056+73C>T NA 1 SNV HGNC HGNC:19966 5 CCDS9911.2 ENSP00000256339 Q9P2D8.125 UPI0000D62441 Q9P2D8-2 6 NA NA PASS SITE 7,114|1,13 NA NA 1 93 40,36 206,221 60,60 24 1.55 NA 10.19 NA FALSE 6.00 20 NA NA NA FALSE NA NA 34.12 6 93692019 HCC1395_HCC1395T 84 0.148 98 28,2 46,11 80,13 NA 0/1 NA NA NA NA 4,80,1,13 C/T PANCANCER NA FALSE UNC79 chr14:93692019:93692020:C:T SNV 5:1 chr14:85529270:97751535:5:1:1 NA NA 0.96 +chr14 94382908 94382909 C G 63 363 0.173553719008264 MODERATE SERPINA1 ENSG00000197249 G missense_variant Transcript ENST00000355814 protein_coding 2/5 ENST00000355814.8:c.330G>C ENSP00000348068.4:p.E110D ENSP00000348068.4 p.E110D 607 330 110 E/D gaG/gaC -1 SNV HGNC HGNC:8941 1 P1 CCDS9925.1 ENSP00000348068 P01009.276 E9KL23.89 UPI000000CBEC P01009-1 1 tolerated(0.05) benign(0.147) PDB-ENSP_mappings:1atu.A&PDB-ENSP_mappings:1d5s.A&PDB-ENSP_mappings:1ezx.A&PDB-ENSP_mappings:1hp7.A&PDB-ENSP_mappings:1iz2.A&PDB-ENSP_mappings:1kct.A&PDB-ENSP_mappings:1oo8.A&PDB-ENSP_mappings:1oph.A&PDB-ENSP_mappings:1psi.A&PDB-ENSP_mappings:1qlp.A&PDB-ENSP_mappings:1qmb.A&PDB-ENSP_mappings:2d26.A&PDB-ENSP_mappings:2qug.A&Gene3D:3.30.497.10&PDB-ENSP_mappings:3cwl.A&PDB-ENSP_mappings:3cwm.A&PDB-ENSP_mappings:3drm.A&PDB-ENSP_mappings:3dru.A&PDB-ENSP_mappings:3dru.B&PDB-ENSP_mappings:3dru.C&PDB-ENSP_mappings:3ndd.A&PDB-ENSP_mappings:3ndf.A&PDB-ENSP_mappings:3ne4.A&PDB-ENSP_mappings:3t1p.A&PDB-ENSP_mappings:4pyw.A&PDB-ENSP_mappings:5io1.A&PDB-ENSP_mappings:5io1.B&PDB-ENSP_mappings:5nbu.A&PDB-ENSP_mappings:5nbv.A&PDB-ENSP_mappings:6hx4.A&PDB-ENSP_mappings:6hx4.B&PDB-ENSP_mappings:6i3z.A&PDB-ENSP_mappings:6i4v.A&PDB-ENSP_mappings:6i7u.A&PDB-ENSP_mappings:6iay.A&PDB-ENSP_mappings:6rod.A&PDB-ENSP_mappings:7ael.AAA&PDB-ENSP_mappings:7api.A&PDB-ENSP_mappings:7npk.A&PDB-ENSP_mappings:7npl.A&PDB-ENSP_mappings:8api.A&PDB-ENSP_mappings:9api.A&AlphaFold_DB_import:AF-P01009-F1&Pfam:PF00079&PANTHER:PTHR11461&SMART:SM00093&Superfamily:SSF56574&CDD:cd02056 6 NA NA PASS SITE 244,217|28,35 NA NA 1 93 20,20 165,155 60,60 25 2.06 NA 33.41 NA FALSE 6.00 93 NA NA NA FALSE NA NA 144.90 6 94382908 HCC1395_HCC1395T 300 0.171 363 89,18 117,23 213,44 NA 0/1 NA NA NA NA 155,145,28,35 C/G PANCANCER NA FALSE SERPINA1_p.E110D chr14:94382908:94382909:C:G SNV 5:1 chr14:85529270:97751535:5:1:1 NA NA 0.96 +chr14 94463232 94463233 G T 97 221 0.438914027149321 MODERATE SERPINA9 ENSG00000170054 T missense_variant Transcript ENST00000298845 protein_coding 6/6 ENST00000298845.12:c.815C>A ENSP00000298845.8:p.T272N ENSP00000298845.8 p.T272N 908 815 272 T/N aCc/aAc -1 SNV HGNC HGNC:15995 1 CCDS41983.2 ENSP00000298845 A0A6Q8JH89.8 UPI0000D62444 tolerated(0.11) possibly_damaging(0.692) AlphaFold_DB_import:AF-A0A6Q8JH89-F1&Pfam:PF00079&PANTHER:PTHR11461&SMART:SM00093&Superfamily:SSF56574&Low_complexity_(Seg):seg 6 NA NA PASS SITE 70,137|33,64 NA NA 1 93 20,20 168,154 60,60 28 1.77 NA 17.16 NA FALSE 6.00 93 NA NA NA FALSE NA NA 255.81 6 94463232 HCC1395_HCC1395T 124 0.429 221 22,19 36,27 91,68 NA 0/1 NA NA NA NA 40,84,33,64 G/T PANCANCER NA FALSE SERPINA9_p.T272N chr14:94463232:94463233:G:T SNV 5:1 chr14:85529270:97751535:5:1:1 NA NA 0.96 +chr14 94624220 94624221 G C 38 259 0.146718146718147 MODIFIER SERPINA3 ENSG00000196136 C downstream_gene_variant Transcript ENST00000393078 protein_coding NA 167 1 SNV HGNC HGNC:16 YES NM_001085.5 1 P1 CCDS32150.1 ENSP00000376793 P01011.246 A0A024R6P0.65 UPI000012509B P01011-1 6 NA NA PASS SITE 186,146|24,14 NA NA 1 93 20,31 166,159 60,60 26 1.59 NA 22.87 NA FALSE 6.00 85 NA NA NA FALSE NA NA 90.18 6 94624220 HCC1395_HCC1395T 221 0.153 259 65,9 87,18 159,28 NA 0/1 NA NA NA NA 124,97,24,14 G/C PANCANCER NA FALSE SERPINA3 chr14:94624220:94624221:G:C SNV 5:1 chr14:85529270:97751535:5:1:1 NA NA 0.96 +chr14 96090629 96090630 C G 50 403 0.124069478908189 MODIFIER C14orf132 ENSG00000227051 G downstream_gene_variant Transcript ENST00000553764 protein_coding NA 3822 1 SNV HGNC HGNC:20346 4 CCDS81849.1 ENSP00000489964 A0A1B0GU51.27 UPI0000E017AD 6 NA NA PASS SITE 259,248|28,22 NA NA 1 93 20,20 155,156 60,60 32 2.00 NA 29.79 NA FALSE 6.00 93 NA NA NA FALSE NA NA 103.18 6 96090629 HCC1395_HCC1395T 353 0.131 403 106,17 105,15 224,33 NA 0/1 NA NA NA NA 181,172,28,22 C/G PANCANCER NA FALSE C14orf132 chr14:96090629:96090630:C:G SNV 5:1 chr14:85529270:97751535:5:1:1 NA NA 0.96 +chr14 104112064 104112065 T C 99 150 0.66 MODIFIER ASPG ENSG00000166183 C intron_variant Transcript ENST00000546892 protein_coding 14/14 ENST00000546892.6:c.1601+64T>C NA 1 SNV HGNC HGNC:20123 1 CCDS91954.1 ENSP00000448911 G3V1Y8.93 UPI0000EE34C4 6 NA NA PASS SITE 88,110|46,53 NA NA 1 93 20,20 149,161 60,60 32 2.00 NA 29.49 NA FALSE 6.00 93 NA NA NA FALSE NA NA 266.86 6 104112064 HCC1395_HCC1395T 51 0.663 150 19,28 13,34 33,66 NA 0/1 NA NA NA NA 22,29,46,53 T/C PANCANCER NA FALSE ASPG chr14:104112064:104112065:T:C SNV 4:0 chr14:97762593:106658177:4:0:1 NA NA 0.96 +chr14 104745001 104745002 C T 26 144 0.180555555555556 MODIFIER ADSS1 ENSG00000185100 T intron_variant Transcript ENST00000330877 protein_coding 11/12 ENST00000330877.7:c.1171+92C>T NA 1 SNV HGNC HGNC:20093 YES NM_152328.5 1 P1 CCDS9990.1 ENSP00000331260 Q8N142.177 UPI000000DC76 Q8N142-1 1 6 NA NA PASS SITE 70,141|9,17 NA NA 1 93 20,20 166,161 60,60 33 1.86 NA 21.02 NA FALSE 6.00 67 NA NA NA FALSE NA NA 55.32 6 104745001 HCC1395_HCC1395T 118 0.182 144 31,6 37,9 80,17 NA 0/1 NA NA NA NA 41,77,9,17 C/T PANCANCER NA FALSE ADSS1 chr14:104745001:104745002:C:T SNV 4:0 chr14:97762593:106658177:4:0:1 NA NA 0.96 +chr14 105311975 105311976 C T 111 111 1 MODIFIER PACS2 ENSG00000179364 T upstream_gene_variant Transcript ENST00000325438 protein_coding NA 2440 1 SNV HGNC HGNC:23794 1 P1 CCDS32168.1 ENSP00000321834 Q86VP3.144 UPI00001FDD1A Q86VP3-1 1 6 NA NA PASS SITE 45,50|45,66 NA NA 1 93 20,20 164,175 60,60 34 1.83 NA 19.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 337.01 6 105311975 HCC1395_HCC1395T 0 0.988 111 0,34 0,43 0,81 NA 0/1 NA NA NA NA 0,0,45,66 C/T PANCANCER NA FALSE PACS2 chr14:105311975:105311976:C:T SNV 4:0 chr14:97762593:106658177:4:0:1 NA NA 0.96 +chr14 105707343 105707344 C T 13 1217 0.0106820049301561 MODERATE IGHA1 ENSG00000211895 T missense_variant Transcript ENST00000390547 IG_C_gene 3/3 ENST00000390547.3:c.887G>A ENSP00000374989.2:p.S296N ENSP00000374989.2 p.S296N 887 887 296 S/N aGc/aAc -1 cds_start_NF SNV HGNC HGNC:5478 A2 ENSP00000374989 P01876.208 UPI000004718D deleterious(0.02) PDB-ENSP_mappings:1iga.A&PDB-ENSP_mappings:1iga.B&PDB-ENSP_mappings:1ow0.A&PDB-ENSP_mappings:1ow0.B&PDB-ENSP_mappings:2esg.A&PDB-ENSP_mappings:2esg.B&PDB-ENSP_mappings:2qej.A&PDB-ENSP_mappings:2qej.B&PDB-ENSP_mappings:3chn.A&PDB-ENSP_mappings:3chn.B&PDB-ENSP_mappings:3chn.C&PDB-ENSP_mappings:3chn.D&PDB-ENSP_mappings:6lx3.A&PDB-ENSP_mappings:6lx3.B&PDB-ENSP_mappings:6lx3.C&PDB-ENSP_mappings:6lx3.D&PDB-ENSP_mappings:6lxw.A&PDB-ENSP_mappings:6lxw.B&PDB-ENSP_mappings:6lxw.C&PDB-ENSP_mappings:6lxw.D&PDB-ENSP_mappings:6ue7.A&PDB-ENSP_mappings:6ue7.B&PDB-ENSP_mappings:6ue7.F&PDB-ENSP_mappings:6ue7.G&PDB-ENSP_mappings:6xja.A&PDB-ENSP_mappings:6xja.B&PDB-ENSP_mappings:7uvl.A&PDB-ENSP_mappings:7uvl.B&AlphaFold_DB_import:AF-P01876-F1 6 NA NA PASS SITE 1191,1005|6,8 NA NA 1 93 20,20 157,156 60,60 31 2.29 NA 198.40 NA FALSE 6.00 11 NA NA NA FALSE NA NA 17.32 6 105707343 HCC1395_HCC1395T 1204 0.012 1217 355,2 435,7 832,9 NA 0/1 NA NA NA NA 644,560,5,8 C/T PANCANCER NA FALSE IGHA1_p.S296N chr14:105707343:105707344:C:T SNV 4:0 chr14:97762593:106658177:4:0:1 NA NA 0.96 +chr14 105855091 105855092 C T 265 265 1 MODERATE IGHM ENSG00000211899 T missense_variant Transcript ENST00000390559 IG_C_gene 3/4 ENST00000390559.6:c.793G>A ENSP00000375001.2:p.E265K ENSP00000375001.2 p.E265K 793 793 265 E/K Gaa/Aaa rs781999492 -1 cds_start_NF SNV HGNC HGNC:5541 A2 ENSP00000375001 P01871.207 UPI00034F239A P01871-1 1 tolerated(0.82) benign(0.007) PDB-ENSP_mappings:6kxs.A&PDB-ENSP_mappings:6kxs.B&PDB-ENSP_mappings:6kxs.C&PDB-ENSP_mappings:6kxs.D&PDB-ENSP_mappings:6kxs.E&PDB-ENSP_mappings:6kxs.F&PDB-ENSP_mappings:6kxs.G&PDB-ENSP_mappings:6kxs.H&PDB-ENSP_mappings:6kxs.K&PDB-ENSP_mappings:6kxs.L&PDB-ENSP_mappings:7k0c.A&PDB-ENSP_mappings:7k0c.B&PDB-ENSP_mappings:7k0c.E&PDB-ENSP_mappings:7k0c.F&PDB-ENSP_mappings:7k0c.G&PDB-ENSP_mappings:7k0c.H&PDB-ENSP_mappings:7k0c.I&PDB-ENSP_mappings:7k0c.J&PDB-ENSP_mappings:7k0c.K&PDB-ENSP_mappings:7k0c.L&AlphaFold_DB_import:AF-P01871-F1 1.625e-05 0 0 0 0 0 3.626e-05 0 0 3.626e-05 gnomADe_NFE 6 NA NA PASS SITE 106,118|118,147 NA NA 1 93 20,20 167,163 60,60 30 2.21 NA 47.55 NA FALSE 6.00 93 NA NA NA FALSE NA NA 835.93 6 105855091 HCC1395_HCC1395T 0 0.995 265 0,76 0,99 0,186 NA 0/1 NA NA NA NA 0,0,118,147 C/T PANCANCER NA FALSE IGHM_p.E265K chr14:105855091:105855092:C:T SNV 4:0 chr14:97762593:106658177:4:0:1 NA NA 0.96 +chr14 106470842 106470843 A G 22 63 0.349206349206349 MODIFIER IGHV3-43 ENSG00000232216 G upstream_gene_variant Transcript ENST00000434710 IG_V_gene NA rs1266597078 42 -1 cds_end_NF SNV HGNC HGNC:5604 YES P1 ENSP00000399826 A0A0B4J1X8.44 UPI000011AACC 0.062 0.081 0.05882 0.03683 0.04947 0.02364 0.09672 0.009434 0.05983 0.06486 0.02586 0.09672 gnomADg_FIN 6 NA NA PASS SITE 3,50|4,18 NA NA 1 42 34,37 227,184 47,40 18 1.09 NA 3.31 NA FALSE 4.61 47 NA NA NA FALSE NA NA 52.33 6 106470842 HCC1395_HCC1395T 41 0.314 63 23,5 15,12 40,18 NA 0/1 NA NA NA NA 2,39,4,18 A/G PANCANCER NA FALSE IGHV3-43 chr14:106470842:106470843:A:G SNV 4:0 chr14:97762593:106658177:4:0:1 NA NA 0.96 +chr14 106537830 106537831 A G 89 128 0.6953125 LOW IGHV3-48 ENSG00000211964 G synonymous_variant Transcript ENST00000390624 IG_V_gene 2/2 ENST00000390624.3:c.333T>C ENSP00000375033.2:p.A111= ENSP00000375033.2 p.A111= 412 333 111 A gcT/gcC rs781796836 -1 cds_end_NF SNV HGNC HGNC:5606 YES P1 ENSP00000375033 P01763.129 UPI000011717D AlphaFold_DB_import:AF-P01763-F1 0.0001256 6.735e-05 2.966e-05 0 0.001382 0 3.722e-05 0 0 0.09611 0.04336 0.2406 0.1009 0.136 0.07429 0.1394 0.03913 0.1244 0.104 0.0846 0.2406 gnomADg_AMI 6 NA NA PASS SITE 140,52|82,7 NA NA 1 93 31,32 165,173 45,40 21 2.05 NA 32.81 NA FALSE 3.38 93 NA NA NA FALSE NA NA 269.17 6 106537830 HCC1395_HCC1395T 39 0.668 128 13,37 26,42 40,82 NA 0/1 NA NA NA NA 39,0,82,7 A/G PANCANCER NA FALSE IGHV3-48_p.A111= chr14:106537830:106537831:A:G SNV 4:0 chr14:97762593:106658177:4:0:1 NA NA 0.96 +chr14 106627335 106627336 T C 74 158 0.468354430379747 MODIFIER IGHV1-58 ENSG00000211968 C upstream_gene_variant Transcript ENST00000390628 IG_V_gene NA rs542713287 4480 -1 cds_end_NF SNV HGNC HGNC:5555 YES P1 ENSP00000375037 A0A0C4DH39.41 UPI000011B547 4.06e-06 6.477e-05 0 0 0 0 0 0 0 0.0993 0.1179 0.2415 0.09455 0.093 0.03059 0.09155 0.02632 0.102 0.09661 0.03539 0.2415 gnomADg_AMI 6 NA NA PASS SITE 117,43|67,7 NA NA 2 93 35,38 202,183 40,40 23 1.88 NA 22.22 NA FALSE 3.91 93 NA NA NA FALSE NA NA 237.03 6 106627335 HCC1395_HCC1395T 84 0.456 158 25,29 42,37 80,67 NA 0/1 NA NA NA NA 66,18,67,7 T/C PANCANCER NA FALSE IGHV1-58 chr14:106627335:106627336:T:C SNV 4:0 chr14:97762593:106658177:4:0:1 NA NA 0.96 +chr15 23039616 23039617 C G 173 173 1 MODIFIER TUBGCP5 ENSG00000275835 G upstream_gene_variant Transcript ENST00000612085 protein_coding NA 2652 -1 cds_start_NF&cds_end_NF SNV HGNC HGNC:18600 3 ENSP00000479530 A0A087WVL9.47 UPI0004620D85 7 NA NA PASS SITE 120,161|72,101 NA NA 1 93 20,20 161,156 60,60 36 2.27 NA 54.73 NA FALSE 6.00 93 NA NA NA FALSE NA NA 516.81 7 23039616 HCC1395_HCC1395T 0 0.991 173 0,55 0,48 0,113 NA 0/1 NA NA NA NA 0,0,72,101 C/G PANCANCER NA FALSE TUBGCP5 chr15:23039616:23039617:C:G SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 28815512 28815513 G A 50 122 0.409836065573771 MODIFIER ENSG00000291258 A non_coding_transcript_exon_variant Transcript ENST00000563202 lncRNA 1/4 ENST00000563202.1:n.167G>A NA 167 rs1485559922 1 SNV 4 8.545e-05 0 0 0.000131 0.003168 0 0 0 0 0 0 0.003168 gnomADg_ASJ 7 NA NA PASS SITE 99,125|22,28 NA NA 2 93 20,20 162,167 60,58 45 1.97 NA 27.69 NA FALSE 4.61 93 NA NA NA FALSE NA NA 113.08 7 28815512 HCC1395_HCC1395T 72 0.396 122 27,15 13,12 45,29 NA 0/1 NA NA NA NA 30,42,22,28 G/A PANCANCER NA FALSE chr15:28815512:28815513:G:A SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 30951922 30951924 T TG 79 157 0.503184713375796 MODIFIER RNU6-466P ENSG00000212526 G downstream_gene_variant Transcript ENST00000391224 snRNA NA 4325 -1 insertion HGNC HGNC:47429 YES 7 NA NA PASS SITE 127,103|47,32 NA NA 2 93 20,20 155,163 60,60 31 1.98 NA 28.25 NA FALSE 6.00 93 2,3 G NA TRUE NA 93 283.68 7 30951922 HCC1395_HCC1395T 78 0.520 157 14,17 29,27 47,51 NA 0|1 0|1 30951922_T_TG NA 30951922 42,36,47,32 T|TG PANCANCER NA FALSE RNU6-466P chr15:30951922:30951924:T:TG indel 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 30951925 30951926 C T 79 157 0.503184713375796 MODIFIER RNU6-466P ENSG00000212526 T downstream_gene_variant Transcript ENST00000391224 snRNA NA 4323 -1 SNV HGNC HGNC:47429 YES 7 NA NA PASS SITE 127,103|47,32 NA NA 2 93 20,20 155,163 60,60 29 1.98 NA 28.26 NA FALSE 6.00 93 NA NA NA FALSE NA NA 283.67 7 30951925 HCC1395_HCC1395T 78 0.520 157 15,16 26,27 47,51 NA 0|1 0|1 30951922_T_TG NA 30951922 42,36,47,32 C|T PANCANCER NA FALSE RNU6-466P chr15:30951925:30951926:C:T SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 33636190 33636192 G GC 28 29 0.96551724137931 MODIFIER RYR3 ENSG00000198838 C intron_variant Transcript ENST00000389232 protein_coding 26/103 ENST00000389232.9:c.3382-186_3382-185insC NA 1 insertion HGNC HGNC:10485 5 A1 ENSP00000373884 A0A0X1KG73.36 UPI000719A1B2 1 7 NA NA PASS SITE 15,2|21,7 NA NA 1 82 38,20 213,188 60,60 27 1.18 NA 4.21 NA FALSE 6.00 93 NA NA NA FALSE NA NA 85.06 7 33636190 HCC1395_HCC1395T 1 0.922 29 0,7 1,12 1,22 NA 0/1 NA NA NA NA 1,0,21,7 G/GC PANCANCER NA FALSE RYR3 chr15:33636190:33636192:G:GC indel 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 39253816 39253817 G C 165 340 0.485294117647059 MODIFIER ENSG00000259345 C intron_variant&non_coding_transcript_variant Transcript ENST00000558209 lncRNA 2/2 ENST00000558209.1:n.451+105973C>G NA -1 SNV 3 7 NA NA PASS SITE 263,183|102,63 NA NA 1 93 20,20 162,167 60,60 32 2.27 NA 55.03 NA FALSE 6.00 93 NA NA NA FALSE NA NA 459.96 7 39253816 HCC1395_HCC1395T 175 0.488 340 46,36 74,78 125,119 NA 0/1 NA NA NA NA 105,70,102,63 G/C PANCANCER NA FALSE chr15:39253816:39253817:G:C SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 39599361 39599362 C T 158 391 0.404092071611253 MODIFIER THBS1 ENSG00000137801 T 3_prime_UTR_variant Transcript ENST00000260356 protein_coding 22/22 ENST00000260356.6:c.*3992C>T NA 7684 1 SNV HGNC HGNC:11785 YES NM_003246.4 1 P1 CCDS32194.1 ENSP00000260356 P07996.253 UPI00001FE219 P07996-1 7 NA NA PASS SITE 291,324|77,82 NA NA 1 93 20,20 171,161 60,60 28 2.44 NA 81.02 NA FALSE 6.00 93 NA NA NA FALSE NA NA 389.18 7 39599361 HCC1395_HCC1395T 233 0.409 391 56,38 94,62 162,112 NA 0/1 NA NA NA NA 105,128,77,81 C/T PANCANCER NA FALSE THBS1 chr15:39599361:39599362:C:T SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 40471063 40471064 G T 2 6 0.333333333333333 MODIFIER CHST14 ENSG00000169105 T 5_prime_UTR_variant Transcript ENST00000306243 protein_coding 1/1 ENST00000306243.7:c.-151G>T NA 80 1 SNV HGNC HGNC:24464 YES NM_130468.4 P1 CCDS10059.1 ENSP00000307297 Q8NCH0.150 UPI000004616D 1 7 NA NA PASS SITE 11,12|1,1 NA NA 1 31 20,36 138,125 60,60 56 1.04 NA 3.01 NA FALSE 6.00 9 NA NA NA FALSE NA NA 6.93 7 40471063 HCC1395_HCC1395T 4 0.396 6 1,1 1,0 2,1 NA 0/1 NA NA NA NA 2,2,1,1 G/T PANCANCER NA FALSE CHST14 chr15:40471063:40471064:G:T SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 40622779 40622781 CC TT 60 137 0.437956204379562 MODERATE KNL1 ENSG00000137812 TT missense_variant Transcript ENST00000346991 protein_coding 11/27 ENST00000346991.9:c.2593_2594delinsTT ENSP00000335463.6:p.P865L ENSP00000335463.6 p.P865L 2983-2984 2593-2594 865 P/L CCa/TTa COSV61162495 1 substitution HGNC HGNC:24054 1 A2 CCDS42023.1 ENSP00000335463 Q8NG31.163 UPI0000E59BD3 Q8NG31-1 1 tolerated(1) benign(0.007) PANTHER:PTHR16520&AlphaFold_DB_import:AF-Q8NG31-F1 1 1 7 NA NA PASS SITE 97,150|23,37 NA NA 1 93 20,34 176,200 60,60 32 2.08 NA 35.52 NA FALSE 6.00 73 NA NA NA FALSE NA NA 228.50 7 40622779 HCC1395_HCC1395T 77 0.438 137 31,11 22,28 59,46 NA 0/1 NA NA NA NA 26,51,23,37 CC/TT PANCANCER NA FALSE KNL1_p.P865L chr15:40622779:40622781:CC:TT indel 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 43149137 43149138 G C 95 95 1 MODERATE TMEM62 ENSG00000137842 C missense_variant Transcript ENST00000260403 protein_coding 7/14 ENST00000260403.7:c.852G>C ENSP00000260403.2:p.W284C ENSP00000260403.2 p.W284C 1069 852 284 W/C tgG/tgC COSV53040791 1 SNV HGNC HGNC:26269 YES NM_024956.4 1 P1 CCDS32210.1 ENSP00000260403 Q0P6H9.105 UPI00004443FD deleterious(0) probably_damaging(1) AlphaFold_DB_import:AF-Q0P6H9-F1&PANTHER:PTHR14795&Superfamily:SSF56300&CDD:cd07401 1 1 7 NA NA PASS SITE 43,68|40,55 NA NA 1 93 20,20 157,169 60,60 30 1.89 NA 22.53 NA FALSE 6.00 93 NA NA NA FALSE NA NA 291.92 7 43149137 HCC1395_HCC1395T 0 0.985 95 0,28 0,34 0,63 NA 0/1 NA NA NA NA 0,0,40,55 G/C PANCANCER NA FALSE TMEM62_p.W284C chr15:43149137:43149138:G:C SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 45133933 45133934 G A 82 82 1 MODIFIER DUOXA1 ENSG00000140254 A upstream_gene_variant Transcript ENST00000267803 protein_coding NA COSV50993345 4074 -1 SNV HGNC HGNC:26507 1 CCDS10119.1 ENSP00000267803 Q1HG43.114 A8K9Q6.116 UPI000006D4D4 Q1HG43-2 1 1 7 NA NA PASS SITE 49,37|46,36 NA NA 1 93 20,20 155,165 60,60 30 1.77 NA 16.55 NA FALSE 6.00 93 NA NA NA FALSE NA NA 259.71 7 45133933 HCC1395_HCC1395T 0 0.983 82 0,19 0,29 0,57 NA 0/1 NA NA NA NA 0,0,46,36 G/A PANCANCER NA FALSE DUOXA1 chr15:45133933:45133934:G:A SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 48251471 48251472 G A 5 11 0.454545454545455 MODIFIER SLC12A1 ENSG00000074803 A intron_variant Transcript ENST00000380993 protein_coding 14/26 ENST00000380993.8:c.1787-144G>A NA 1 SNV HGNC HGNC:10910 YES NM_000338.3 5 A1 CCDS10129.2 ENSP00000370381 Q13621.196 UPI0000229BFB Q13621-1 1 7 NA NA PASS SITE 15,0|5,0 NA NA 1 26 39,36 213,245 60,60 50 1.000 NA 2.71 NA FALSE 6.00 45 NA NA NA FALSE NA NA 16.84 7 48251471 HCC1395_HCC1395T 6 0.462 11 2,2 4,3 6,5 NA 0/1 NA NA NA NA 6,0,5,0 G/A PANCANCER NA FALSE SLC12A1 chr15:48251471:48251472:G:A SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 48437746 48437747 G A 11 20 0.55 MODIFIER FBN1 ENSG00000166147 A intron_variant Transcript ENST00000316623 protein_coding 51/65 ENST00000316623.10:c.6313+22C>T NA -1 SNV HGNC HGNC:3603 YES NM_000138.5 1 P1 CCDS32232.1 ENSP00000325527 P35555.248 UPI0000EE4EBC 1 7 NA NA PASS SITE 20,4|9,2 NA NA 1 36 38,37 198,206 60,60 27 1.16 NA 3.91 NA FALSE 6.00 37 NA NA NA FALSE NA NA 32.33 7 48437746 HCC1395_HCC1395T 9 0.526 20 3,2 5,6 8,9 NA 0/1 NA NA NA NA 7,2,9,2 G/A PANCANCER NA FALSE FBN1 chr15:48437746:48437747:G:A SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 48992964 48992965 C G 4 19 0.210526315789474 MODIFIER SECISBP2L ENSG00000138593 G intron_variant Transcript ENST00000261847 protein_coding 16/16 ENST00000261847.7:c.2489-38G>C NA COSV55934933 -1 SNV HGNC HGNC:28997 1 A1 CCDS32234.1 ENSP00000261847 Q93073.162 UPI00004E901A Q93073-2 1 1 7 NA NA PASS SITE 0,31|0,4 NA NA 1 55 39,40 215,223 60,60 45 1.24 NA 4.81 NA FALSE 6.00 57 NA NA NA FALSE NA NA 12.73 7 48992964 HCC1395_HCC1395T 15 0.240 19 5,2 9,2 15,4 NA 0/1 NA NA NA NA 0,15,0,4 C/G PANCANCER NA FALSE SECISBP2L chr15:48992964:48992965:C:G SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 49282071 49282072 G T 157 157 1 MODERATE GALK2 ENSG00000156958 T missense_variant Transcript ENST00000327171 protein_coding 6/10 ENST00000327171.7:c.556G>T ENSP00000316632.3:p.A186S ENSP00000316632.3 p.A186S 788 556 186 A/S Gca/Tca COSV59100879 1 SNV HGNC HGNC:4119 1 CCDS32236.1 ENSP00000316632 Q01415.192 UPI00001B3E97 Q01415-2 deleterious(0) possibly_damaging(0.789) Gene3D:3.30.230.10&AlphaFold_DB_import:AF-Q01415-F1&PIRSF:PIRSF000530&Prints:PR00959&PANTHER:PTHR10457&Superfamily:SSF54211&TIGRFAM:TIGR00131 1 1 7 NA NA PASS SITE 66,83|64,93 NA NA 1 93 20,20 166,147 60,60 40 1.99 NA 29.15 NA FALSE 6.00 93 NA NA NA FALSE NA NA 444.49 7 49282071 HCC1395_HCC1395T 0 0.991 157 0,30 0,64 0,103 NA 0/1 NA NA NA NA 0,0,64,93 G/T PANCANCER NA FALSE GALK2_p.A186S chr15:49282071:49282072:G:T SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 50047462 50047463 A G 62 62 1 LOW ATP8B4 ENSG00000104043 G splice_region_variant&synonymous_variant Transcript ENST00000284509 protein_coding 4/28 ENST00000284509.11:c.90T>C ENSP00000284509.6:p.D30= ENSP00000284509.6 p.D30= 243 90 30 D gaT/gaC COSV52709738&COSV52713583 -1 SNV HGNC HGNC:13536 YES NM_024837.4 5 P1 CCDS32238.1 ENSP00000284509 Q8TF62.171 UPI0000055904 CDD:cd02073&PANTHER:PTHR24092&Pfam:PF16209&TIGRFAM:TIGR01652&Superfamily:SSF81665&AlphaFold_DB_import:AF-Q8TF62-F1 1&1 1&1 7 NA NA PASS SITE 51,43|34,28 NA NA 1 93 20,20 165,158 60,60 34 1.78 NA 17.66 NA FALSE 6.00 93 NA NA NA FALSE NA NA 188.75 7 50047462 HCC1395_HCC1395T 0 0.977 62 0,17 0,22 0,41 NA 0/1 NA NA NA NA 0,0,34,28 A/G PANCANCER NA FALSE ATP8B4_p.D30= chr15:50047462:50047463:A:G SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 50643417 50643418 T G 84 190 0.442105263157895 MODERATE TRPM7 ENSG00000092439 G missense_variant Transcript ENST00000560955 protein_coding 5/39 ENST00000560955.5:c.458A>C ENSP00000453277.1:p.K153T ENSP00000453277.1 p.K153T 696 458 153 K/T aAg/aCg -1 SNV HGNC HGNC:17994 1 P4 CCDS73725.1 ENSP00000453277 H0YLN8.93 UPI00000497D6 1 deleterious_low_confidence(0) possibly_damaging(0.726) Pfam:PF18139&PANTHER:PTHR13800 7 NA NA PASS SITE 151,124|41,43 NA NA 1 93 20,20 157,155 60,60 32 2.03 NA 31.31 NA FALSE 6.00 93 NA NA NA FALSE NA NA 210.50 7 50643417 HCC1395_HCC1395T 106 0.452 190 29,16 38,36 68,56 NA 0/1 NA NA NA NA 62,44,41,43 T/G PANCANCER NA FALSE TRPM7_p.K153T chr15:50643417:50643418:T:G SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 51751672 51751673 G A 103 103 1 MODIFIER TMOD2 ENSG00000128872 A 5_prime_UTR_variant Transcript ENST00000249700 protein_coding 1/10 ENST00000249700.9:c.-110G>A NA 76 1 SNV HGNC HGNC:11872 YES NM_014548.4 1 P1 CCDS10144.1 ENSP00000249700 Q9NZR1.159 UPI0000137080 Q9NZR1-1 7 NA NA PASS SITE 125,114|54,49 NA NA 1 93 20,20 146,144 60,60 31 2.14 NA 41.54 NA FALSE 6.00 93 NA NA NA FALSE NA NA 261.23 7 51751672 HCC1395_HCC1395T 0 0.983 103 0,20 0,34 0,57 NA 0/1 NA NA NA NA 0,0,54,49 G/A PANCANCER NA FALSE TMOD2 chr15:51751672:51751673:G:A SNV 2:0 chr15:19964897:55545690:2:0:1 TRUE NA 0.96 +chr15 56464272 56464273 G T 14 30 0.466666666666667 MODIFIER MNS1 ENSG00000138587 T intron_variant Transcript ENST00000260453 protein_coding 1/9 ENST00000260453.4:c.4-25C>A NA -1 SNV HGNC HGNC:29636 YES NM_018365.4 1 P1 CCDS10158.1 ENSP00000260453 Q8NEH6.128 UPI0000070061 1 7 NA NA PASS SITE 0,30|0,14 NA NA 1 40 39,36 230,227 60,60 15 1.19 NA 4.21 NA FALSE 6.00 51 NA NA NA FALSE NA NA 45.11 7 56464272 HCC1395_HCC1395T 16 0.471 30 3,3 12,10 16,14 NA 0/1 NA NA NA NA 0,16,0,14 G/T PANCANCER NA FALSE MNS1 chr15:56464272:56464273:G:T SNV 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 58173042 58173043 C T 6 349 0.0171919770773639 MODIFIER AQP9 ENSG00000103569 T intron_variant Transcript ENST00000219919 protein_coding 2/5 ENST00000219919.9:c.239-26C>T NA 1 SNV HGNC HGNC:643 YES NM_020980.5 1 P1 CCDS10165.1 ENSP00000219919 O43315.183 UPI000013C796 7 NA NA PASS SITE 307,233|2,4 NA NA 1 93 20,20 156,171 60,60 42 2.09 NA 36.98 NA FALSE 6.00 26 NA NA NA FALSE NA NA 8.23 7 58173042 HCC1395_HCC1395T 343 0.021 349 93,2 121,2 226,4 NA 0/1 NA NA NA NA 198,145,2,4 C/T PANCANCER NA FALSE AQP9 chr15:58173042:58173043:C:T SNV 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 58691359 58691360 ATATATATTACCTCGAAGCCCTTCTTCCACT A 152 383 0.39686684073107 MODIFIER ADAM10 ENSG00000137845 - intron_variant Transcript ENST00000260408 protein_coding 2/15 ENST00000260408.8:c.207-9075_207-9046del NA -1 deletion HGNC HGNC:188 YES NM_001110.4 1 P1 CCDS10167.1 ENSP00000260408 O14672.216 A0A024R5U5.68 UPI00001254C8 O14672-1 1 7 NA NA PASS SITE 249,191|94,58 NA NA 1 93 20,34 162,187 60,60 41 2.13 NA 38.88 NA FALSE 6.00 93 NA NA NA FALSE NA NA 610.38 7 58691359 HCC1395_HCC1395T 231 0.434 383 44,42 49,55 145,109 NA 0/1 NA NA NA NA 132,99,94,58 ATATATATTACCTCGAAGCCCTTCTTCCACT/A PANCANCER NA FALSE ADAM10 chr15:58691359:58691360:ATATATATTACCTCGAAGCCCTTCTTCCACT:A indel 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 59135873 59135874 G C 371 754 0.492042440318302 MODIFIER MYO1E ENSG00000157483 C 3_prime_UTR_variant Transcript ENST00000288235 protein_coding 28/28 ENST00000288235.9:c.*1507C>G NA 5205 -1 SNV HGNC HGNC:7599 YES NM_004998.4 1 P1 CCDS32254.1 ENSP00000288235 Q12965.197 Q4KMR3.151 UPI00001FE590 1 7 NA NA PASS SITE 315,412|165,206 NA NA 1 93 20,20 159,166 60,60 33 2.37 NA 69.23 NA FALSE 6.00 93 NA NA NA FALSE NA NA 970.27 7 59135873 HCC1395_HCC1395T 383 0.489 754 93,87 147,143 255,244 NA 0/1 NA NA NA NA 162,221,165,206 G/C PANCANCER NA FALSE MYO1E chr15:59135873:59135874:G:C SNV 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 62247006 62247007 C A 38 88 0.431818181818182 MODIFIER ENSG00000291297 A upstream_gene_variant Transcript ENST00000561706 lncRNA NA 3924 -1 SNV YES 3 7 NA NA PASS SITE 69,36|28,10 NA NA 1 93 20,31 176,188 60,60 29 1.64 NA 12.04 NA FALSE 6.00 93 NA NA NA FALSE NA NA 102.93 7 62247006 HCC1395_HCC1395T 50 0.456 88 17,16 16,12 36,30 NA 0/1 NA NA NA NA 33,17,28,10 C/A PANCANCER NA FALSE chr15:62247006:62247007:C:A SNV 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 62819537 62819538 G A 205 381 0.538057742782152 MODIFIER MIR190A ENSG00000211137 A upstream_gene_variant Transcript ENST00000388402 miRNA NA COSV60888713 4420 1 SNV HGNC HGNC:31560 YES 1 1 7 NA NA PASS SITE 195,180|95,110 NA NA 1 93 20,20 163,154 60,60 36 2.11 NA 37.88 NA FALSE 6.00 93 NA NA NA FALSE NA NA 502.15 7 62819537 HCC1395_HCC1395T 176 0.537 381 52,54 52,64 109,127 NA 0/1 NA NA NA NA 91,85,95,110 G/A PANCANCER NA FALSE MIR190A chr15:62819537:62819538:G:A SNV 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 65150921 65150922 GAAAAGCCATGTTTGTTTTTTTAAAATAAAAAATGGAGGTAAACATGATCTTTAAAATCA G 52 111 0.468468468468468 LOW CLPX ENSG00000166855 - splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000300107 protein_coding 13/13 ENST00000300107.7:c.1812-67_1812-9del NA -1 deletion HGNC HGNC:2088 YES NM_006660.5 1 P1 CCDS10202.1 ENSP00000300107 O76031.189 A0A024R5X7.55 UPI0000127B73 1 7 NA NA PASS SITE 29,74|8,44 NA NA 1 60 20,40 182,202 60,60 40 1.49 NA 8.12 NA FALSE 6.00 93 NA NA NA FALSE NA NA 208.71 7 65150921 HCC1395_HCC1395T 59 0.468 111 10,7 18,16 45,41 NA 0/1 NA NA NA NA 15,44,8,44 GAAAAGCCATGTTTGTTTTTTTAAAATAAAAAATGGAGGTAAACATGATCTTTAAAATCA/G PANCANCER NA FALSE CLPX chr15:65150921:65150922:GAAAAGCCATGTTTGTTTTTTTAAAATAAAAAATGGAGGTAAACATGATCTTTAAAATCA:G indel 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 67823497 67823498 C T 26 45 0.577777777777778 MODIFIER SKOR1 ENSG00000188779 T intron_variant Transcript ENST00000341418 protein_coding 2/14 ENST00000341418.10:c.271-462C>T NA 1 SNV HGNC HGNC:21326 1 ENSP00000343200 P84550.140 UPI00001987EE P84550-2 7 NA NA PASS SITE 39,27|16,10 NA NA 1 84 20,20 148,134 60,60 42 1.48 NA 8.73 NA FALSE 6.00 85 NA NA NA FALSE NA NA 63.59 7 67823497 HCC1395_HCC1395T 19 0.567 45 3,8 8,8 12,16 NA 0/1 NA NA NA NA 11,8,16,10 C/T PANCANCER NA FALSE SKOR1 chr15:67823497:67823498:C:T SNV 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 69049034 69049035 G C 47 118 0.398305084745763 MODERATE NOX5 ENSG00000255346 C missense_variant Transcript ENST00000388866 protein_coding 14/16 ENST00000388866.8:c.1975G>C ENSP00000373518.3:p.D659H ENSP00000373518.3 p.D659H 2016 1975 659 D/H Gac/Cac COSV52987537 1 SNV HGNC HGNC:14874 YES NM_024505.4 1 CCDS32276.2 ENSP00000373518 Q96PH1.166 UPI000006DDBD Q96PH1-1 deleterious(0) possibly_damaging(0.83) Gene3D:3.40.50.80&PDB-ENSP_mappings:6sz5.B&PDB-ENSP_mappings:6sz5.C&AlphaFold_DB_import:AF-Q96PH1-F1&Pfam:PF08030&PANTHER:PTHR11972&SFLD:SFLDG01168&SFLD:SFLDG01169&SFLD:SFLDS00052&Superfamily:SSF52343&CDD:cd06186 1 1 7 NA NA PASS SITE 82,88|23,24 NA NA 1 93 20,20 159,171 60,60 37 1.82 NA 18.96 NA FALSE 6.00 93 NA NA NA FALSE NA NA 114.92 7 69049034 HCC1395_HCC1395T 71 0.397 118 19,13 23,15 46,30 NA 0/1 NA NA NA NA 34,37,23,24 G/C PANCANCER NA FALSE NOX5_p.D659H chr15:69049034:69049035:G:C SNV 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 70060783 70060784 G T 45 95 0.473684210526316 MODIFIER TLE3 ENSG00000140332 T intron_variant Transcript ENST00000317509 protein_coding 8/19 ENST00000317509.12:c.595-134C>A NA -1 SNV HGNC HGNC:11839 1 A1 CCDS58375.1 ENSP00000319233 Q04726.215 UPI000002B569 Q04726-2 7 NA NA PASS SITE 38,91|9,36 NA NA 1 93 20,34 179,179 60,60 26 1.75 NA 16.51 NA FALSE 6.00 93 NA NA NA FALSE NA NA 132.08 7 70060783 HCC1395_HCC1395T 50 0.493 95 14,14 22,13 38,37 NA 0/1 NA NA NA NA 14,36,9,36 G/T PANCANCER NA FALSE TLE3 chr15:70060783:70060784:G:T SNV 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 70895626 70895627 C G 24 53 0.452830188679245 MODIFIER THAP10 ENSG00000129028 G upstream_gene_variant Transcript ENST00000249861 protein_coding NA 3193 -1 SNV HGNC HGNC:23193 YES NM_020147.4 1 P1 CCDS10237.1 ENSP00000249861 Q9P2Z0.142 UPI0000071917 7 NA NA PASS SITE 28,31|13,11 NA NA 1 52 20,20 167,155 60,60 41 1.28 NA 5.42 NA FALSE 6.00 63 NA NA NA FALSE NA NA 57.52 7 70895626 HCC1395_HCC1395T 29 0.444 53 3,4 15,10 19,15 NA 0/1 NA NA NA NA 14,15,13,11 C/G PANCANCER NA FALSE THAP10 chr15:70895626:70895627:C:G SNV 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 71824289 71824290 T C 101 732 0.137978142076503 MODIFIER MYO9A ENSG00000066933 C 3_prime_UTR_variant Transcript ENST00000356056 protein_coding 42/42 ENST00000356056.10:c.*2291A>G NA 10480 rs1377287632 -1 SNV HGNC HGNC:7608 YES NM_006901.4 1 P2 CCDS10239.1 ENSP00000348349 B2RTY4.131 UPI000013D213 B2RTY4-1 1 6.571e-06 0 0 0 0 0 0 0 1.47e-05 0 0 1.47e-05 gnomADg_NFE 7 NA NA PASS SITE 567,431|61,40 NA NA 1 93 20,20 167,173 60,60 34 2.39 NA 71.59 NA FALSE 6.00 93 NA NA NA FALSE NA NA 221.06 7 71824289 HCC1395_HCC1395T 631 0.141 732 144,26 262,41 419,69 NA 0/1 NA NA NA NA 365,266,61,40 T/C PANCANCER NA FALSE MYO9A chr15:71824289:71824290:T:C SNV 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 73888523 73888524 C T 15 46 0.326086956521739 MODIFIER TBC1D21 ENSG00000167139 T intron_variant Transcript ENST00000300504 protein_coding 10/10 ENST00000300504.7:c.978+10C>T NA 1 SNV HGNC HGNC:28536 YES NM_153356.3 1 P1 CCDS10252.1 ENSP00000300504 Q8IYX1.131 UPI00000741CB Q8IYX1-1 7 NA NA PASS SITE 31,40|8,7 NA NA 1 84 20,20 164,177 60,60 38 1.43 NA 7.82 NA FALSE 6.00 47 NA NA NA FALSE NA NA 33.77 7 73888523 HCC1395_HCC1395T 31 0.338 46 7,3 12,6 20,10 NA 0/1 NA NA NA NA 13,18,8,7 C/T PANCANCER NA FALSE TBC1D21 chr15:73888523:73888524:C:T SNV 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 74280669 74280670 G T 53 89 0.595505617977528 MODERATE CCDC33 ENSG00000140481 T missense_variant&splice_region_variant Transcript ENST00000398814 protein_coding 9/19 ENST00000398814.8:c.891G>T ENSP00000381795.3:p.M297I ENSP00000381795.3 p.M297I 1285 891 297 M/I atG/atT 1 SNV HGNC HGNC:26552 YES NM_025055.5 2 P2 CCDS42058.1 ENSP00000381795 Q8N5R6.139 UPI0000E671FE Q8N5R6-6 deleterious(0) benign(0.11) AlphaFold_DB_import:AF-Q8N5R6-F1&PANTHER:PTHR21623 7 NA NA PASS SITE 70,57|35,18 NA NA 1 93 20,20 152,184 60,60 34 1.76 NA 16.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 149.40 7 74280669 HCC1395_HCC1395T 36 0.609 89 5,17 18,21 24,38 NA 0/1 NA NA NA NA 19,17,35,18 G/T PANCANCER NA FALSE CCDC33_p.M297I chr15:74280669:74280670:G:T SNV 2:2 chr15:55614284:77634194:2:2:1 FALSE NA 0.96 +chr15 78131522 78131523 C T 5 23 0.217391304347826 MODIFIER CIB2 ENSG00000136425 T upstream_gene_variant Transcript ENST00000258930 protein_coding NA 77 -1 SNV HGNC HGNC:24579 YES NM_006383.4 1 P1 CCDS10296.1 ENSP00000258930 O75838.173 UPI000000DBE0 O75838-1 1 7 NA NA PASS SITE 17,29|2,3 NA NA 1 55 20,38 152,189 60,60 45 1.30 NA 5.72 NA FALSE 6.00 26 NA NA NA FALSE NA NA 13.30 7 78131522 HCC1395_HCC1395T 18 0.263 23 4,1 6,3 13,4 NA 0/1 NA NA NA NA 8,10,2,3 C/T PANCANCER NA FALSE CIB2 chr15:78131522:78131523:C:T SNV 2:1 chr15:77690778:82659790:2:1:1 TRUE NA 0.96 +chr15 78475939 78475940 T A 146 662 0.220543806646526 MODIFIER IREB2 ENSG00000136381 A intron_variant Transcript ENST00000258886 protein_coding 8/21 ENST00000258886.13:c.1024-249T>A NA 1 SNV HGNC HGNC:6115 YES NM_004136.4 1 P1 CCDS10302.1 ENSP00000258886 P48200.190 UPI0004620DD2 P48200-1 1 7 NA NA PASS SITE 551,438|81,65 NA NA 1 93 20,20 158,163 60,60 29 2.48 NA 89.60 NA FALSE 6.00 93 NA NA NA FALSE NA NA 341.22 7 78475939 HCC1395_HCC1395T 516 0.229 662 119,36 202,61 332,98 NA 0/1 NA NA NA NA 294,222,81,65 T/A PANCANCER NA FALSE IREB2 chr15:78475939:78475940:T:A SNV 2:1 chr15:77690778:82659790:2:1:1 TRUE NA 0.96 +chr15 78999882 78999883 G A 24 138 0.173913043478261 LOW RASGRF1 ENSG00000058335 A synonymous_variant Transcript ENST00000394745 protein_coding 4/14 ENST00000394745.3:c.303C>T ENSP00000378228.3:p.V101= ENSP00000378228.3 p.V101= 1481 303 101 V gtC/gtT rs766127449 -1 SNV HGNC HGNC:9875 1 CCDS42065.1 ENSP00000378228 Q13972.205 UPI000002F89F Q13972-2 PANTHER:PTHR23113&SMART:SM00229&AlphaFold_DB_import:AF-Q13972-F1 2.386e-05 0 2.892e-05 0 0 0 8.791e-06 0 0.0001307 2.628e-05 0 0 0 0 0 0 0 1.47e-05 0 0.0006214 0.0006214 gnomADg_SAS 7 NA NA PASS SITE 135,130|11,13 NA NA 1 93 20,20 162,164 60,60 37 1.99 NA 28.89 NA FALSE 6.00 48 NA NA NA FALSE NA NA 54.24 7 78999882 HCC1395_HCC1395T 114 0.181 138 33,5 40,10 76,16 NA 0/1 NA NA NA NA 60,54,11,13 G/A PANCANCER NA FALSE RASGRF1_p.V101= chr15:78999882:78999883:G:A SNV 2:1 chr15:77690778:82659790:2:1:1 TRUE NA 0.96 +chr15 80120246 80120247 T C 36 179 0.201117318435754 MODIFIER ZFAND6 ENSG00000086666 C intron_variant Transcript ENST00000261749 protein_coding 2/6 ENST00000261749.11:c.-17-82T>C NA 1 SNV HGNC HGNC:30164 YES NM_019006.4 1 P1 CCDS10313.1 ENSP00000261749 Q6FIF0.143 UPI0000073A48 Q6FIF0-1 7 NA NA PASS SITE 163,126|26,10 NA NA 1 93 20,25 185,173 60,60 31 2.03 NA 31.25 NA FALSE 6.00 93 NA NA NA FALSE NA NA 89.53 7 80120246 HCC1395_HCC1395T 143 0.213 179 39,13 61,15 106,28 NA 0/1 NA NA NA NA 83,60,26,10 T/C PANCANCER NA FALSE ZFAND6 chr15:80120246:80120247:T:C SNV 2:1 chr15:77690778:82659790:2:1:1 TRUE NA 0.96 +chr15 84036951 84036952 A T 79 301 0.262458471760797 MODERATE ADAMTSL3 ENSG00000156218 T missense_variant Transcript ENST00000286744 protein_coding 29/30 ENST00000286744.10:c.4933A>T ENSP00000286744.5:p.I1645F ENSP00000286744.5 p.I1645F 5120 4933 1645 I/F Att/Ttt COSV54473043&COSV54475588 1 SNV HGNC HGNC:14633 YES NM_207517.3 1 P1 CCDS10326.1 ENSP00000286744 P82987.144 UPI00001615A5 P82987-1 tolerated(0.05) benign(0) Pfam:PF19030&Gene3D:2.20.100.10&Superfamily:SSF82895&AlphaFold_DB_import:AF-P82987-F1 1&1 1&1 7 NA NA PASS SITE 179,233|33,47 NA NA 1 93 20,20 161,161 60,60 32 -7.728e-02 NA 33.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 177.90 7 84036951 HCC1395_HCC1395T 222 0.267 301 51,15 78,34 144,52 NA 0/1 NA NA NA NA 100,122,33,46 A/T PANCANCER NA FALSE ADAMTSL3_p.I1645F chr15:84036951:84036952:A:T SNV 3:1 chr15:82687507:92165073:3:1:1 NA NA 0.96 +chr15 89196959 89196960 TACTTTAAA T 164 605 0.271074380165289 MODIFIER ABHD2 ENSG00000140526 - 3_prime_UTR_variant Transcript ENST00000352732 protein_coding 11/11 ENST00000352732.10:c.*1538_*1545del NA 3029-3036 1 deletion HGNC HGNC:18717 YES NM_152924.5 1 P1 CCDS10348.1 ENSP00000268129 P08910.178 A0A024RC89.55 UPI000012E24E 1 7 NA NA PASS SITE 392,424|72,92 NA NA 1 93 20,20 165,177 60,60 38 2.40 NA 72.72 NA FALSE 6.00 93 NA NA NA FALSE NA NA 637.73 7 89196959 HCC1395_HCC1395T 441 0.274 605 110,32 119,50 287,107 NA 0/1 NA NA NA NA 210,231,72,92 TACTTTAAA/T PANCANCER NA FALSE ABHD2 chr15:89196959:89196960:TACTTTAAA:T indel 3:1 chr15:82687507:92165073:3:1:1 NA NA 0.96 +chr15 89305954 89305955 C G 6 33 0.181818181818182 MODIFIER FANCI ENSG00000140525 G intron_variant Transcript ENST00000300027 protein_coding 30/36 ENST00000300027.12:c.3170-53C>G NA 1 SNV HGNC HGNC:25568 5 CCDS10349.2 ENSP00000300027 Q9NVI1.168 UPI0000603C25 Q9NVI1-1 1 7 NA NA PASS SITE 35,15|5,1 NA NA 1 54 36,39 173,191 60,60 25 1.33 NA 5.97 NA FALSE 6.00 34 NA NA NA FALSE NA NA 16.45 7 89305954 HCC1395_HCC1395T 27 0.214 33 3,1 18,4 21,5 NA 0/1 NA NA NA NA 17,10,5,1 C/G PANCANCER NA FALSE FANCI chr15:89305954:89305955:C:G SNV 3:1 chr15:82687507:92165073:3:1:1 NA NA 0.96 +chr15 89671702 89671703 C A 12 54 0.222222222222222 MODIFIER PLIN1 ENSG00000166819 A intron_variant Transcript ENST00000300055 protein_coding 3/8 ENST00000300055.10:c.251-138G>T NA -1 SNV HGNC HGNC:9076 YES NM_002666.5 1 P1 CCDS10353.1 ENSP00000300055 O60240.173 UPI000013E61C 1 7 NA NA PASS SITE 33,55|3,9 NA NA 1 93 32,26 173,198 60,60 25 1.56 NA 10.53 NA FALSE 6.00 31 NA NA NA FALSE NA NA 27.90 7 89671702 HCC1395_HCC1395T 42 0.232 54 5,3 25,5 32,9 NA 0/1 NA NA NA NA 16,26,3,9 C/A PANCANCER NA FALSE PLIN1 chr15:89671702:89671703:C:A SNV 3:1 chr15:82687507:92165073:3:1:1 NA NA 0.96 +chr15 92466729 92466730 C T 26 165 0.157575757575758 MODIFIER ST8SIA2 ENSG00000140557 T 3_prime_UTR_variant Transcript ENST00000268164 protein_coding 6/6 ENST00000268164.8:c.*2344C>T NA 3656 rs1414799597 1 SNV HGNC HGNC:10870 YES NM_006011.4 1 P1 CCDS10372.1 ENSP00000268164 Q92186.172 B2R9U8.113 UPI0000135970 6.571e-06 2.413e-05 0 0 0 0 0 0 0 0 0 2.413e-05 gnomADg_AFR 7 NA NA PASS SITE 105,115|13,13 NA NA 1 93 20,20 162,158 60,60 40 1.73 NA 15.95 NA FALSE 4.61 65 NA NA NA FALSE NA NA 49.83 7 92466729 HCC1395_HCC1395T 139 0.147 165 38,8 46,6 95,16 NA 0/1 NA NA NA NA 64,75,13,13 C/T PANCANCER NA FALSE ST8SIA2 chr15:92466729:92466730:C:T SNV 4:1 chr15:92165320:101684138:4:1:1 NA NA 0.96 +chr15 94399983 94399984 G T 31 200 0.155 MODERATE MCTP2 ENSG00000140563 T missense_variant Transcript ENST00000357742 protein_coding 16/23 ENST00000357742.10:c.1953G>T ENSP00000350377.4:p.K651N ENSP00000350377.4 p.K651N 2122 1953 651 K/N aaG/aaT COSV59145329 1 SNV HGNC HGNC:25636 YES NM_001385001.1 1 P1 CCDS32338.1 ENSP00000350377 Q6DN12.140 UPI0000D613A2 Q6DN12-1 1 deleterious(0) AlphaFold_DB_import:AF-Q6DN12-F1&PANTHER:PTHR45911 1 1 7 NA NA PASS SITE 110,183|13,18 NA NA 1 93 20,20 165,145 60,60 25 1.92 NA 24.64 NA FALSE 6.00 70 NA NA NA FALSE NA NA 63.44 7 94399983 HCC1395_HCC1395T 169 0.153 200 43,10 63,9 115,20 NA 0/1 NA NA NA NA 61,108,13,18 G/T PANCANCER NA FALSE MCTP2_p.K651N chr15:94399983:94399984:G:T SNV 4:1 chr15:92165320:101684138:4:1:1 NA NA 0.96 +chr15 100580747 100580748 G C 197 334 0.589820359281437 LOW LINS1 ENSG00000140471 C synonymous_variant Transcript ENST00000314742 protein_coding 2/7 ENST00000314742.13:c.96C>G ENSP00000318423.8:p.L32= ENSP00000318423.8 p.L32= 263 96 32 L ctC/ctG COSV100130617&COSV104633298 -1 SNV HGNC HGNC:30922 YES NM_001040616.3 5 P1 CCDS10385.1 ENSP00000318423 Q8NG48.127 UPI000013D795 Q8NG48-1 1 PANTHER:PTHR16057&AlphaFold_DB_import:AF-Q8NG48-F1 1&1 1&1 7 NA NA PASS SITE 171,167|99,98 NA NA 1 93 20,20 154,162 60,60 33 2.11 NA 37.88 NA FALSE 6.00 93 NA NA NA FALSE NA NA 526.60 7 100580747 HCC1395_HCC1395T 137 0.585 334 34,43 55,77 92,130 NA 0/1 NA NA NA NA 68,69,99,98 G/C PANCANCER NA FALSE LINS1_p.L32= chr15:100580747:100580748:G:C SNV 4:1 chr15:92165320:101684138:4:1:1 NA NA 0.96 +chr15 100900577 100900578 G T 43 102 0.42156862745098 MODERATE ALDH1A3 ENSG00000184254 T missense_variant&splice_region_variant Transcript ENST00000329841 protein_coding 9/13 ENST00000329841.10:c.886G>T ENSP00000332256.5:p.D296Y ENSP00000332256.5 p.D296Y 963 886 296 D/Y Gac/Tac 1 SNV HGNC HGNC:409 YES NM_000693.4 1 P1 CCDS10389.1 ENSP00000332256 P47895.192 A0A024RC95.64 UPI00001AFAF8 1 deleterious_low_confidence(0) possibly_damaging(0.523) PDB-ENSP_mappings:5fhz.A&PDB-ENSP_mappings:5fhz.B&PDB-ENSP_mappings:5fhz.C&PDB-ENSP_mappings:5fhz.D&PDB-ENSP_mappings:5fhz.E&PDB-ENSP_mappings:5fhz.F&PDB-ENSP_mappings:5fhz.G&PDB-ENSP_mappings:5fhz.H&PDB-ENSP_mappings:6s6w.A&PDB-ENSP_mappings:6s6w.B&PDB-ENSP_mappings:6te5.A&PDB-ENSP_mappings:6te5.B&PDB-ENSP_mappings:6tgw.A&PDB-ENSP_mappings:6tgw.B&PDB-ENSP_mappings:6tgw.C&PDB-ENSP_mappings:6tgw.D&PDB-ENSP_mappings:6try.A&PDB-ENSP_mappings:6try.B&PDB-ENSP_mappings:7a6q.A&PDB-ENSP_mappings:7a6q.B&PDB-ENSP_mappings:7qk7.A&PDB-ENSP_mappings:7qk7.B&PDB-ENSP_mappings:7qk8.A&PDB-ENSP_mappings:7qk8.B&PDB-ENSP_mappings:7qk9.A&PDB-ENSP_mappings:7qk9.B&CDD:cd07141&PANTHER:PTHR11699&Gene3D:3.40.309.10&Pfam:PF00171&Gene3D:3.40.605.10&Superfamily:SSF53720&AlphaFold_DB_import:AF-P47895-F1 7 NA NA PASS SITE 65,58|23,20 NA NA 1 93 20,20 167,175 60,60 26 1.67 NA 13.54 NA FALSE 6.00 93 NA NA NA FALSE NA NA 108.68 7 100900577 HCC1395_HCC1395T 59 0.424 102 24,14 15,18 44,32 NA 0/1 NA NA NA NA 33,26,23,20 G/T PANCANCER NA FALSE ALDH1A3_p.D296Y chr15:100900577:100900578:G:T SNV 4:1 chr15:92165320:101684138:4:1:1 NA NA 0.96 +chr15 101653790 101653791 C G 113 516 0.218992248062016 MODIFIER TM2D3 ENSG00000184277 G upstream_gene_variant Transcript ENST00000333202 protein_coding NA rs914555452 1409 -1 SNV HGNC HGNC:24128 YES NM_078474.3 1 A1 CCDS10393.1 ENSP00000330433 Q9BRN9.126 UPI00001B02BE Q9BRN9-1 7 NA NA PASS SITE 389,278|66,47 NA NA 1 93 20,20 175,175 60,60 33 2.26 NA 53.58 NA FALSE 6.00 93 NA NA NA FALSE NA NA 274.20 7 101653790 HCC1395_HCC1395T 403 0.209 516 106,24 186,53 296,78 NA 0/1 NA NA NA NA 247,156,66,47 C/G PANCANCER NA FALSE TM2D3 chr15:101653790:101653791:C:G SNV 4:1 chr15:92165320:101684138:4:1:1 NA NA 0.96 +chr16 79675 79676 C A 21 102 0.205882352941176 MODERATE MPG ENSG00000103152 A missense_variant Transcript ENST00000219431 protein_coding 3/5 ENST00000219431.4:c.290C>A ENSP00000219431.4:p.P97H ENSP00000219431.4 p.P97H 521 290 97 P/H cCc/cAc 1 SNV HGNC HGNC:7211 3 A2 CCDS32346.1 ENSP00000219431 P29372.226 Q1W6H1.136 UPI000002A2C0 P29372-1 tolerated(0.11) benign(0.005) PDB-ENSP_mappings:1bnk.A&PDB-ENSP_mappings:1ewn.A&PDB-ENSP_mappings:1f4r.A&PDB-ENSP_mappings:1f6o.A&Gene3D:3.10.300.10&PDB-ENSP_mappings:3qi5.A&PDB-ENSP_mappings:3qi5.B&PDB-ENSP_mappings:3uby.A&PDB-ENSP_mappings:3uby.B&AlphaFold_DB_import:AF-P29372-F1&HAMAP:MF_00527&Pfam:PF02245&PANTHER:PTHR10429&Superfamily:SSF50486&TIGRFAM:TIGR00567&CDD:cd00540 8 NA NA PASS SITE 66,90|10,11 NA NA 1 93 20,20 162,166 60,60 27 1.70 NA 14.75 NA FALSE 6.00 47 NA NA NA FALSE NA NA 46.71 8 79675 HCC1395_HCC1395T 81 0.206 102 21,5 31,9 57,14 NA 0/1 NA NA NA NA 37,44,10,11 C/A PANCANCER NA FALSE MPG_p.P97H chr16:79675:79676:C:A SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 634075 634076 G A 68 205 0.331707317073171 MODIFIER RAB40C ENSG00000197562 A downstream_gene_variant Transcript ENST00000248139 protein_coding NA rs755549268 4807 1 SNV HGNC HGNC:18285 YES NM_021168.5 1 P1 CCDS10413.1 ENSP00000248139 Q96S21.185 UPI0000133002 Q96S21-1 2.476e-05 0 0 0 0 0 0 0.0002463 0.0001646 3.942e-05 0 0 0 0 0 0 0 0 0 0.001241 0.001241 gnomADg_SAS 8 NA NA PASS SITE 150,166|29,39 NA NA 1 93 20,20 165,179 60,60 31 2.09 NA 35.77 NA FALSE 6.00 87 NA NA NA FALSE NA NA 170.89 8 634075 HCC1395_HCC1395T 137 0.355 205 34,15 49,27 88,48 NA 0/1 NA NA NA NA 70,67,29,39 G/A PANCANCER NA FALSE RAB40C chr16:634075:634076:G:A SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 1320437 1320438 G C 176 273 0.644688644688645 HIGH UBE2I ENSG00000103275 C splice_acceptor_variant Transcript ENST00000325437 protein_coding 5/6 ENST00000325437.9:c.334-1G>C NA COSV57648832 1 SNV HGNC HGNC:12485 3 P1 CCDS10433.1 ENSP00000324897 P63279.196 UPI00000010F8 1 1 8 NA NA PASS SITE 184,107|113,63 NA NA 1 93 20,20 156,175 60,60 30 2.15 NA 41.14 NA FALSE 6.00 93 NA NA NA FALSE NA NA 515.57 8 1320437 HCC1395_HCC1395T 97 0.657 273 29,46 35,76 66,127 NA 0/1 NA NA NA NA 58,39,113,63 G/C PANCANCER NA FALSE UBE2I chr16:1320437:1320438:G:C SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 2175291 2175292 C T 15 35 0.428571428571429 LOW TRAF7 ENSG00000131653 T splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000326181 protein_coding 15/20 ENST00000326181.11:c.1387-10C>T NA rs774614180&COSV58219666 1 SNV HGNC HGNC:20456 YES NM_032271.3 1 P1 CCDS10461.1 ENSP00000318944 Q6Q0C0.183 UPI000014186F Q6Q0C0-1 1 3.987e-06 0 0 0 0 0 0 0 3.267e-05 3.267e-05 gnomADe_SAS 0&1 0&1 8 NA NA PASS SITE 33,21|11,4 NA NA 1 77 28,36 154,138 60,60 18 1.43 NA 7.51 NA FALSE 6.00 81 NA NA NA FALSE NA NA 40.76 8 2175291 HCC1395_HCC1395T 20 0.436 35 9,6 6,6 16,12 NA 0/1 NA NA NA NA 13,7,11,4 C/T PANCANCER NA FALSE TRAF7 chr16:2175291:2175292:C:T SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 2295601 2295602 C G 236 450 0.524444444444444 MODERATE ABCA3 ENSG00000167972 G missense_variant Transcript ENST00000301732 protein_coding 18/33 ENST00000301732.10:c.2403G>C ENSP00000301732.5:p.E801D ENSP00000301732.5 p.E801D 3097 2403 801 E/D gaG/gaC COSV57050107&COSV57060020&COSV57061484 -1 SNV HGNC HGNC:33 YES NM_001089.3 1 P1 CCDS10466.1 ENSP00000301732 Q99758.187 UPI0000001232 Q99758-1 1 tolerated(0.06) benign(0.094) PDB-ENSP_mappings:7w01.A&PDB-ENSP_mappings:7w02.A&AlphaFold_DB_import:AF-Q99758-F1 1&1&1 1&1&1 8 NA NA PASS SITE 371,265|143,93 NA NA 1 93 20,20 155,150 60,60 32 2.44 NA 81.48 NA FALSE 6.00 93 NA NA NA FALSE NA NA 636.22 8 2295601 HCC1395_HCC1395T 214 0.540 450 62,70 66,84 133,156 NA 0/1 NA NA NA NA 126,88,143,93 C/G PANCANCER NA FALSE ABCA3_p.E801D chr16:2295601:2295602:C:G SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 2762718 2762719 G C 22 181 0.121546961325967 LOW SRRM2 ENSG00000167978 C synonymous_variant Transcript ENST00000301740 protein_coding 11/15 ENST00000301740.13:c.2190G>C ENSP00000301740.8:p.R730= ENSP00000301740.8 p.R730= 2430 2190 730 R cgG/cgC COSV57072155 1 SNV HGNC HGNC:16639 YES NM_016333.4 1 P1 CCDS32373.1 ENSP00000301740 Q9UQ35.183 A0A140VK53.32 UPI000049DDFC Q9UQ35-1 1 PDB-ENSP_mappings:5mqf.S&PDB-ENSP_mappings:5xjc.U&PDB-ENSP_mappings:5yzg.U&PDB-ENSP_mappings:5z56.U&PDB-ENSP_mappings:5z57.U&PDB-ENSP_mappings:6ff4.S&PDB-ENSP_mappings:6ff7.S&PDB-ENSP_mappings:6icz.U&PDB-ENSP_mappings:6zym.S&PDB-ENSP_mappings:7a5p.S&PDB-ENSP_mappings:7dvq.U&PDB-ENSP_mappings:7w59.U&PDB-ENSP_mappings:7w5a.U&PDB-ENSP_mappings:7w5b.U&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg 1 1 8 NA NA PASS SITE 176,129|13,9 NA NA 1 93 20,37 163,185 60,60 22 2.00 NA 29.79 NA FALSE 6.00 72 NA NA NA FALSE NA NA 55.97 8 2762718 HCC1395_HCC1395T 159 0.135 181 44,9 63,6 108,16 NA 0/1 NA NA NA NA 95,64,13,9 G/C PANCANCER NA FALSE SRRM2_p.R730= chr16:2762718:2762719:G:C SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 2820901 2820902 C T 60 163 0.368098159509202 MODIFIER PRSS21 ENSG00000007038 T intron_variant Transcript ENST00000005995 protein_coding 4/5 ENST00000005995.8:c.551-54C>T NA 1 SNV HGNC HGNC:9485 YES NM_006799.4 1 P1 CCDS10478.1 ENSP00000005995 Q9Y6M0.183 UPI000004813E Q9Y6M0-1 8 NA NA PASS SITE 181,59|49,11 NA NA 1 93 35,37 177,186 60,60 26 2.03 NA 31.30 NA FALSE 6.00 84 NA NA NA FALSE NA NA 175.53 8 2820901 HCC1395_HCC1395T 103 0.384 163 37,14 43,35 82,51 NA 0/1 NA NA NA NA 81,22,49,11 C/T PANCANCER NA FALSE PRSS21 chr16:2820901:2820902:C:T SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 3204225 3204226 C G 54 92 0.58695652173913 LOW OR1F1 ENSG00000168124 G splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000304646 protein_coding 3/3 ENST00000304646.3:c.-12-10C>G NA rs1045433609 1 SNV HGNC HGNC:8194 YES P1 CCDS10496.1 ENSP00000305424 O43749.180 UPI00000015B4 8 NA NA PASS SITE 87,67|27,27 NA NA 1 93 20,20 157,161 60,60 40 1.86 NA 21.67 NA FALSE 6.00 85 NA NA NA FALSE NA NA 133.02 8 3204225 HCC1395_HCC1395T 38 0.585 92 9,8 14,20 23,33 NA 0/1 NA NA NA NA 21,17,27,27 C/G PANCANCER NA FALSE OR1F1 chr16:3204225:3204226:C:G SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 3751904 3751905 G A 17 81 0.209876543209877 MODIFIER CREBBP ENSG00000005339 A intron_variant Transcript ENST00000262367 protein_coding 19/30 ENST00000262367.10:c.3699-98C>T NA -1 SNV HGNC HGNC:2348 YES NM_004380.3 1 P1 CCDS10509.1 ENSP00000262367 Q92793.254 UPI0000000620 Q92793-1 1 8 NA NA PASS SITE 53,74|8,9 NA NA 1 93 20,20 169,162 60,60 31 1.65 NA 12.94 NA FALSE 6.00 36 NA NA NA FALSE NA NA 40.60 8 3751904 HCC1395_HCC1395T 64 0.236 81 16,3 20,7 41,12 NA 0/1 NA NA NA NA 29,35,8,9 G/A PANCANCER TRUE FALSE CREBBP chr16:3751904:3751905:G:A SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 3792126 3792127 T A 46 105 0.438095238095238 MODIFIER CREBBP ENSG00000005339 A intron_variant Transcript ENST00000262367 protein_coding 4/30 ENST00000262367.10:c.1217-32A>T NA -1 SNV HGNC HGNC:2348 YES NM_004380.3 1 P1 CCDS10509.1 ENSP00000262367 Q92793.254 UPI0000000620 Q92793-1 1 8 NA NA PASS SITE 43,102|14,32 NA NA 1 93 35,34 175,176 60,60 23 1.82 NA 19.26 NA FALSE 6.00 93 NA NA NA FALSE NA NA 124.53 8 3792126 HCC1395_HCC1395T 59 0.429 105 17,15 21,13 47,35 NA 0/1 NA NA NA NA 14,45,14,32 T/A PANCANCER TRUE FALSE CREBBP chr16:3792126:3792127:T:A SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 4114370 4114371 A G 10 542 0.018450184501845 MODERATE ADCY9 ENSG00000162104 G missense_variant Transcript ENST00000294016 protein_coding 2/11 ENST00000294016.8:c.1073T>C ENSP00000294016.3:p.V358A ENSP00000294016.3 p.V358A 1869 1073 358 V/A gTc/gCc -1 SNV HGNC HGNC:240 YES NM_001116.4 1 P1 CCDS32382.1 ENSP00000294016 O60503.189 UPI000012887F tolerated(0.82) benign(0.005) Gene3D:3.30.70.1230&AlphaFold_DB_import:AF-O60503-F1&PANTHER:PTHR45627&SMART:SM00044&MobiDB_lite:mobidb-lite 8 NA NA PASS SITE 476,415|4,6 NA NA 1 93 20,20 158,160 60,60 24 2.37 NA 68.49 NA FALSE 6.00 14 NA NA NA FALSE NA NA 15.93 8 4114370 HCC1395_HCC1395T 532 0.022 542 110,2 216,5 346,7 NA 0/1 NA NA NA NA 279,253,4,6 A/G PANCANCER NA FALSE ADCY9_p.V358A chr16:4114370:4114371:A:G SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 4416467 4416468 G C 7 401 0.0174563591022444 MODERATE CORO7 ENSG00000262246 C missense_variant Transcript ENST00000251166 protein_coding 1/28 ENST00000251166.9:c.52C>G ENSP00000251166.4:p.R18G ENSP00000251166.4 p.R18G 130 52 18 R/G Cgc/Ggc rs749326506 -1 SNV HGNC HGNC:26161 YES NM_024535.5 1 P1 CCDS10513.1 ENSP00000251166 P57737.179 UPI00001FF898 P57737-1 deleterious(0.02) benign(0.158) Gene3D:2.130.10.10&AlphaFold_DB_import:AF-P57737-F1&Pfam:PF08953&PANTHER:PTHR10856&SMART:SM01166 1.009e-05 0 0 0 0 0 0 0 7.528e-05 7.528e-05 gnomADe_SAS 8 NA NA PASS SITE 487,351|5,2 NA NA 1 93 20,33 157,206 60,60 20 2.48 NA 86.60 NA FALSE 6.00 47 NA NA NA FALSE NA NA 10.97 8 4416467 HCC1395_HCC1395T 394 0.027 401 107,3 131,2 249,6 NA 0/1 NA NA NA NA 232,162,5,2 G/C PANCANCER NA FALSE CORO7_p.R18G chr16:4416467:4416468:G:C SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 4454855 4454856 G T 74 111 0.666666666666667 HIGH DNAJA3 ENSG00000103423 T stop_gained Transcript ENST00000262375 protein_coding 11/12 ENST00000262375.11:c.1384G>T ENSP00000262375.4:p.E462* ENSP00000262375.4 p.E462* 1398 1384 462 E/* Gag/Tag COSV52164764 1 SNV HGNC HGNC:11808 YES NM_005147.6 1 P3 CCDS10515.1 ENSP00000262375 Q96EY1.201 Q53G26.156 UPI0000043C38 Q96EY1-1 HAMAP:MF_01152&PANTHER:PTHR44145&MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-Q96EY1-F1 1 1 8 NA NA PASS SITE 86,54|48,26 NA NA 1 93 20,20 163,170 60,60 34 1.84 NA 20.17 NA FALSE 6.00 93 NA NA NA FALSE NA NA 208.04 8 4454855 HCC1395_HCC1395T 37 0.665 111 11,21 14,31 26,52 NA 0/1 NA NA NA NA 25,12,48,26 G/T PANCANCER NA FALSE DNAJA3_p.E462* chr16:4454855:4454856:G:T SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 4578850 4578851 G C 5 14 0.357142857142857 MODIFIER C16orf96 ENSG00000205832 C intron_variant Transcript ENST00000444310 protein_coding 5/15 ENST00000444310.5:c.2156-90G>C NA 1 SNV HGNC HGNC:40031 YES NM_001145011.2 5 P1 CCDS53986.1 ENSP00000415027 A6NNT2.88 UPI0001929538 8 NA NA PASS SITE 17,0|5,0 NA NA 1 25 40,37 205,198 60,60 11 0.954 NA 2.41 NA FALSE 6.00 64 NA NA NA FALSE NA NA 16.31 8 4578850 HCC1395_HCC1395T 9 0.375 14 5,2 4,3 9,5 NA 0/1 NA NA NA NA 9,0,5,0 G/C PANCANCER NA FALSE C16orf96 chr16:4578850:4578851:G:C SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 4767171 4767172 G A 60 201 0.298507462686567 MODIFIER ZNF500 ENSG00000103199 A upstream_gene_variant Transcript ENST00000219478 protein_coding NA rs542541514 9 -1 SNV HGNC HGNC:23716 YES NM_021646.4 2 P1 CCDS32383.1 ENSP00000219478 O60304.184 UPI00001C1FB0 O60304-1 3.941e-05 0 0 0.0003926 0 0 0 0 0 0 0 0.0003926 gnomADg_AMR 8 NA NA PASS SITE 190,179|28,32 NA NA 1 93 20,20 150,156 60,60 35 2.15 NA 42.14 NA FALSE 6.00 93 NA NA NA FALSE NA NA 141.26 8 4767171 HCC1395_HCC1395T 141 0.306 201 33,22 57,17 92,40 NA 0/1 NA NA NA NA 77,64,28,32 G/A PANCANCER NA FALSE ZNF500 chr16:4767171:4767172:G:A SNV 2:1 chr16:47354:9822347:2:1:1 TRUE NA 0.96 +chr16 11548047 11548048 G T 12 903 0.0132890365448505 MODIFIER LITAF ENSG00000189067 T 3_prime_UTR_variant Transcript ENST00000339430 protein_coding 4/4 ENST00000339430.9:c.*1590C>A NA 2309 -1 SNV HGNC HGNC:16841 1 P1 CCDS32386.1 ENSP00000340118 Q99732.192 UPI000007094D Q99732-1 1 8 NA NA PASS SITE 707,609|9,3 NA NA 1 93 20,27 165,176 60,60 24 2.46 NA 84.49 NA FALSE 6.00 37 NA NA NA FALSE NA NA 16.84 8 11548047 HCC1395_HCC1395T 891 0.016 903 238,5 331,4 607,9 NA 0/1 NA NA NA NA 476,415,9,3 G/T PANCANCER NA FALSE LITAF chr16:11548047:11548048:G:T SNV 4:1 chr16:10431373:19121458:4:1:1 NA NA 0.96 +chr16 12910638 12910639 T G 53 230 0.230434782608696 MODIFIER SHISA9 ENSG00000237515 G 3_prime_UTR_variant Transcript ENST00000423335 protein_coding 2/2 ENST00000423335.2:c.*2057T>G NA 3031 1 SNV HGNC HGNC:37231 1 CCDS45418.2 ENSP00000395245 B4DS77.99 UPI000047D8EB B4DS77-3 8 NA NA PASS SITE 164,97|31,22 NA NA 1 93 34,24 184,183 60,60 25 1.81 NA 18.66 NA FALSE 6.00 93 NA NA NA FALSE NA NA 137.15 8 12910638 HCC1395_HCC1395T 177 0.227 230 51,14 90,27 142,41 NA 0/1 NA NA NA NA 117,60,31,22 T/G PANCANCER NA FALSE SHISA9 chr16:12910638:12910639:T:G SNV 4:1 chr16:10431373:19121458:4:1:1 NA NA 0.96 +chr16 16261699 16261700 T C 47 173 0.271676300578035 MODIFIER NOMO3 ENSG00000103226 C intron_variant Transcript ENST00000263012 protein_coding 12/31 ENST00000263012.10:c.1395+23T>C NA 1 SNV HGNC HGNC:25242 1 ENSP00000263012 J3KN36.76 UPI00001AE864 8 NA NA PASS SITE 58,146|14,33 NA NA 1 93 20,20 165,161 42,42 29 1.76 NA 17.15 NA FALSE 6.00 53 NA NA NA FALSE NA NA 108.66 8 16261699 HCC1395_HCC1395T 126 0.268 173 44,23 38,7 91,33 NA 0/1 NA NA NA NA 35,91,14,33 T/C PANCANCER NA FALSE NOMO3 chr16:16261699:16261700:T:C SNV 4:1 chr16:10431373:19121458:4:1:1 NA NA 0.96 +chr16 19266917 19266918 C T 23 124 0.185483870967742 LOW SYT17 ENSG00000103528 T synonymous_variant Transcript ENST00000355377 protein_coding 8/8 ENST00000355377.7:c.1266C>T ENSP00000347538.2:p.I422= ENSP00000347538.2 p.I422= 1673 1266 422 I atC/atT rs765529724&COSV62546217 1 SNV HGNC HGNC:24119 YES NM_016524.4 1 P1 CCDS10575.1 ENSP00000347538 Q9BSW7.161 UPI000007297F Gene3D:2.60.40.150&AlphaFold_DB_import:AF-Q9BSW7-F1&Pfam:PF00168&Prints:PR00399&PROSITE_profiles:PS50004&PANTHER:PTHR10024&SMART:SM00239&Superfamily:SSF49562&CDD:cd08410 3.982e-05 0.0001231 2.893e-05 0 0.0002175 0 8.81e-06 0 6.535e-05 3.95e-05 9.675e-05 0 0.0001311 0 0 0 0 0 0 0 0.0002175 gnomADe_EAS 0&1 0&1 8 NA NA PASS SITE 77,67|13,10 NA NA 1 67 20,20 156,163 60,60 31 1.46 NA 8.43 NA FALSE 4.61 66 NA NA NA FALSE NA NA 56.85 8 19266917 HCC1395_HCC1395T 101 0.214 124 23,6 37,9 65,17 NA 0/1 NA NA NA NA 54,47,13,10 C/T PANCANCER NA FALSE SYT17_p.I422= chr16:19266917:19266918:C:T SNV 4:2 chr16:19170223:21679238:4:2:1 NA NA 0.96 +chr16 19551340 19551341 TTA T 183 637 0.287284144427002 MODIFIER VPS35L ENSG00000103544 - upstream_gene_variant Transcript ENST00000251143 protein_coding NA 4073 1 deletion HGNC HGNC:24641 1 ENSP00000251143 E7EWW0.81 UPI0001E1129C 1 8 NA NA PASS SITE 393,265|114,69 NA NA 2 93 20,35 169,187 60,60 39 2.17 NA 44.18 NA FALSE 6.00 93 NA NA NA FALSE NA NA 697.41 8 19551340 HCC1395_HCC1395T 454 0.285 637 111,33 155,80 331,131 NA 0|1 0|1 19551340_TTA_T NA 19551340 275,179,114,69 TTA|T PANCANCER NA FALSE VPS35L chr16:19551340:19551341:TTA:T indel 4:2 chr16:19170223:21679238:4:2:1 NA NA 0.96 +chr16 19551343 19551344 CACAGACAAAGTGACATCAGAAGG C 183 788 0.232233502538071 MODIFIER VPS35L ENSG00000103544 - upstream_gene_variant Transcript ENST00000251143 protein_coding NA 4049 1 deletion HGNC HGNC:24641 1 ENSP00000251143 E7EWW0.81 UPI0001E1129C 1 8 NA NA PASS SITE 514,363|114,69 NA NA 2 93 20,37 168,187 60,60 38 2.27 NA 55.10 NA FALSE 6.00 93 NA NA NA FALSE NA NA 686.50 8 19551343 HCC1395_HCC1395T 605 0.242 788 113,33 163,78 415,131 NA 0|1 0|1 19551340_TTA_T NA 19551340 359,246,114,69 CACAGACAAAGTGACATCAGAAGG|C PANCANCER NA FALSE VPS35L chr16:19551343:19551344:CACAGACAAAGTGACATCAGAAGG:C indel 4:2 chr16:19170223:21679238:4:2:1 NA NA 0.96 +chr16 20790936 20790937 G A 37 241 0.153526970954357 MODIFIER ACSM3 ENSG00000005187 A intron_variant Transcript ENST00000289416 protein_coding 10/13 ENST00000289416.10:c.1326+248G>A NA 1 SNV HGNC HGNC:10522 YES NM_005622.4 1 P1 CCDS10589.1 ENSP00000289416 Q53FZ2.136 UPI0000251DAA Q53FZ2-1 8 NA NA PASS SITE 126,150|17,20 NA NA 1 93 20,20 160,172 60,60 32 1.68 NA 13.85 NA FALSE 6.00 29 NA NA NA FALSE NA NA 86.23 8 20790936 HCC1395_HCC1395T 204 0.172 241 45,5 76,22 134,27 NA 0/1 NA NA NA NA 90,114,17,20 G/A PANCANCER NA FALSE ACSM3 chr16:20790936:20790937:G:A SNV 4:2 chr16:19170223:21679238:4:2:1 NA NA 0.96 +chr16 21278464 21278465 G C 27 46 0.58695652173913 MODIFIER CRYM ENSG00000103316 C intron_variant Transcript ENST00000219599 protein_coding 2/9 ENST00000219599.8:c.-85-128C>G NA -1 SNV HGNC HGNC:2418 1 P1 CCDS10597.1 ENSP00000219599 Q14894.190 UPI00001284E5 1 8 NA NA PASS SITE 8,35|5,22 NA NA 1 73 39,38 195,203 60,60 22 1.34 NA 6.32 NA FALSE 6.00 92 NA NA NA FALSE NA NA 85.53 8 21278464 HCC1395_HCC1395T 19 0.575 46 4,6 11,15 16,22 NA 0/1 NA NA NA NA 4,15,5,22 G/C PANCANCER NA FALSE CRYM chr16:21278464:21278465:G:C SNV 4:2 chr16:19170223:21679238:4:2:1 NA NA 0.96 +chr16 21402776 21402777 G A 5 6 0.833333333333333 MODIFIER NPIPB3 ENSG00000169246 A downstream_gene_variant Transcript ENST00000419180 protein_coding NA 2397 -1 cds_end_NF SNV HGNC HGNC:28989 3 ENSP00000413141 C9K082.66 UPI000204A921 8 NA NA PASS SITE 0,22|0,5 NA NA 1 69 40,39 246,174 21,40 31 1.35 NA 6.30 NA FALSE 6.00 16 NA NA NA FALSE NA NA 19.43 8 21402776 HCC1395_HCC1395T 1 0.754 6 0,2 1,0 1,5 NA 0/1 NA NA NA NA 0,1,0,5 G/A PANCANCER NA FALSE NPIPB3 chr16:21402776:21402777:G:A SNV 4:2 chr16:19170223:21679238:4:2:1 NA NA 0.96 +chr16 22116742 22116743 T C 185 659 0.280728376327769 MODIFIER VWA3A ENSG00000175267 C upstream_gene_variant Transcript ENST00000299840 nonsense_mediated_decay NA 4282 1 cds_start_NF SNV HGNC HGNC:27088 1 ENSP00000299840 H7BXL8.46 UPI0002467085 8 NA NA PASS SITE 395,323|103,82 NA NA 1 93 20,20 161,157 60,60 32 2.21 NA 48.72 NA FALSE 6.00 93 NA NA NA FALSE NA NA 433.91 8 22116742 HCC1395_HCC1395T 474 0.282 659 109,45 170,66 302,118 NA 0/1 NA NA NA NA 256,218,103,82 T/C PANCANCER NA FALSE VWA3A chr16:22116742:22116743:T:C SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 22297675 22297676 C G 9 26 0.346153846153846 MODIFIER POLR3E ENSG00000058600 G intron_variant Transcript ENST00000299853 protein_coding 1/20 ENST00000299853.10:c.-39+138C>G NA 1 SNV HGNC HGNC:30347 YES NM_018119.4 1 P1 CCDS10605.1 ENSP00000299853 Q9NVU0.174 UPI000006D8F8 Q9NVU0-1 8 NA NA PASS SITE 2,26|1,8 NA NA 1 36 32,40 197,198 60,60 39 1.08 NA 3.31 NA FALSE 6.00 38 NA NA NA FALSE NA NA 28.49 8 22297675 HCC1395_HCC1395T 17 0.362 26 6,1 4,7 15,8 NA 0/1 NA NA NA NA 2,15,1,8 C/G PANCANCER NA FALSE POLR3E chr16:22297675:22297676:C:G SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 22305469 22305470 A T 28 163 0.171779141104294 MODIFIER POLR3E ENSG00000058600 T intron_variant Transcript ENST00000299853 protein_coding 3/20 ENST00000299853.10:c.87+263A>T NA 1 SNV HGNC HGNC:30347 YES NM_018119.4 1 P1 CCDS10605.1 ENSP00000299853 Q9NVU0.174 UPI000006D8F8 Q9NVU0-1 8 NA NA PASS SITE 60,140|7,21 NA NA 1 93 20,20 168,168 60,60 27 1.71 NA 14.70 NA FALSE 6.00 21 NA NA NA FALSE NA NA 65.90 8 22305469 HCC1395_HCC1395T 135 0.180 163 28,2 66,14 97,21 NA 0/1 NA NA NA NA 42,93,7,21 A/T PANCANCER NA FALSE POLR3E chr16:22305469:22305470:A:T SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 23596226 23596227 C T 13 678 0.0191740412979351 MODERATE NDUFAB1 ENSG00000004779 T missense_variant Transcript ENST00000007516 protein_coding 1/5 ENST00000007516.8:c.65G>A ENSP00000007516.2:p.R22Q ENSP00000007516.2 p.R22Q 91 65 22 R/Q cGg/cAg rs990053933 -1 SNV HGNC HGNC:7694 YES NM_005003.3 1 P1 CCDS10614.1 ENSP00000007516 O14561.203 UPI0000125321 tolerated(0.21) benign(0.161) PDB-ENSP_mappings:5ool.w&PDB-ENSP_mappings:5oom.w&PDB-ENSP_mappings:7a5h.w&PDB-ENSP_mappings:7a5j.w&PDB-ENSP_mappings:7o9k.w&PDB-ENSP_mappings:7o9m.w&PDB-ENSP_mappings:7odr.w&PDB-ENSP_mappings:7ods.w&PDB-ENSP_mappings:7odt.w&PDB-ENSP_mappings:7of0.w&PDB-ENSP_mappings:7of2.w&PDB-ENSP_mappings:7of3.w&PDB-ENSP_mappings:7of5.w&PDB-ENSP_mappings:7of7.w&PDB-ENSP_mappings:7oi6.w&PDB-ENSP_mappings:7oi7.w&PDB-ENSP_mappings:7oi8.w&PDB-ENSP_mappings:7oi9.w&PDB-ENSP_mappings:7oic.w&PDB-ENSP_mappings:7oid.w&PDB-ENSP_mappings:7oie.w&PDB-ENSP_mappings:7pd3.w&PDB-ENSP_mappings:7po4.zc&PDB-ENSP_mappings:7qh6.w&AlphaFold_DB_import:AF-O14561-F1 4.352e-06 0 2.984e-05 0 0 0 0 0 0 2.984e-05 gnomADe_AMR 8 NA NA PASS SITE 627,591|8,5 NA NA 1 93 20,20 157,181 60,60 36 2.58 NA 112.13 NA FALSE 6.00 23 NA NA NA FALSE NA NA 20.08 8 23596226 HCC1395_HCC1395T 665 0.022 678 201,6 221,3 448,9 NA 0/1 NA NA NA NA 348,317,8,5 C/T PANCANCER NA FALSE NDUFAB1_p.R22Q chr16:23596226:23596227:C:T SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 24215029 24215030 C A 50 98 0.510204081632653 MODIFIER PRKCB ENSG00000166501 A intron_variant Transcript ENST00000321728 protein_coding 16/16 ENST00000321728.12:c.1864-4932C>A NA 1 SNV HGNC HGNC:9395 1 A1 CCDS10618.1 ENSP00000318315 P05771.255 UPI000012DF67 P05771-1 1 8 NA NA PASS SITE 48,49|23,27 NA NA 1 93 34,30 177,173 60,60 20 1.58 NA 10.79 NA FALSE 6.00 87 NA NA NA FALSE NA NA 138.43 8 24215029 HCC1395_HCC1395T 48 0.482 98 15,13 23,21 40,37 NA 0/1 NA NA NA NA 27,21,23,27 C/A PANCANCER NA FALSE PRKCB chr16:24215029:24215030:C:A SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 24806461 24806462 T A 135 240 0.5625 MODIFIER TNRC6A ENSG00000090905 A intron_variant Transcript ENST00000315183 protein_coding 15/23 ENST00000315183.11:c.4183-113T>A NA 1 SNV HGNC HGNC:11969 5 P4 CCDS81959.1 ENSP00000326900 Q8NDV7.191 UPI000155D53E Q8NDV7-6 1 8 NA NA PASS SITE 134,82|87,48 NA NA 1 93 20,36 174,186 60,60 34 1.89 NA 22.83 NA FALSE 6.00 93 NA NA NA FALSE NA NA 413.55 8 24806461 HCC1395_HCC1395T 105 0.565 240 34,36 49,68 83,108 NA 0/1 NA NA NA NA 73,32,87,48 T/A PANCANCER NA FALSE TNRC6A chr16:24806461:24806462:T:A SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 25221523 25221524 G C 51 231 0.220779220779221 MODERATE AQP8 ENSG00000103375 C missense_variant Transcript ENST00000219660 protein_coding 3/6 ENST00000219660.6:c.327G>C ENSP00000219660.5:p.M109I ENSP00000219660.5 p.M109I 426 327 109 M/I atG/atC 1 SNV HGNC HGNC:642 YES NM_001169.3 1 P2 CCDS10626.1 ENSP00000219660 O94778.173 UPI00001697EC deleterious(0.02) benign(0.176) Gene3D:1.20.1080.10&AlphaFold_DB_import:AF-O94778-F1&Pfam:PF00230&Prints:PR00783&Prints:PR02020&PANTHER:PTHR45665&Superfamily:SSF81338&Transmembrane_helices:TMhelix 8 NA NA PASS SITE 141,192|20,31 NA NA 1 93 20,20 154,178 60,60 32 2.01 NA 30.10 NA FALSE 6.00 93 NA NA NA FALSE NA NA 124.91 8 25221523 HCC1395_HCC1395T 180 0.242 231 48,14 55,18 112,35 NA 0/1 NA NA NA NA 72,108,20,31 G/C PANCANCER NA FALSE AQP8_p.M109I chr16:25221523:25221524:G:C SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 25246938 25246939 C T 250 538 0.464684014869888 MODERATE ZKSCAN2 ENSG00000155592 T missense_variant Transcript ENST00000328086 protein_coding 5/7 ENST00000328086.12:c.1258G>A ENSP00000331626.7:p.E420K ENSP00000331626.7 p.E420K 1976 1258 420 E/K Gag/Aag COSV100048419&COSV60156433 -1 SNV HGNC HGNC:25677 YES NM_001012981.5 1 P1 CCDS32410.1 ENSP00000331626 Q63HK3.148 UPI0000229E7F Q63HK3-1 deleterious(0.02) probably_damaging(0.989) AlphaFold_DB_import:AF-Q63HK3-F1&Pfam:PF13837 1&1 1&1 8 NA NA PASS SITE 308,259|140,110 NA NA 1 93 20,20 162,162 60,60 32 2.27 NA 55.64 NA FALSE 6.00 93 NA NA NA FALSE NA NA 628.62 8 25246938 HCC1395_HCC1395T 288 0.455 538 64,58 126,100 197,165 NA 0/1 NA NA NA NA 155,133,140,110 C/T PANCANCER NA FALSE ZKSCAN2_p.E420K chr16:25246938:25246939:C:T SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 27850590 27850591 G C 47 118 0.398305084745763 MODIFIER GSG1L ENSG00000169181 C intron_variant Transcript ENST00000380897 protein_coding 2/5 ENST00000380897.7:c.86-5529C>G NA -1 SNV HGNC HGNC:28283 1 CCDS10631.1 ENSP00000370282 Q6UXU4.123 UPI000006D72C Q6UXU4-2 8 NA NA PASS SITE 68,82|18,29 NA NA 1 93 20,31 158,178 60,60 41 1.73 NA 15.61 NA FALSE 6.00 93 NA NA NA FALSE NA NA 128.38 8 27850590 HCC1395_HCC1395T 71 0.456 118 15,11 27,22 44,37 NA 0/1 NA NA NA NA 31,40,18,29 G/C PANCANCER NA FALSE GSG1L chr16:27850590:27850591:G:C SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 29980814 29980815 G A 105 249 0.421686746987952 MODIFIER TAOK2 ENSG00000149930 A intron_variant Transcript ENST00000279394 protein_coding 8/18 ENST00000279394.7:c.656-847G>A NA 1 SNV HGNC HGNC:16835 1 P1 CCDS10662.1 ENSP00000279394 Q9UL54.189 UPI0000073D88 Q9UL54-2 8 NA NA PASS SITE 161,136|57,48 NA NA 1 93 20,20 183,188 60,60 24 2.07 NA 34.87 NA FALSE 6.00 93 NA NA NA FALSE NA NA 269.70 8 29980814 HCC1395_HCC1395T 144 0.412 249 26,25 78,49 109,76 NA 0/1 NA NA NA NA 84,60,57,48 G/A PANCANCER NA FALSE TAOK2 chr16:29980814:29980815:G:A SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 30091658 30091659 T A 8 340 0.0235294117647059 MODIFIER TBX6 ENSG00000149922 A upstream_gene_variant Transcript ENST00000279386 protein_coding NA 409 -1 SNV HGNC HGNC:11605 1 P1 CCDS10670.1 ENSP00000279386 O95947.192 UPI000013DBC7 O95947-1 1 8 NA NA PASS SITE 285,249|4,4 NA NA 1 93 20,20 151,169 60,60 35 2.13 NA 39.43 NA FALSE 6.00 13 NA NA NA FALSE NA NA 11.19 8 30091658 HCC1395_HCC1395T 332 0.028 340 75,1 128,4 210,5 NA 0/1 NA NA NA NA 177,155,4,4 T/A PANCANCER NA FALSE TBX6 chr16:30091658:30091659:T:A SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 30894580 30894581 G C 129 293 0.440273037542662 MODIFIER BCL7C ENSG00000099385 C upstream_gene_variant Transcript ENST00000215115 protein_coding NA 503 -1 SNV HGNC HGNC:1006 YES NM_004765.4 1 P4 CCDS10693.1 ENSP00000215115 Q8WUZ0.131 UPI000006F931 Q8WUZ0-1 8 NA NA PASS SITE 189,165|62,67 NA NA 1 93 20,20 169,165 60,60 33 2.12 NA 39.09 NA FALSE 6.00 93 NA NA NA FALSE NA NA 345.18 8 30894580 HCC1395_HCC1395T 164 0.440 293 42,26 65,60 112,88 NA 0/1 NA NA NA NA 88,76,62,67 G/C PANCANCER NA FALSE BCL7C chr16:30894580:30894581:G:C SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 30924354 30924355 T C 26 105 0.247619047619048 MODIFIER FBXL19 ENSG00000099364 C 5_prime_UTR_variant Transcript ENST00000338343 protein_coding 1/11 ENST00000338343.10:c.-130T>C NA 783 1 SNV HGNC HGNC:25300 YES NM_001382779.1 5 P1 CCDS92142.1 ENSP00000339712 H3BPZ0.88 UPI00004E188A 8 NA NA PASS SITE 112,56|15,11 NA NA 1 93 29,36 167,165 60,60 25 1.82 NA 19.47 NA FALSE 6.00 74 NA NA NA FALSE NA NA 68.62 8 30924354 HCC1395_HCC1395T 79 0.244 105 15,8 47,12 64,20 NA 0/1 NA NA NA NA 55,24,15,11 T/C PANCANCER NA FALSE FBXL19 chr16:30924354:30924355:T:C SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 31034332 31034333 G T 47 109 0.431192660550459 LOW STX4 ENSG00000103496 T splice_region_variant&intron_variant Transcript ENST00000313843 protein_coding 3/10 ENST00000313843.8:c.232+7G>T NA 1 SNV HGNC HGNC:11439 YES NM_004604.5 1 P1 CCDS10700.1 ENSP00000317714 Q12846.204 UPI0000136162 Q12846-1 8 NA NA PASS SITE 69,76|23,24 NA NA 1 93 20,33 168,167 60,60 27 1.76 NA 16.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 130.07 8 31034332 HCC1395_HCC1395T 62 0.452 109 20,17 23,18 44,36 NA 0/1 NA NA NA NA 30,32,23,24 G/T PANCANCER NA FALSE STX4 chr16:31034332:31034333:G:T SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 31416199 31416200 C G 49 220 0.222727272727273 LOW ITGAD ENSG00000156886 G splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000389202 protein_coding 18/29 ENST00000389202.3:c.2284-14C>G NA 1 SNV HGNC HGNC:6146 YES NM_005353.3 1 P1 CCDS32438.1 ENSP00000373854 Q13349.190 UPI000004B27A 8 NA NA PASS SITE 148,168|23,26 NA NA 1 93 20,20 158,156 60,60 33 1.98 NA 28.30 NA FALSE 6.00 67 NA NA NA FALSE NA NA 110.97 8 31416199 HCC1395_HCC1395T 171 0.233 220 30,7 67,20 110,33 NA 0/1 NA NA NA NA 77,94,23,26 C/G PANCANCER NA FALSE ITGAD chr16:31416199:31416200:C:G SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 31473862 31473863 G A 13 458 0.0283842794759825 LOW TGFB1I1 ENSG00000140682 A synonymous_variant Transcript ENST00000361773 protein_coding 4/11 ENST00000361773.7:c.159G>A ENSP00000355117.3:p.K53= ENSP00000355117.3 p.K53= 213 159 53 K aaG/aaA 1 SNV HGNC HGNC:11767 1 CCDS10713.1 ENSP00000355117 O43294.172 A0A024QZE7.66 UPI000006F14C O43294-2 AlphaFold_DB_import:AF-O43294-F1&Pfam:PF03535&PIRSF:PIRSF037881&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg 8 NA NA PASS SITE 387,328|7,7 NA NA 1 93 20,20 164,153 60,60 24 2.29 NA 57.64 NA FALSE 6.00 42 NA NA NA FALSE NA NA 18.75 8 31473862 HCC1395_HCC1395T 445 0.030 458 141,4 167,5 319,9 NA 0/1 NA NA NA NA 246,199,7,6 G/A PANCANCER NA FALSE TGFB1I1_p.K53= chr16:31473862:31473863:G:A SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 31755396 31755397 T C 54 257 0.21011673151751 MODIFIER KRBOX5 ENSG00000197302 C intron_variant Transcript ENST00000316491 protein_coding 4/4 ENST00000316491.14:c.361+1496T>C NA rs1415096020 1 SNV HGNC HGNC:26987 YES NM_001130913.2 1 CCDS45473.1 ENSP00000319222 Q7Z2F6.146 UPI000003603E Q7Z2F6-1 5.07e-06 0 0 0 0 0 0 0 3.842e-05 3.842e-05 gnomADe_SAS 8 NA NA PASS SITE 147,174|24,30 NA NA 1 93 20,30 170,205 60,60 33 1.93 NA 25.24 NA FALSE 6.00 91 NA NA NA FALSE NA NA 130.75 8 31755396 HCC1395_HCC1395T 203 0.226 257 53,14 84,25 147,43 NA 0/1 NA NA NA NA 94,109,24,30 T/C PANCANCER NA FALSE KRBOX5 chr16:31755396:31755397:T:C SNV 2:2 chr16:21719128:32066216:2:2:1 FALSE NA 0.96 +chr16 48235018 48235019 G A 92 156 0.58974358974359 MODIFIER ABCC11 ENSG00000121270 A intron_variant Transcript ENST00000353782 protein_coding 1/28 ENST00000353782.9:c.-19+114C>T NA rs13336625 -1 SNV HGNC HGNC:14639 1 CCDS10733.1 ENSP00000311326 Q96J66.169 A0A024R6R9.63 UPI000013F0F6 Q96J66-2 1 0.1100 0.2458 0.0893 0.0188 0.1014 0.044 0.1307 0.2339 0.06031 0.09826 0.09983 0.01521 0.1145 0.1519 0.09478 0.1171 0.05436 0.2458 AFR 1 27903959 8 NA NA PASS SITE 101,43|71,21 NA NA 1 93 20,34 163,179 60,60 19 1.76 NA 16.86 NA FALSE 0.873 82 NA NA NA FALSE NA NA 274.85 8 48235018 HCC1395_HCC1395T 64 0.612 156 18,17 27,56 47,74 NA 0/1 NA NA NA NA 47,17,71,21 G/A PANCANCER NA FALSE ABCC11 chr16:48235018:48235019:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 48235209 48235210 TAGAGATGCAA T 63 97 0.649484536082474 MODIFIER ABCC11 ENSG00000121270 - upstream_gene_variant Transcript ENST00000353782 protein_coding NA rs398088092 33 -1 deletion HGNC HGNC:14639 1 CCDS10733.1 ENSP00000311326 Q96J66.169 A0A024R6R9.63 UPI000013F0F6 Q96J66-2 1 0.1122 0.2458 0.0893 0.0298 0.1014 0.044 0.1305 0.2327 0.06031 0.09779 0.09977 0.02408 0.1142 0.1519 0.09469 0.1165 0.05477 0.2458 AFR 30766545 8 NA NA PASS SITE 12,54|7,56 NA NA 1 4 31,35 195,221 60,60 40 1.53 NA 8.18 NA FALSE 0.876 93 3,2 AGAGATGCAA NA TRUE NA 93 253.78 8 48235209 HCC1395_HCC1395T 34 0.696 97 5,5 6,16 26,58 NA 0/1 NA NA NA NA 8,26,7,56 TAGAGATGCAA/T PANCANCER NA FALSE ABCC11 chr16:48235209:48235210:TAGAGATGCAA:T indel 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 48352353 48352354 A G 154 235 0.65531914893617 MODIFIER LONP2 ENSG00000102910 G 3_prime_UTR_variant Transcript ENST00000285737 protein_coding 15/15 ENST00000285737.9:c.*551A>G NA 3199 rs28515165 1 SNV HGNC HGNC:20598 YES NM_031490.5 1 P1 CCDS10734.1 ENSP00000285737 Q86WA8.169 UPI000000DCD1 Q86WA8-1 0.0613 0.0711 0.0706 0.0198 0.1004 0.044 0.08341 0.07359 0.06031 0.07705 0.0732 0.01405 0.1148 0.1266 0.09391 0.08469 0.05385 0.1266 gnomADg_MID 8 NA NA PASS SITE 63,105|43,111 NA NA 1 93 20,20 174,178 60,60 27 1.76 NA 16.81 NA FALSE 1.03 93 NA NA NA FALSE NA NA 463.64 8 48352353 HCC1395_HCC1395T 81 0.663 235 12,24 20,25 58,115 NA 0/1 NA NA NA NA 29,52,43,111 A/G PANCANCER NA FALSE LONP2 chr16:48352353:48352354:A:G SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 48354877 48354882 C CAGTT 486 703 0.691322901849218 MODIFIER LONP2 ENSG00000102910 AGTT 3_prime_UTR_variant Transcript ENST00000285737 protein_coding 15/15 ENST00000285737.9:c.*3078_*3081dup NA 5723-5724 rs3083559 1 insertion HGNC HGNC:20598 YES NM_031490.5 1 P1 CCDS10734.1 ENSP00000285737 Q86WA8.169 UPI000000DCD1 Q86WA8-1 6 0.1200 0.205 0.1311 0.0198 0.162 0.0573 0.164 0.2082 0.1593 0.1363 0.178 0.01388 0.1664 0.2707 0.1594 0.1694 0.07539 0.2707 gnomADg_MID 8 NA NA PASS SITE 221,219|257,229 NA NA 1 93 20,20 161,157 60,60 36 2.19 NA 44.90 NA FALSE 0.767 93 1,2 AGTT NA TRUE NA 93 1912.96 8 48354877 HCC1395_HCC1395T 217 0.684 703 43,124 70,143 144,313 NA 0/1 NA NA NA NA 112,105,257,229 C/CAGTT PANCANCER NA FALSE LONP2 chr16:48354877:48354882:C:CAGTT indel 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 48355125 48355130 G GAAGT 81 124 0.653225806451613 MODIFIER LONP2 ENSG00000102910 AAGT 3_prime_UTR_variant Transcript ENST00000285737 protein_coding 15/15 ENST00000285737.9:c.*3324_*3327dup NA 5971-5972 rs148672925 1 insertion HGNC HGNC:20598 YES NM_031490.5 1 P1 CCDS10734.1 ENSP00000285737 Q86WA8.169 UPI000000DCD1 Q86WA8-1 4 0.0613 0.0711 0.0706 0.0198 0.1004 0.044 0.08342 0.07367 0.05824 0.07831 0.07324 0.01407 0.1138 0.1266 0.09375 0.08437 0.05454 0.1266 gnomADg_MID 8 NA NA PASS SITE 39,44|40,41 NA NA 1 9 20,20 180,178 60,60 29 1.50 NA 8.75 NA FALSE 1.03 93 1,2 AAGT NA TRUE NA 93 325.67 8 48355125 HCC1395_HCC1395T 43 0.644 124 9,20 17,24 32,59 NA 0/1 NA NA NA NA 23,20,40,41 G/GAAGT PANCANCER NA FALSE LONP2 chr16:48355125:48355130:G:GAAGT indel 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 48356869 48356870 TA T 206 319 0.64576802507837 MODIFIER LONP2 ENSG00000102910 - 3_prime_UTR_variant Transcript ENST00000285737 protein_coding 15/15 ENST00000285737.9:c.*5070del NA 7716 rs150126658 1 deletion HGNC HGNC:20598 YES NM_031490.5 1 P1 CCDS10734.1 ENSP00000285737 Q86WA8.169 UPI000000DCD1 Q86WA8-1 2 0.0601 0.0673 0.0692 0.0198 0.1004 0.044 0.08172 0.06899 0.06031 0.07567 0.07122 0.01404 0.1136 0.1234 0.09363 0.08182 0.05397 0.1234 gnomADg_MID 8 NA NA PASS SITE 131,95|126,82 NA NA 1 93 20,20 161,156 60,60 40 1.86 NA 21.02 NA FALSE 1.04 93 3,2 A NA TRUE NA 93 390.48 8 48356869 HCC1395_HCC1395T 113 0.647 319 28,34 40,93 74,136 NA 0/1 NA NA NA NA 67,46,125,81 TA/T PANCANCER NA FALSE LONP2 chr16:48356869:48356870:TA:T indel 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 48356980 48356981 C T 162 274 0.591240875912409 MODIFIER LONP2 ENSG00000102910 T 3_prime_UTR_variant Transcript ENST00000285737 protein_coding 15/15 ENST00000285737.9:c.*5178C>T NA 7826 rs10221107 1 SNV HGNC HGNC:20598 YES NM_031490.5 1 P1 CCDS10734.1 ENSP00000285737 Q86WA8.169 UPI000000DCD1 Q86WA8-1 0.1683 0.3775 0.1455 0.0198 0.165 0.0583 0.2048 0.3487 0.1648 0.1528 0.1768 0.01404 0.1672 0.3006 0.1602 0.1969 0.07643 0.3775 AFR 8 NA NA PASS SITE 111,93|91,71 NA NA 1 93 30,35 185,199 60,60 22 1.85 NA 20.77 NA FALSE 0.690 93 NA NA NA FALSE NA NA 491.96 8 48356980 HCC1395_HCC1395T 112 0.605 274 28,41 53,85 86,132 NA 0/1 NA NA NA NA 61,51,91,71 C/T PANCANCER NA FALSE LONP2 chr16:48356980:48356981:C:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 48360715 48360716 C T 49 77 0.636363636363636 MODIFIER LONP2 ENSG00000102910 T downstream_gene_variant Transcript ENST00000285737 protein_coding NA rs8190 3366 1 SNV HGNC HGNC:20598 YES NM_031490.5 1 P1 CCDS10734.1 ENSP00000285737 Q86WA8.169 UPI000000DCD1 Q86WA8-1 0.1687 0.379 0.147 0.0198 0.165 0.0573 0.2052 0.3501 0.1645 0.1533 0.1769 0.01403 0.1676 0.3006 0.1602 0.1967 0.07593 0.379 AFR 24889829 8 NA NA PASS SITE 45,35|31,18 NA NA 1 59 37,36 191,207 60,60 30 1.60 NA 11.74 NA FALSE 0.688 93 NA NA NA FALSE NA NA 146.64 8 48360715 HCC1395_HCC1395T 28 0.608 77 10,13 13,24 24,38 NA 0/1 NA NA NA NA 15,13,31,18 C/T PANCANCER NA FALSE LONP2 chr16:48360715:48360716:C:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 49279042 49279043 A G 298 434 0.686635944700461 MODIFIER CBLN1 ENSG00000102924 G 3_prime_UTR_variant Transcript ENST00000219197 protein_coding 3/3 ENST00000219197.11:c.*362T>C NA 1317 rs77591139 -1 SNV HGNC HGNC:1543 YES NM_004352.4 1 P1 CCDS10736.1 ENSP00000219197 P23435.173 UPI0000127506 0.0064 0.0015 0.0043 0 0.0149 0.0123 0.01219 0.003619 0.03509 0.009755 0.01297 0 0.003581 0.01266 0.01961 0.009091 0.01742 0.03509 gnomADg_AMI 8 NA NA PASS SITE 114,126|139,160 NA NA 1 93 20,20 173,175 60,60 27 1.88 NA 22.17 NA FALSE 1.96 93 NA NA NA FALSE NA NA 880.21 8 49279042 HCC1395_HCC1395T 136 0.682 434 13,41 44,88 104,224 NA 0/1 NA NA NA NA 60,76,138,160 A/G PANCANCER NA FALSE CBLN1 chr16:49279042:49279043:A:G SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 49281351 49281352 C T 98 252 0.388888888888889 MODERATE CBLN1 ENSG00000102924 T missense_variant Transcript ENST00000219197 protein_coding 1/3 ENST00000219197.11:c.115G>A ENSP00000219197.5:p.D39N ENSP00000219197.5 p.D39N 488 115 39 D/N Gac/Aac COSV54653999 -1 SNV HGNC HGNC:1543 YES NM_004352.4 1 P1 CCDS10736.1 ENSP00000219197 P23435.173 UPI0000127506 deleterious_low_confidence(0) possibly_damaging(0.891) PDB-ENSP_mappings:5kc6.A&PDB-ENSP_mappings:5kc6.B&PDB-ENSP_mappings:5kc6.C&PDB-ENSP_mappings:5kc7.A&PDB-ENSP_mappings:5kc7.B&PDB-ENSP_mappings:5kc7.C&PDB-ENSP_mappings:5kc7.D&PANTHER:PTHR22923&AlphaFold_DB_import:AF-P23435-F1 1 1 8 NA NA PASS SITE 89,164|40,58 NA NA 1 93 20,20 164,167 60,60 24 1.87 NA 21.27 NA FALSE 6.00 93 NA NA NA FALSE NA NA 234.53 8 49281351 HCC1395_HCC1395T 154 0.367 252 37,27 58,32 109,63 NA 0/1 NA NA NA NA 55,99,40,58 C/T PANCANCER NA FALSE CBLN1_p.D39N chr16:49281351:49281352:C:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 49488483 49488484 A G 29 61 0.475409836065574 MODIFIER ZNF423 ENSG00000102935 G downstream_gene_variant Transcript ENST00000535559 protein_coding NA rs73580811 2304 -1 SNV HGNC HGNC:16762 2 CCDS81979.1 ENSP00000442321 F5H7S1.98 UPI0001892633 1 0.1460 0.1475 0.1254 0.1806 0.159 0.1094 0.1402 0.1522 0.08662 0.1394 0.1277 0.1705 0.1035 0.2261 0.1389 0.1577 0.1133 0.2261 gnomADg_MID 8 NA NA PASS SITE 32,30|14,15 NA NA 1 10 20,20 153,158 60,60 37 1.30 NA 5.72 NA FALSE 0.863 93 NA NA NA FALSE NA NA 74.46 8 49488483 HCC1395_HCC1395T 32 0.525 61 8,9 10,10 18,20 NA 0/1 NA NA NA NA 15,17,14,15 A/G PANCANCER NA FALSE ZNF423 chr16:49488483:49488484:A:G SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 49489061 49489062 A G 62 109 0.568807339449541 MODIFIER ZNF423 ENSG00000102935 G downstream_gene_variant Transcript ENST00000535559 protein_coding NA rs9933065 1726 -1 SNV HGNC HGNC:16762 2 CCDS81979.1 ENSP00000442321 F5H7S1.98 UPI0001892633 1 0.1280 0.0794 0.1225 0.1806 0.16 0.1104 0.1239 0.08905 0.08681 0.1356 0.1311 0.1707 0.1036 0.231 0.1417 0.1487 0.1145 0.231 gnomADg_MID 8 NA NA PASS SITE 62,63|34,28 NA NA 1 93 20,20 160,164 60,60 27 1.72 NA 15.35 NA FALSE 0.910 92 NA NA NA FALSE NA NA 168.88 8 49489061 HCC1395_HCC1395T 47 0.589 109 15,13 13,28 29,42 NA 0/1 NA NA NA NA 23,24,34,28 A/G PANCANCER NA FALSE ZNF423 chr16:49489061:49489062:A:G SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 50025028 50025029 G C 24 77 0.311688311688312 MODIFIER CNEP1R1 ENSG00000205423 C upstream_gene_variant Transcript ENST00000389134 nonsense_mediated_decay NA 206 1 SNV HGNC HGNC:26759 3 ENSP00000373786 H3BLY8.45 UPI0002466F30 8 NA NA PASS SITE 43,48|11,13 NA NA 2 81 20,39 170,182 60,60 23 1.19 NA 8.13 NA FALSE 6.00 93 NA NA NA FALSE NA NA 59.11 8 50025028 HCC1395_HCC1395T 53 0.313 77 12,7 23,10 42,19 NA 1|0 1|0 50025027_CG_AC NA 50025027 25,28,11,13 C|G PANCANCER NA FALSE CNEP1R1 chr16:50025028:50025029:G:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 50025257 50025258 G C 166 262 0.633587786259542 MODIFIER CNEP1R1 ENSG00000205423 C 5_prime_UTR_variant&NMD_transcript_variant Transcript ENST00000389134 nonsense_mediated_decay 1/6 ENST00000389134.9:c.-59G>C NA 24 rs186131518 1 SNV HGNC HGNC:26759 3 ENSP00000373786 H3BLY8.45 UPI0002466F30 0.0042 0 0.0014 0 0.0129 0.0072 0.01095 0.002581 0.004386 0.006869 0.0193 0 0.03108 0.01274 0.01468 0.01292 0.004762 0.03108 gnomADg_FIN 8 NA NA PASS SITE 117,110|75,91 NA NA 1 93 20,20 159,162 60,60 29 1.97 NA 27.39 NA FALSE 1.89 93 NA NA NA FALSE NA NA 422.55 8 50025257 HCC1395_HCC1395T 96 0.629 262 30,40 30,64 65,111 NA 0/1 NA NA NA NA 49,47,75,91 G/C PANCANCER NA FALSE CNEP1R1 chr16:50025257:50025258:G:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 50105983 50105984 G A 168 283 0.593639575971731 MODIFIER HEATR3 ENSG00000155393 A 3_prime_UTR_variant Transcript ENST00000299192 protein_coding 15/15 ENST00000299192.8:c.*922G>A NA 3127 rs3188026 1 SNV HGNC HGNC:26087 YES NM_182922.4 1 P1 CCDS10739.1 ENSP00000299192 Q7Z4Q2.154 UPI0000071B6C Q7Z4Q2-1 1 0.0050 0 0.0014 0 0.0169 0.0072 0.01088 0.002582 0.004386 0.006941 0.0193 0 0.03111 0.01266 0.01453 0.01292 0.00476 0.03111 gnomADg_FIN 8 NA NA PASS SITE 118,84|102,66 NA NA 1 93 20,20 164,163 60,60 34 1.75 NA 16.55 NA FALSE 1.89 93 NA NA NA FALSE NA NA 437.91 8 50105983 HCC1395_HCC1395T 115 0.597 283 23,31 49,77 74,110 NA 0/1 NA NA NA NA 69,46,102,66 G/A PANCANCER NA FALSE HEATR3 chr16:50105983:50105984:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 50230143 50230144 T C 51 78 0.653846153846154 MODIFIER TENT4B ENSG00000121274 C 3_prime_UTR_variant&NMD_transcript_variant Transcript ENST00000357464 nonsense_mediated_decay 10/10 ENST00000357464.4:c.*1156T>C NA 2066 rs62028293 1 cds_start_NF SNV HGNC HGNC:30758 5 ENSP00000350054 E9PC61.61 UPI0004620AE7 0.0050 0.0015 0.0058 0 0.0159 0.0031 0.00981 0.00268 0.02083 0.01113 0.002592 0 0.0201 0.01266 0.01369 0.009551 0.00331 0.02083 gnomADg_AMI 8 NA NA PASS SITE 20,37|22,29 NA NA 1 22 30,20 189,196 60,60 31 1.36 NA 6.62 NA FALSE 2.00 45 NA NA NA FALSE NA NA 133.97 8 50230143 HCC1395_HCC1395T 27 0.617 78 3,3 7,12 23,38 NA 0/1 NA NA NA NA 9,18,22,29 T/C PANCANCER NA FALSE TENT4B chr16:50230143:50230144:T:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 50636271 50636272 G C 70 105 0.666666666666667 MODIFIER NKD1 ENSG00000140807 C 3_prime_UTR_variant Transcript ENST00000268459 protein_coding 10/10 ENST00000268459.6:c.*2490G>C NA 4061 rs745230 1 SNV HGNC HGNC:17045 YES NM_033119.5 1 P1 CCDS10743.1 ENSP00000268459 Q969G9.153 UPI0000073F02 0.5184 0.4887 0.487 0.4831 0.7087 0.4213 0.6012 0.4888 0.7901 0.5384 0.6827 0.5319 0.7497 0.6083 0.6697 0.5939 0.4524 0.7901 gnomADg_AMI 12019468 8 NA NA PASS SITE 42,45|34,36 NA NA 1 27 20,20 154,149 60,60 37 1.51 NA 9.33 NA FALSE 0.201 93 NA NA NA FALSE NA NA 180.14 8 50636271 HCC1395_HCC1395T 35 0.657 105 8,16 15,29 23,45 NA 0/1 NA NA NA NA 15,20,34,36 G/C PANCANCER NA FALSE NKD1 chr16:50636271:50636272:G:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 50732975 50732976 G A 131 212 0.617924528301887 MODIFIER NOD2 ENSG00000167207 A 3_prime_UTR_variant Transcript ENST00000300589 protein_coding 12/12 ENST00000300589.6:c.*1156G>A NA 4384 rs3135500&CR1414299 1 SNV HGNC HGNC:5331 1 CCDS10746.1 ENSP00000300589 Q9HC29.213 UPI000005027A Q9HC29-1 1 0.3522 0.5787 0.3256 0.1756 0.4185 0.1789 0.4348 0.5561 0.5154 0.4016 0.5239 0.1861 0.4104 0.3671 0.402 0.4075 0.2209 0.5787 AFR benign 1&1 31637880&24465869&16600026&27775822&18576390&29516665&22957492&27426943&25342389&20350193&25933107&16008671&22563200&30950247&22139875&24297055&25148897&29881342&28726756&23850724&26164662&30579343&28366820&25475103&33904676&32581566&34173079&33399167&35327350&36118798&36189256&35401568 8 NA NA PASS SITE 91,54|76,55 NA NA 1 93 38,35 204,192 60,60 25 1.72 NA 15.65 NA FALSE 0.373 93 NA NA NA FALSE NA NA 399.67 8 50732975 HCC1395_HCC1395T 81 0.628 212 24,41 37,61 65,111 NA 0/1 NA NA NA NA 53,28,76,55 G/A PANCANCER NA FALSE NOD2 chr16:50732975:50732976:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 51646548 51646549 A C 63 97 0.649484536082474 MODERATE HNRNPA1L3 ENSG00000224578 C missense_variant Transcript ENST00000565308 protein_coding 2/2 ENST00000565308.3:c.731A>C ENSP00000493805.2:p.Y244S ENSP00000493805.2 p.Y244S 1340 731 244 Y/S tAt/tCt rs369938434&COSV68940722 1 SNV HGNC HGNC:48778 YES P1 CCDS92159.1 ENSP00000493805 A0A2R8Y4L2.22 UPI0000140F43 deleterious_low_confidence(0.03) benign(0) AlphaFold_DB_import:AF-A0A2R8Y4L2-F1&PANTHER:PTHR48026&Low_complexity_(Seg):seg 3.286e-05 7.241e-05 0 0 0 0 0 0 2.94e-05 0 0 7.241e-05 gnomADg_AFR 0&1 0&1 8 NA NA PASS SITE 23,34|33,30 NA NA 1 42 33,20 185,158 41,41 32 1.32 NA 6.02 NA FALSE 4.61 93 NA NA NA FALSE NA NA 177.57 8 51646548 HCC1395_HCC1395T 34 0.649 97 7,18 18,26 25,47 NA 0/1 NA NA NA NA 15,19,33,30 A/C PANCANCER NA FALSE HNRNPA1L3_p.Y244S chr16:51646548:51646549:A:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 55464778 55464780 CC AA 21 43 0.488372093023256 MODIFIER MMP2-AS1 ENSG00000260135 AA upstream_gene_variant Transcript ENST00000569037 lncRNA NA rs71380431 2481 -1 substitution HGNC HGNC:53142 YES 5 8 NA NA PASS SITE 12,25|9,12 NA NA 2 33 20,20 167,161 60,60 36 1.04 NA 3.01 NA FALSE 6.00 52 NA NA NA FALSE NA NA 85.46 8 55464778 HCC1395_HCC1395T 22 0.467 43 4,6 6,3 15,13 NA 1|0 1|0 55464753_GC_TG NA 55464753 7,15,9,12 AA|CC PANCANCER NA FALSE MMP2-AS1 chr16:55464778:55464780:CC:AA indel 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 55509301 55509302 G T 102 384 0.265625 MODIFIER MMP2 ENSG00000087245 T downstream_gene_variant Transcript ENST00000219070 protein_coding NA 2610 1 SNV HGNC HGNC:7166 YES NM_004530.6 1 P1 CCDS10752.1 ENSP00000219070 P08253.251 A0A024R6R4.69 UPI00000422C4 P08253-1 1 8 NA NA PASS SITE 194,263|45,57 NA NA 1 93 20,20 155,151 60,60 39 2.04 NA 32.46 NA FALSE 6.00 93 NA NA NA FALSE NA NA 227.01 8 55509301 HCC1395_HCC1395T 282 0.267 384 75,26 89,35 184,67 NA 0/1 NA NA NA NA 118,164,45,57 G/T PANCANCER NA FALSE MMP2 chr16:55509301:55509302:G:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 55810705 55810706 G A 98 162 0.604938271604938 MODIFIER CES1 ENSG00000198848 A intron_variant Transcript ENST00000360526 protein_coding 10/13 ENST00000360526.8:c.1171-41C>T NA rs2244614&COSV62087129 -1 SNV HGNC HGNC:1863 YES NM_001025195.2 1 P4 CCDS32450.1 ENSP00000353720 P23141.214 UPI000054B390 P23141-2 1 0.3644 0.2345 0.5317 0.1865 0.6133 0.3487 0.5185 0.2674 0.5419 0.5775 0.2084 0.6495 0.6117 0.5512 0.3488 0.4945 0.2731 0.4424 0.5664 0.5511 0.2058 0.6472 0.4589 0.6206 0.5005 0.3418 0.6495 gnomADe_FIN 0&1 0&1 27662362&32458030&36453946 8 NA NA PASS SITE 50,77|38,60 NA NA 1 54 20,20 167,147 60,60 33 1.61 NA 11.74 NA FALSE 0.287 93 NA NA NA FALSE NA NA 257.79 8 55810705 HCC1395_HCC1395T 64 0.582 162 13,21 21,31 45,63 NA 0/1 NA NA NA NA 20,44,38,60 G/A PANCANCER NA FALSE CES1 chr16:55810705:55810706:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 56429830 56429831 G A 363 557 0.651705565529623 MODIFIER AMFR ENSG00000159461 A upstream_gene_variant Transcript ENST00000290649 protein_coding NA rs79677185 4285 -1 SNV HGNC HGNC:463 YES NM_001144.6 1 P1 CCDS10758.1 ENSP00000290649 Q9UKV5.192 UPI000013EDCA 0.0769 0.0197 0.0403 0.1597 0.0268 0.1462 0.0418 0.03029 0.007675 0.03428 0.01472 0.1562 0.04863 0.02215 0.03589 0.04358 0.1354 0.1597 EAS 8 NA NA PASS SITE 190,200|196,167 NA NA 1 93 20,20 166,162 60,60 32 2.14 NA 40.33 NA FALSE 1.38 93 NA NA NA FALSE NA NA 984.53 8 56429830 HCC1395_HCC1395T 194 0.632 557 46,73 79,153 140,241 NA 0/1 NA NA NA NA 89,105,196,167 G/A PANCANCER NA FALSE AMFR chr16:56429830:56429831:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 56431490 56431491 C G 419 687 0.609898107714702 MODIFIER NUDT21 ENSG00000167005 G 3_prime_UTR_variant Transcript ENST00000300291 protein_coding 7/7 ENST00000300291.10:c.*1222G>C NA 2036 rs78002423 -1 SNV HGNC HGNC:13870 YES NM_007006.3 1 P1 CCDS10760.1 ENSP00000300291 O43809.195 A0A024R6W2.64 UPI0000073E79 0.0611 0.0189 0.0432 0.1379 0.0288 0.0849 0.04149 0.03 0.007675 0.03605 0.01498 0.1271 0.05109 0.02215 0.04099 0.03916 0.07906 0.1379 EAS 8 NA NA PASS SITE 264,279|195,227 NA NA 2 93 20,20 158,163 60,60 33 -2.109e+00 NA 43.55 NA FALSE 1.36 93 NA NA NA FALSE NA NA 1161.19 8 56431490 HCC1395_HCC1395T 268 0.621 687 60,82 103,182 170,279 NA 0/1 NA NA NA NA 126,142,193,226 C/G PANCANCER NA FALSE NUDT21 chr16:56431490:56431491:C:G SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 56431513 56431514 C T 360 598 0.602006688963211 MODIFIER NUDT21 ENSG00000167005 T 3_prime_UTR_variant Transcript ENST00000300291 protein_coding 7/7 ENST00000300291.10:c.*1199G>A NA 2013 rs8059717 -1 SNV HGNC HGNC:13870 YES NM_007006.3 1 P1 CCDS10760.1 ENSP00000300291 O43809.195 A0A024R6W2.64 UPI0000073E79 0.7198 0.9713 0.5706 0.6101 0.5537 0.7699 0.6675 0.9201 0.589 0.5993 0.5467 0.5969 0.4425 0.5063 0.5741 0.6332 0.7262 0.9713 AFR 8 NA NA PASS SITE 226,269|154,210 NA NA 2 93 20,20 159,173 60,60 29 -3.571e+00 NA 38.27 NA FALSE 0.194 93 NA NA NA FALSE NA NA 951.56 8 56431513 HCC1395_HCC1395T 238 0.614 598 49,56 82,148 154,246 NA 0/1 NA NA NA NA 104,134,152,208 C/T PANCANCER NA FALSE NUDT21 chr16:56431513:56431514:C:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 56431716 56431717 T C 262 393 0.666666666666667 MODIFIER NUDT21 ENSG00000167005 C 3_prime_UTR_variant Transcript ENST00000300291 protein_coding 7/7 ENST00000300291.10:c.*996A>G NA 1810 rs76464820 -1 SNV HGNC HGNC:13870 YES NM_007006.3 1 P1 CCDS10760.1 ENSP00000300291 O43809.195 A0A024R6W2.64 UPI0000073E79 0.0611 0.0189 0.0432 0.1379 0.0288 0.0849 0.04146 0.02992 0.007692 0.03606 0.01527 0.1272 0.05101 0.02215 0.04097 0.03923 0.07857 0.1379 EAS 8 NA NA PASS SITE 164,103|153,109 NA NA 2 93 20,20 180,176 60,60 27 2.00 NA 29.45 NA FALSE 1.36 93 NA NA NA FALSE NA NA 752.98 8 56431716 HCC1395_HCC1395T 131 0.667 393 39,65 50,107 92,185 NA 0/1 NA NA NA NA 81,50,153,109 T/C PANCANCER NA FALSE NUDT21 chr16:56431716:56431717:T:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 56431749 56431752 G GTA 342 520 0.657692307692308 MODIFIER NUDT21 ENSG00000167005 TA 3_prime_UTR_variant Transcript ENST00000300291 protein_coding 7/7 ENST00000300291.10:c.*962_*963insTA NA 1776-1777 rs74311713 -1 insertion HGNC HGNC:13870 YES NM_007006.3 1 P1 CCDS10760.1 ENSP00000300291 O43809.195 A0A024R6W2.64 UPI0000073E79 0.0921 0.0681 0.0461 0.1637 0.0288 0.1483 0.0565 0.07205 0.007675 0.04194 0.01529 0.1558 0.05085 0.02229 0.04105 0.05086 0.1366 0.1637 EAS 8 NA NA PASS SITE 197,151|204,138 NA NA 2 93 20,20 168,171 60,60 36 2.09 NA 35.55 NA FALSE 1.24 93 NA NA NA FALSE NA NA 1042.26 8 56431749 HCC1395_HCC1395T 178 0.652 520 47,77 62,127 124,233 NA 0/1 NA NA NA NA 102,76,204,138 G/GTA PANCANCER NA FALSE NUDT21 chr16:56431749:56431752:G:GTA indel 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 56477154 56477155 A G 99 148 0.668918918918919 MODIFIER OGFOD1 ENSG00000087263 G downstream_gene_variant Transcript ENST00000336111 nonsense_mediated_decay NA rs10438565 25 1 SNV HGNC HGNC:25585 2 ENSP00000337196 J3KNR5.48 UPI0002467066 0.0795 0.0174 0.0461 0.1647 0.0288 0.1513 0.04435 0.02381 0.007675 0.03503 0.01964 0.1563 0.05329 0.02848 0.04431 0.04195 0.1369 0.1647 EAS 8 NA NA PASS SITE 66,37|63,36 NA NA 1 63 20,20 160,174 60,60 18 1.60 NA 11.44 NA FALSE 1.33 93 NA NA NA FALSE NA NA 255.45 8 56477154 HCC1395_HCC1395T 49 0.651 148 11,21 24,33 38,72 NA 0/1 NA NA NA NA 34,15,63,36 A/G PANCANCER NA FALSE OGFOD1 chr16:56477154:56477155:A:G SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 56477824 56477825 T C 66 101 0.653465346534653 MODIFIER OGFOD1 ENSG00000087263 C downstream_gene_variant Transcript ENST00000336111 nonsense_mediated_decay NA rs4783941 695 1 SNV HGNC HGNC:25585 2 ENSP00000337196 J3KNR5.48 UPI0002467066 0.7264 0.9667 0.5778 0.6071 0.5825 0.7781 0.6857 0.9213 0.589 0.6069 0.5816 0.5972 0.4736 0.5348 0.6041 0.6549 0.7395 0.9667 AFR 18635565 8 NA NA PASS SITE 35,30|36,30 NA NA 1 9 35,40 207,201 60,60 35 1.41 NA 7.52 NA FALSE 0.179 76 NA NA NA FALSE NA NA 236.99 8 56477824 HCC1395_HCC1395T 35 0.639 101 10,13 24,45 34,61 NA 0/1 NA NA NA NA 18,17,36,30 T/C PANCANCER NA FALSE OGFOD1 chr16:56477824:56477825:T:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 56478099 56478100 C T 17 28 0.607142857142857 MODIFIER OGFOD1 ENSG00000087263 T downstream_gene_variant Transcript ENST00000336111 nonsense_mediated_decay NA rs78452195 970 1 SNV HGNC HGNC:25585 2 ENSP00000337196 J3KNR5.48 UPI0002467066 0.0028 0 0.0101 0 0.007 0 0.008911 0.002872 0 0.007856 0.008646 0 0.003491 0.006329 0.01515 0.006692 0.0006214 0.01515 gnomADg_NFE 8 NA NA PASS SITE 13,16|11,6 NA NA 2 8 38,36 213,181 60,60 32 1.23 NA 4.82 NA FALSE 2.01 52 NA NA NA FALSE NA NA 55.43 8 56478099 HCC1395_HCC1395T 11 0.616 28 1,3 5,9 9,15 NA 0/1 NA NA NA NA 4,7,11,6 C/T PANCANCER NA FALSE OGFOD1 chr16:56478099:56478100:C:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57121291 57121292 C T 29 44 0.659090909090909 MODIFIER CPNE2 ENSG00000140848 T intron_variant Transcript ENST00000290776 protein_coding 8/15 ENST00000290776.13:c.780+100C>T NA 1 SNV HGNC HGNC:2315 YES NM_152727.6 1 P1 CCDS10774.1 ENSP00000290776 Q96FN4.161 UPI000017DA4F Q96FN4-1 8 NA NA PASS SITE 21,21|14,15 NA NA 1 52 20,25 162,165 60,60 27 1.30 NA 5.42 NA FALSE 6.00 89 NA NA NA FALSE NA NA 91.51 8 57121291 HCC1395_HCC1395T 15 0.667 44 6,7 3,12 10,21 NA 0/1 NA NA NA NA 6,9,14,15 C/T PANCANCER NA FALSE CPNE2 chr16:57121291:57121292:C:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57186833 57186834 G A 66 107 0.616822429906542 MODIFIER PSME3IP1 ENSG00000172775 A upstream_gene_variant Transcript ENST00000309137 protein_coding NA rs11076181 794 -1 SNV HGNC HGNC:29856 YES NM_024946.4 1 P1 CCDS42168.1 ENSP00000335808 Q9GZU8.144 A0A024R6T8.62 UPI000003620C 0.3980 0.41 0.4524 0.3919 0.493 0.2515 0.4398 0.4128 0.3505 0.4455 0.4278 0.407 0.4558 0.4715 0.4689 0.4606 0.2525 0.493 EUR 8 NA NA PASS SITE 46,46|36,30 NA NA 1 30 20,35 163,182 60,60 35 1.51 NA 9.33 NA FALSE 0.350 93 NA NA NA FALSE NA NA 202.93 8 57186833 HCC1395_HCC1395T 41 0.654 107 10,21 14,28 27,52 NA 0/1 NA NA NA NA 22,19,36,30 G/A PANCANCER NA FALSE PSME3IP1 chr16:57186833:57186834:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57416065 57416066 T C 67 108 0.62037037037037 MODIFIER CCL17 ENSG00000102970 C downstream_gene_variant Transcript ENST00000219244 protein_coding NA rs117566975 2 1 SNV HGNC HGNC:10615 YES NM_002987.3 1 P1 CCDS10780.1 ENSP00000219244 Q92583.184 UPI00001362D9 0.0014 0 0.0029 0 0.005 0 0.002293 0.00082 0 0.004055 0 0 0 0 0.003645 0.002388 0 0.005 EUR 8 NA NA PASS SITE 40,70|27,40 NA NA 1 93 20,20 167,168 60,60 29 1.68 NA 14.14 NA FALSE 2.77 93 NA NA NA FALSE NA NA 182.57 8 57416065 HCC1395_HCC1395T 41 0.597 108 15,13 10,24 30,45 NA 0/1 NA NA NA NA 14,27,27,40 T/C PANCANCER NA FALSE CCL17 chr16:57416065:57416066:T:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57475272 57475273 G A 65 82 0.792682926829268 MODIFIER POLR2C ENSG00000102978 A downstream_gene_variant Transcript ENST00000219252 protein_coding NA rs147240098 3263 1 SNV HGNC HGNC:9189 YES NM_032940.3 1 P1 CCDS10782.1 ENSP00000219252 P19387.220 Q6FGR6.145 UPI00000012C1 0.0106 0 0.0231 0 0.0358 0.001 0.02389 0.005876 0.004386 0.02672 0.01786 0 0.0522 0.02532 0.03355 0.02876 0.002693 0.0522 gnomADg_FIN 8 NA NA PASS SITE 18,37|29,36 NA NA 1 53 20,20 160,172 60,60 31 1.45 NA 8.13 NA FALSE 1.60 93 NA NA NA FALSE NA NA 173.62 8 57475272 HCC1395_HCC1395T 17 0.781 82 2,12 7,20 11,42 NA 0/1 NA NA NA NA 6,11,29,36 G/A PANCANCER NA FALSE POLR2C chr16:57475272:57475273:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57529199 57529200 A G 125 201 0.621890547263682 MODIFIER CCDC102A ENSG00000135736 G 5_prime_UTR_variant Transcript ENST00000258214 protein_coding 2/9 ENST00000258214.3:c.-22T>C NA 198 rs4784815&COSV50779554 -1 SNV HGNC HGNC:28097 YES NM_033212.4 1 P1 CCDS10784.1 ENSP00000258214 Q96A19.132 UPI000013CFBA 0.5363 0.9297 0.3256 0.3155 0.4165 0.5051 0.3822 1 0.25 0.3778 0.25 0.5133 0.848 0.4901 0.371 0.3533 0.2761 0.3589 0.4459 0.393 0.4823 0.5048 1 gnomADe_AFR 0&1 0&1 8 NA NA PASS SITE 100,92|69,56 NA NA 1 93 20,20 160,162 60,60 27 1.90 NA 23.43 NA FALSE 0.316 93 NA NA NA FALSE NA NA 343.66 8 57529199 HCC1395_HCC1395T 76 0.603 201 28,38 22,41 55,84 NA 0/1 NA NA NA NA 35,41,69,56 A/G PANCANCER NA FALSE CCDC102A chr16:57529199:57529200:A:G SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57542646 57542647 GAAGCTAC G 56 121 0.462809917355372 MODIFIER ADGRG5 ENSG00000159618 - upstream_gene_variant Transcript ENST00000340339 protein_coding NA rs11277477 36 1 deletion HGNC HGNC:19010 1 P1 CCDS10785.1 ENSP00000342981 Q8IZF4.157 UPI0000039944 0.3516 0.4123 0.3905 0.4157 0.2863 0.2434 0.3562 0.4129 0.4143 0.3851 0.327 0.4521 0.3802 0.3608 0.3113 0.3544 0.2684 0.4521 gnomADg_EAS 1 32888493 8 NA NA PASS SITE 55,61|33,23 NA NA 1 40 20,20 171,163 60,60 26 1.60 NA 11.42 NA FALSE 0.446 93 NA NA NA FALSE NA NA 156.94 8 57542646 HCC1395_HCC1395T 65 0.476 121 17,18 16,18 45,41 NA 0/1 NA NA NA NA 29,36,33,23 GAAGCTAC/G PANCANCER NA FALSE ADGRG5 chr16:57542646:57542647:GAAGCTAC:G indel 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57561934 57561935 G A 40 147 0.272108843537415 MODIFIER ADGRG5 ENSG00000159618 A intron_variant Transcript ENST00000340339 protein_coding 1/11 ENST00000340339.4:c.-38-122G>A NA 1 SNV HGNC HGNC:19010 1 P1 CCDS10785.1 ENSP00000342981 Q8IZF4.157 UPI0000039944 8 NA NA PASS SITE 109,58|27,13 NA NA 1 93 20,20 162,158 60,60 30 1.65 NA 12.90 NA FALSE 6.00 72 NA NA NA FALSE NA NA 93.53 8 57561934 HCC1395_HCC1395T 107 0.290 147 27,9 45,19 74,30 NA 0/1 NA NA NA NA 68,39,27,13 G/A PANCANCER NA FALSE ADGRG5 chr16:57561934:57561935:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57656381 57656382 C T 23 36 0.638888888888889 MODIFIER ADGRG1 ENSG00000205336 T intron_variant Transcript ENST00000388813 protein_coding 9/14 ENST00000388813.9:c.1063+110C>T NA rs113013178 1 SNV HGNC HGNC:4512 1 P4 CCDS32461.1 ENSP00000373465 Q9Y653.190 A0A0S2Z517.51 UPI00001FF2A9 Q9Y653-2 1 0.0010 0.0008 0 0 0.004 0 0.002019 0.0007974 0 0.0004585 0 0 0.000943 0.003165 0.003558 0 0.002908 0.004 EUR 8 NA NA PASS SITE 5,22|5,18 NA NA 1 7 39,38 203,166 60,60 14 1.18 NA 4.21 NA FALSE 2.63 69 NA NA NA FALSE NA NA 77.33 8 57656381 HCC1395_HCC1395T 13 0.636 36 3,5 7,12 11,20 NA 0/1 NA NA NA NA 3,10,5,18 C/T PANCANCER NA FALSE ADGRG1 chr16:57656381:57656382:C:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57664802 57664803 C A 80 117 0.683760683760684 MODIFIER ADGRG3 ENSG00000182885 A upstream_gene_variant Transcript ENST00000333493 protein_coding NA rs80206511 3504 1 SNV HGNC HGNC:13728 YES NM_170776.5 1 P2 CCDS10786.1 ENSP00000332900 Q86Y34.155 UPI000003C9E1 0.0405 0.0265 0.072 0.0288 0.0278 0.0624 0.04036 0.03059 0.05714 0.04328 0.02823 0.03712 0.04634 0.009494 0.04428 0.03629 0.05963 0.072 AMR benign 1 8 NA NA PASS SITE 32,57|36,44 NA NA 1 68 20,20 180,154 60,60 30 1.61 NA 11.74 NA FALSE 1.37 93 NA NA NA FALSE NA NA 217.34 8 57664802 HCC1395_HCC1395T 37 0.656 117 9,17 18,34 28,54 NA 0/1 NA NA NA NA 14,23,36,44 C/A PANCANCER NA FALSE ADGRG3 chr16:57664802:57664803:C:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57753151 57753152 G C 296 496 0.596774193548387 LOW KATNB1 ENSG00000140854 C synonymous_variant Transcript ENST00000379661 protein_coding 11/20 ENST00000379661.8:c.930G>C ENSP00000368982.3:p.T310= ENSP00000368982.3 p.T310= 1282 930 310 T acG/acC rs147460464 1 SNV HGNC HGNC:6217 YES NM_005886.3 5 P1 CCDS10788.1 ENSP00000368982 Q9BVA0.180 UPI000007388F 1 Gene3D:2.130.10.10&HAMAP:MF_03022&PANTHER:PTHR19845&AlphaFold_DB_import:AF-Q9BVA0-F1 0.0008 0 0.0029 0 0.002 0 0.001744 0.0004996 0.001044 0.001504 0 0.002183 0.002802 0.002483 0 0.001584 0.0004343 0 0.0005234 0.002016 0 0.0016 0 0.002807 0 0 0.0029 AMR benign/likely_benign&likely_benign 1 8 NA NA PASS SITE 215,251|153,143 NA NA 1 93 20,20 155,159 60,60 31 2.25 NA 52.62 NA FALSE 2.78 93 NA NA NA FALSE NA NA 759.15 8 57753151 HCC1395_HCC1395T 200 0.592 496 63,85 55,96 131,190 NA 0/1 NA NA NA NA 91,109,153,143 G/C PANCANCER NA FALSE KATNB1_p.T310= chr16:57753151:57753152:G:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57775080 57775081 C T 124 220 0.563636363636364 MODIFIER KIFC3 ENSG00000140859 T intron_variant Transcript ENST00000379655 protein_coding 3/18 ENST00000379655.8:c.316-2792G>A NA rs56302643 -1 SNV HGNC HGNC:6326 1 P4 CCDS10789.2 ENSP00000368976 Q9BVG8.189 UPI000059D399 Q9BVG8-3 0.0801 0.0053 0.1009 0.1369 0.1054 0.0818 0.08117 0.02083 0.08662 0.1108 0.07316 0.1268 0.0996 0.1266 0.1046 0.08821 0.08499 0.1369 EAS 8 NA NA PASS SITE 100,104|53,71 NA NA 1 93 20,20 156,160 60,60 34 1.84 NA 20.42 NA FALSE 1.08 93 NA NA NA FALSE NA NA 316.58 8 57775080 HCC1395_HCC1395T 96 0.575 220 27,35 31,41 61,83 NA 0/1 NA NA NA NA 49,47,53,71 C/T PANCANCER NA FALSE KIFC3 chr16:57775080:57775081:C:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57788741 57788742 G A 47 82 0.573170731707317 MODIFIER KIFC3 ENSG00000140859 A intron_variant Transcript ENST00000379655 protein_coding 3/18 ENST00000379655.8:c.315+6258C>T NA rs58082302&COSV65551461 -1 SNV HGNC HGNC:6326 1 P4 CCDS10789.2 ENSP00000368976 Q9BVG8.189 UPI000059D399 Q9BVG8-3 0.0905 0.0492 0.0893 0.1379 0.1064 0.0818 0.09546 0.06598 0.08631 0.08246 0.1243 0.1026 0.1031 0.1 0.0847 0.09112 0.0616 0.08462 0.1007 0.07316 0.127 0.09906 0.1329 0.1043 0.09503 0.08316 0.1379 EAS 0&1 0&1 8 NA NA PASS SITE 24,52|13,34 NA NA 1 36 20,20 165,181 60,60 24 1.48 NA 8.68 NA FALSE 1.03 93 NA NA NA FALSE NA NA 134.97 8 57788741 HCC1395_HCC1395T 35 0.581 82 12,14 11,21 25,35 NA 0/1 NA NA NA NA 10,25,13,34 G/A PANCANCER NA FALSE KIFC3 chr16:57788741:57788742:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57816237 57816238 C G 77 123 0.626016260162602 MODIFIER ENSG00000187185 G non_coding_transcript_exon_variant Transcript ENST00000335616 lncRNA 4/4 ENST00000335616.3:n.608C>G NA 608 rs1477404 1 SNV 2 0.2496 0.2927 0.1744 0.1042 0.2972 0.3456 0.262 0.2995 0.1821 0.2547 0.09893 0.3554 0.2861 0.2732 0.3284 0.2869 0.3094 0.2374 0.2161 0.2625 0.09907 0.3577 0.2943 0.2918 0.2785 0.3255 0.3577 gnomADg_FIN 8 NA NA PASS SITE 60,59|37,40 NA NA 1 75 20,20 148,159 60,60 39 1.66 NA 13.54 NA FALSE 0.529 93 NA NA NA FALSE NA NA 190.49 8 57816237 HCC1395_HCC1395T 46 0.607 123 12,26 18,19 31,48 NA 0/1 NA NA NA NA 23,23,37,40 C/G PANCANCER NA FALSE chr16:57816237:57816238:C:G SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57958367 57958368 C G 63 176 0.357954545454545 MODIFIER CNGB1 ENSG00000070729 G intron_variant Transcript ENST00000251102 protein_coding 11/32 ENST00000251102.13:c.837+43G>C NA -1 SNV HGNC HGNC:2151 YES NM_001297.5 1 P4 CCDS42169.1 ENSP00000251102 Q14028.187 UPI000013CCDF Q14028-1 1 8 NA NA PASS SITE 120,84|39,24 NA NA 1 93 20,20 155,158 60,60 25 1.78 NA 17.76 NA FALSE 6.00 93 NA NA NA FALSE NA NA 160.18 8 57958367 HCC1395_HCC1395T 113 0.353 176 35,25 37,14 78,42 NA 0/1 NA NA NA NA 67,46,39,24 C/G PANCANCER NA FALSE CNGB1 chr16:57958367:57958368:C:G SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57959937 57959938 C T 22 34 0.647058823529412 MODERATE CNGB1 ENSG00000070729 T missense_variant Transcript ENST00000251102 protein_coding 10/33 ENST00000251102.13:c.712G>A ENSP00000251102.8:p.G238S ENSP00000251102.8 p.G238S 789 712 238 G/S Ggc/Agc rs61745888&COSV51899889 -1 SNV HGNC HGNC:2151 YES NM_001297.5 1 P4 CCDS42169.1 ENSP00000251102 Q14028.187 UPI000013CCDF Q14028-1 1 tolerated_low_confidence(0.7) benign(0) AlphaFold_DB_import:AF-Q14028-F1&MobiDB_lite:mobidb-lite 0.0114 0.0023 0.0159 0 0.0288 0.0143 0.01669 0.003152 0.01225 0.01281 0.0003015 0.01402 0.02255 0.01665 0.02049 0.01451 0.003672 0 0.01708 0.01326 0.0003862 0.01473 0.0443 0.02149 0.01676 0.01637 0.0443 gnomADg_MID benign&likely_benign 0&1 1&1 23757202&30098192 8 NA NA PASS SITE 23,11|12,10 NA NA 1 6 20,20 154,156 60,60 44 1.23 NA 4.82 NA FALSE 1.85 85 NA NA NA FALSE NA NA 56.31 8 57959937 HCC1395_HCC1395T 12 0.601 34 2,6 6,7 9,14 NA 0/1 NA NA NA NA 9,3,12,10 C/T PANCANCER NA FALSE CNGB1_p.G238S chr16:57959937:57959938:C:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 57960043 57960044 T C 74 124 0.596774193548387 LOW CNGB1 ENSG00000070729 C synonymous_variant Transcript ENST00000251102 protein_coding 10/33 ENST00000251102.13:c.606A>G ENSP00000251102.8:p.E202= ENSP00000251102.8 p.E202= 683 606 202 E gaA/gaG rs76788887&COSV51899900 -1 SNV HGNC HGNC:2151 YES NM_001297.5 1 P4 CCDS42169.1 ENSP00000251102 Q14028.187 UPI000013CCDF Q14028-1 1 AlphaFold_DB_import:AF-Q14028-F1&MobiDB_lite:mobidb-lite 0.0100 0.0023 0.0144 0 0.0288 0.0082 0.01508 0.003066 0.01237 0.009249 7.673e-05 0.01397 0.02139 0.01641 0.01459 0.0139 0.003601 0 0.01636 0.009233 0.0001936 0.01473 0.04114 0.02101 0.01583 0.01036 0.04114 gnomADg_MID benign&likely_benign 0&1 1&1 23757202 8 NA NA PASS SITE 54,44|42,33 NA NA 1 39 20,20 147,162 60,60 38 1.43 NA 8.33 NA FALSE 1.85 67 NA NA NA FALSE NA NA 180.62 8 57960043 HCC1395_HCC1395T 50 0.567 124 12,10 21,33 34,45 NA 0/1 NA NA NA NA 28,22,42,32 T/C PANCANCER NA FALSE CNGB1_p.E202= chr16:57960043:57960044:T:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 58282793 58282794 G A 64 79 0.810126582278481 MODIFIER CCDC113 ENSG00000103021 A 3_prime_UTR_variant Transcript ENST00000219299 protein_coding 9/9 ENST00000219299.8:c.*3016G>A NA 4229 rs138079638 1 SNV HGNC HGNC:25002 YES NM_014157.4 1 P1 CCDS10795.1 ENSP00000219299 Q9H0I3.141 UPI000007254E Q9H0I3-1 0.0048 0.0015 0.0072 0 0.0109 0.0061 0.008425 0.002148 0 0.008441 0.02477 0.0003854 0.002732 0.006329 0.01308 0.01194 0.006221 0.02477 gnomADg_ASJ 8 NA NA PASS SITE 30,27|37,27 NA NA 1 68 20,20 166,174 60,60 33 1.48 NA 8.73 NA FALSE 2.10 93 NA NA NA FALSE NA NA 186.06 8 58282793 HCC1395_HCC1395T 15 0.810 79 4,15 6,29 10,46 NA 0/1 NA NA NA NA 7,8,37,27 G/A PANCANCER NA FALSE CCDC113 chr16:58282793:58282794:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 58512393 58512394 C T 89 124 0.717741935483871 MODIFIER SETD6 ENSG00000103037 T upstream_gene_variant Transcript ENST00000219315 protein_coding NA rs1058132 3124 1 SNV HGNC HGNC:26116 YES NM_001160305.4 1 CCDS54013.1 ENSP00000219315 Q8TBK2.147 UPI000013C779 Q8TBK2-1 0.4750 0.6619 0.2968 0.5546 0.3121 0.4346 0.3814 0.5861 0.1371 0.3168 0.3474 0.5656 0.2531 0.4842 0.28 0.375 0.414 0.6619 AFR 8 NA NA PASS SITE 52,49|53,36 NA NA 1 80 20,32 163,171 60,60 27 1.67 NA 13.50 NA FALSE 0.439 93 NA NA NA FALSE NA NA 273.54 8 58512393 HCC1395_HCC1395T 35 0.734 124 4,24 15,42 24,68 NA 0/1 NA NA NA NA 16,19,53,36 C/T PANCANCER NA FALSE SETD6 chr16:58512393:58512394:C:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 58515417 58515418 G C 71 113 0.628318584070796 MODIFIER SETD6 ENSG00000103037 C upstream_gene_variant Transcript ENST00000219315 protein_coding NA rs34676074 100 1 SNV HGNC HGNC:26116 YES NM_001160305.4 1 CCDS54013.1 ENSP00000219315 Q8TBK2.147 UPI000013C779 Q8TBK2-1 0.0379 0.0053 0.0288 0 0.0865 0.0777 0.05037 0.01288 0.05921 0.04814 0.088 0.0001928 0.06549 0.09177 0.07054 0.06399 0.0785 0.09177 gnomADg_MID 8 NA NA PASS SITE 67,35|46,25 NA NA 2 71 20,20 173,153 60,60 34 1.63 NA 12.25 NA FALSE 1.28 93 NA NA NA FALSE NA NA 191.31 8 58515417 HCC1395_HCC1395T 42 0.607 113 15,22 11,24 31,48 NA 0/1 NA NA NA NA 27,15,46,25 G/C PANCANCER NA FALSE SETD6 chr16:58515417:58515418:G:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 58519873 58519874 G A 238 339 0.702064896755162 MODIFIER SETD6 ENSG00000103037 A 3_prime_UTR_variant Transcript ENST00000219315 protein_coding 8/8 ENST00000219315.9:c.*844G>A NA 2287 rs3200575 1 SNV HGNC HGNC:26116 YES NM_001160305.4 1 CCDS54013.1 ENSP00000219315 Q8TBK2.147 UPI000013C779 Q8TBK2-1 0.4854 0.6702 0.2939 0.5694 0.3211 0.454 0.3892 0.5891 0.1414 0.3201 0.3745 0.5731 0.2642 0.4873 0.2898 0.3816 0.4282 0.6702 AFR 33119910 8 NA NA PASS SITE 81,136|91,147 NA NA 1 93 20,20 167,162 60,60 31 1.91 NA 23.78 NA FALSE 0.429 93 NA NA NA FALSE NA NA 647.55 8 58519873 HCC1395_HCC1395T 101 0.702 339 24,53 41,96 68,162 NA 0/1 NA NA NA NA 36,65,91,147 G/A PANCANCER NA FALSE SETD6 chr16:58519873:58519874:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 58560430 58560431 G A 3 15 0.2 MODIFIER CNOT1 ENSG00000125107 A intron_variant Transcript ENST00000317147 protein_coding 16/48 ENST00000317147.10:c.1980-68C>T NA rs1403760336 -1 SNV HGNC HGNC:7877 YES NM_016284.5 1 P3 CCDS10799.1 ENSP00000320949 A5YKK6.140 UPI00001FF2F6 A5YKK6-1 1 1.019e-05 0 0 0 0 0 0 0 0 0 0.0003147 0.0003147 gnomADg_SAS 8 NA NA PASS SITE 2,19|0,3 NA NA 1 29 37,35 231,204 60,60 25 1.02 NA 2.71 NA FALSE 6.00 8 NA NA NA FALSE NA NA 6.81 8 58560430 HCC1395_HCC1395T 12 0.265 15 1,0 3,0 10,3 NA 0/1 NA NA NA NA 2,10,0,3 G/A PANCANCER NA FALSE CNOT1 chr16:58560430:58560431:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 58665158 58665159 C T 60 89 0.674157303370786 MODIFIER SLC38A7 ENSG00000103042 T 3_prime_UTR_variant Transcript ENST00000219320 protein_coding 12/12 ENST00000219320.9:c.*2227G>A NA 4009 rs117711557 -1 SNV HGNC HGNC:25582 YES NM_018231.3 1 P1 CCDS10800.1 ENSP00000219320 Q9NVC3.156 UPI000004EC72 Q9NVC3-1 0.0104 0.0212 0.0058 0 0.0119 0.0082 0.01176 0.01763 0.004396 0.008519 0.03489 0 0.0008491 0.03165 0.01033 0.01437 0.01077 0.03489 gnomADg_ASJ 8 NA NA PASS SITE 54,31|37,23 NA NA 1 53 20,20 150,157 60,60 27 1.52 NA 9.63 NA FALSE 1.96 80 NA NA NA FALSE NA NA 156.40 8 58665158 HCC1395_HCC1395T 29 0.640 89 7,10 14,28 22,40 NA 0/1 NA NA NA NA 22,7,37,23 C/T PANCANCER NA FALSE SLC38A7 chr16:58665158:58665159:C:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 58707311 58707312 A T 62 88 0.704545454545455 MODIFIER GOT2 ENSG00000125166 T 3_prime_UTR_variant Transcript ENST00000245206 protein_coding 10/10 ENST00000245206.10:c.*860T>A NA 2241 rs11861897 -1 SNV HGNC HGNC:4433 YES NM_002080.4 1 P1 CCDS10801.1 ENSP00000245206 P00505.226 UPI000013CB99 P00505-1 1 0.0593 0.1831 0.0317 0 0.0239 0.0092 0.0554 0.1543 0.004386 0.03287 0.0438 0.0001927 0.001226 0.07278 0.01742 0.0489 0.01306 0.1831 AFR 8 NA NA PASS SITE 47,24|41,21 NA NA 1 52 34,35 178,197 60,60 26 1.54 NA 9.93 NA FALSE 1.35 93 NA NA NA FALSE NA NA 200.13 8 58707311 HCC1395_HCC1395T 26 0.700 88 3,15 17,35 22,52 NA 0/1 NA NA NA NA 18,8,41,21 A/T PANCANCER NA FALSE GOT2 chr16:58707311:58707312:A:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 58709715 58709716 G A 22 36 0.611111111111111 MODIFIER GOT2 ENSG00000125166 A intron_variant Transcript ENST00000245206 protein_coding 8/9 ENST00000245206.10:c.1020-148C>T NA -1 SNV HGNC HGNC:4433 YES NM_002080.4 1 P1 CCDS10801.1 ENSP00000245206 P00505.226 UPI000013CB99 P00505-1 1 8 NA NA PASS SITE 2,21|3,19 NA NA 1 22 38,37 203,196 60,60 23 0.954 NA 2.41 NA FALSE 6.00 49 NA NA NA FALSE NA NA 71.19 8 58709715 HCC1395_HCC1395T 14 0.588 36 5,4 7,15 13,19 NA 0/1 NA NA NA NA 1,13,3,19 G/A PANCANCER NA FALSE GOT2 chr16:58709715:58709716:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 61648049 61648050 G C 111 374 0.296791443850267 MODIFIER CDH8 ENSG00000150394 C intron_variant Transcript ENST00000299345 protein_coding 12/12 ENST00000299345.10:c.2127-161C>G NA -1 SNV HGNC HGNC:1767 5 ENSP00000299345 X6R3Y6.54 UPI0002466E90 8 NA NA PASS SITE 192,149|61,50 NA NA 1 93 20,20 156,176 60,60 31 1.72 NA 15.05 NA FALSE 6.00 93 NA NA NA FALSE NA NA 275.80 8 61648049 HCC1395_HCC1395T 263 0.309 374 72,26 89,45 171,76 NA 0/1 NA NA NA NA 147,116,61,50 G/C PANCANCER NA FALSE CDH8 chr16:61648049:61648050:G:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 61651938 61651939 G C 28 90 0.311111111111111 MODIFIER CDH8 ENSG00000150394 C intron_variant Transcript ENST00000299345 protein_coding 12/12 ENST00000299345.10:c.2126+1944C>G NA -1 SNV HGNC HGNC:1767 5 ENSP00000299345 X6R3Y6.54 UPI0002466E90 8 NA NA PASS SITE 21,71|7,21 NA NA 1 66 34,29 174,163 60,60 27 1.36 NA 6.62 NA FALSE 6.00 48 NA NA NA FALSE NA NA 77.03 8 61651938 HCC1395_HCC1395T 62 0.306 90 7,3 33,15 49,21 NA 0/1 NA NA NA NA 13,49,7,21 G/C PANCANCER NA FALSE CDH8 chr16:61651938:61651939:G:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 61725569 61725570 A G 581 877 0.66248574686431 MODIFIER CDH8 ENSG00000150394 G intron_variant Transcript ENST00000299345 protein_coding 9/12 ENST00000299345.10:c.1536+1525T>C NA rs79574106 -1 SNV HGNC HGNC:1767 5 ENSP00000299345 X6R3Y6.54 UPI0002466E90 0.1116 0.0356 0.1427 0.1389 0.1193 0.1564 0.1129 0.04778 0.1495 0.1455 0.1111 0.1551 0.1291 0.1529 0.1362 0.1054 0.159 0.159 gnomADg_SAS 8 NA NA PASS SITE 230,272|254,327 NA NA 1 93 20,20 159,165 60,60 39 2.14 NA 40.58 NA FALSE 0.921 93 NA NA NA FALSE NA NA 1607.14 8 61725569 HCC1395_HCC1395T 296 0.660 877 60,129 116,230 198,385 NA 0/1 NA NA NA NA 135,161,254,327 A/G PANCANCER NA FALSE CDH8 chr16:61725569:61725570:A:G SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 66730166 66730167 G A 89 160 0.55625 LOW DYNC1LI2 ENSG00000135720 A synonymous_variant Transcript ENST00000258198 protein_coding 8/13 ENST00000258198.7:c.987C>T ENSP00000258198.2:p.T329= ENSP00000258198.2 p.T329= 1005 987 329 T acC/acT rs34706526 -1 SNV HGNC HGNC:2966 YES NM_006141.3 1 P1 CCDS10818.1 ENSP00000258198 O43237.174 A0A024R6Z0.49 UPI0000129A0D O43237-1 PDB-ENSP_mappings:6f1t.i&PDB-ENSP_mappings:6f1t.j&PDB-ENSP_mappings:6f1t.q&PDB-ENSP_mappings:6f1t.r&PDB-ENSP_mappings:6f1y.j&PDB-ENSP_mappings:6f38.i&PDB-ENSP_mappings:6f38.j&PDB-ENSP_mappings:6f38.q&PDB-ENSP_mappings:6f38.r&PDB-ENSP_mappings:6f3a.j&PDB-ENSP_mappings:7z8f.i&PDB-ENSP_mappings:7z8f.j&PDB-ENSP_mappings:7z8f.q&PDB-ENSP_mappings:7z8f.r&PDB-ENSP_mappings:7z8i.j&PDB-ENSP_mappings:7z8i.r&PDB-ENSP_mappings:7z8j.j&PDB-ENSP_mappings:7z8j.r&PDB-ENSP_mappings:7z8k.i&PDB-ENSP_mappings:7z8l.q&PANTHER:PTHR12688&Pfam:PF05783&AlphaFold_DB_import:AF-O43237-F1 1.993e-05 0 0 0 0 0 4.402e-05 0 0 6.573e-06 0 0 0 0 0 0 0 1.47e-05 0 0 4.402e-05 gnomADe_NFE 8 NA NA PASS SITE 71,67|48,41 NA NA 1 93 20,20 151,165 60,60 34 1.67 NA 13.54 NA FALSE 6.00 93 NA NA NA FALSE NA NA 239.57 8 66730166 HCC1395_HCC1395T 71 0.583 160 21,21 19,36 42,59 NA 0/1 NA NA NA NA 36,35,48,41 G/A PANCANCER NA FALSE DYNC1LI2_p.T329= chr16:66730166:66730167:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 67146163 67146165 CT GA 104 178 0.584269662921348 MODIFIER PHAF1 ENSG00000125149 GA intron_variant Transcript ENST00000219139 protein_coding 14/15 ENST00000219139.8:c.1110-115_1110-114delinsGA NA 1 substitution HGNC HGNC:29564 YES NM_025187.5 1 P1 CCDS10828.1 ENSP00000219139 Q9BSU1.141 A0A024R6W4.52 UPI0000137911 Q9BSU1-1 8 NA NA PASS SITE 94,55|70,34 NA NA 1 93 20,20 165,164 60,60 32 1.44 NA 15.65 NA FALSE 6.00 93 NA NA NA FALSE NA NA 343.78 8 67146163 HCC1395_HCC1395T 74 0.583 178 21,23 25,48 52,73 NA 0/1 NA NA NA NA 47,27,70,34 CT/GA PANCANCER NA FALSE PHAF1 chr16:67146163:67146165:CT:GA indel 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 67188925 67188926 A T 235 386 0.60880829015544 MODIFIER MATCAP1 ENSG00000196123 T upstream_gene_variant Transcript ENST00000290881 protein_coding NA rs117403380&COSV52048761 4885 -1 SNV HGNC HGNC:34408 5 P1 CCDS42177.1 ENSP00000290881 Q68EN5.127 UPI00001AEB6A Q68EN5-1 0.0022 0 0.0029 0 0.0089 0 0.00738 0.0006825 0.002868 0.001197 5.445e-05 0.03146 0.008316 0.0059 0.002255 0.006838 0.0006276 0.002193 0.0053 0.00173 0 0.02811 0.009494 0.008707 0.008118 0.003104 0.03146 gnomADe_FIN 0&1 0&1 8 NA NA PASS SITE 191,165|126,109 NA NA 1 93 20,20 156,159 60,60 35 2.15 NA 41.53 NA FALSE 2.07 93 NA NA NA FALSE NA NA 618.63 8 67188925 HCC1395_HCC1395T 151 0.601 386 41,61 56,84 102,154 NA 0/1 NA NA NA NA 82,69,126,109 A/T PANCANCER NA FALSE MATCAP1 chr16:67188925:67188926:A:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 67376909 67376910 G A 135 210 0.642857142857143 MODIFIER LRRC36 ENSG00000159708 A intron_variant Transcript ENST00000329956 protein_coding 11/13 ENST00000329956.11:c.1806+37G>A NA 1 SNV HGNC HGNC:25615 YES NM_018296.6 1 P1 CCDS32467.1 ENSP00000329943 Q1X8D7.121 UPI0000409634 Q1X8D7-1 8 NA NA PASS SITE 60,76|63,72 NA NA 1 93 20,20 149,158 60,60 34 1.67 NA 13.54 NA FALSE 6.00 93 NA NA NA FALSE NA NA 372.30 8 67376909 HCC1395_HCC1395T 75 0.653 210 17,36 28,51 49,93 NA 0/1 NA NA NA NA 36,39,63,72 G/A PANCANCER NA FALSE LRRC36 chr16:67376909:67376910:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 67457668 67457669 T C 108 139 0.776978417266187 MODIFIER ATP6V0D1 ENSG00000159720 C intron_variant Transcript ENST00000290949 protein_coding 1/7 ENST00000290949.8:c.131-3953A>G NA rs749242 -1 SNV HGNC HGNC:13724 YES NM_004691.5 1 P1 CCDS10838.1 ENSP00000290949 P61421.166 UPI0000138041 0.0425 0.0061 0.1499 0 0.0765 0.0245 0.06555 0.01266 0.1221 0.02649 0.0002873 0.09344 0.07414 0.06719 0.03651 0.05572 0.01361 0.09539 0.089 0.02506 0.0003855 0.09859 0.03503 0.07385 0.0616 0.03517 0.1499 AMR 8 NA NA PASS SITE 36,62|47,61 NA NA 1 93 20,20 168,168 60,60 28 1.66 NA 13.55 NA FALSE 1.24 93 NA NA NA FALSE NA NA 280.54 8 67457668 HCC1395_HCC1395T 31 0.767 139 9,29 9,35 20,68 NA 0/1 NA NA NA NA 11,20,47,61 T/C PANCANCER NA FALSE ATP6V0D1 chr16:67457668:67457669:T:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 67893377 67893378 G A 57 71 0.802816901408451 LOW PSKH1 ENSG00000159792 A splice_donor_region_variant&intron_variant Transcript ENST00000291041 protein_coding 1/2 ENST00000291041.6:c.-71+6G>A NA rs538467132 1 SNV HGNC HGNC:9529 YES NM_006742.3 1 P1 CCDS10851.1 ENSP00000291041 P11801.197 UPI000012DFE0 0.0008 0 0 0 0.004 0 0.004126 0.0001688 0.002193 0.0003271 0.002016 0.0001925 0.0263 0 0.004514 0.001434 0.003514 0.0263 gnomADg_FIN 8 NA NA PASS SITE 25,28|27,30 NA NA 1 47 20,20 148,156 60,60 40 1.39 NA 6.88 NA FALSE 2.22 93 NA NA NA FALSE NA NA 142.94 8 67893377 HCC1395_HCC1395T 14 0.787 71 4,16 3,16 9,36 NA 0/1 NA NA NA NA 7,7,27,30 G/A PANCANCER NA FALSE PSKH1 chr16:67893377:67893378:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 68834619 68834620 T C 60 77 0.779220779220779 MODIFIER CDH1 ENSG00000039068 C 3_prime_UTR_variant Transcript ENST00000261769 protein_coding 16/16 ENST00000261769.10:c.*1120T>C NA 3893 rs13689&COSV55740499 1 SNV HGNC HGNC:1748 YES NM_004360.5 1 P1 CCDS10869.1 ENSP00000261769 P12830.256 A0A0U2ZQU7.41 UPI00000341EF P12830-1 1 0.1514 0.1467 0.1499 0.1567 0.1918 0.1115 0.1776 0.1521 0.1162 0.1795 0.1841 0.1564 0.2122 0.2437 0.1945 0.1611 0.1102 0.2437 gnomADg_MID benign 0&1 1&1 26959740&29963112&20044998&26285011&29433565&22535324&22330421&30405831&19834798&21459793&27192129&24660577&25150394&26511186 8 NA NA PASS SITE 35,27|35,25 NA NA 1 45 20,20 159,160 60,60 31 1.48 NA 8.73 NA FALSE 0.745 84 NA NA NA FALSE NA NA 166.64 8 68834619 HCC1395_HCC1395T 17 0.769 77 3,10 8,28 11,39 NA 0/1 NA NA NA NA 10,7,35,25 T/C PANCANCER TRUE FALSE CDH1 chr16:68834619:68834620:T:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 69085210 69085211 C G 12 38 0.315789473684211 MODIFIER TANGO6 ENSG00000103047 G downstream_gene_variant Transcript ENST00000261778 protein_coding NA 28 1 SNV HGNC HGNC:25749 YES NM_024562.2 1 P1 CCDS45516.1 ENSP00000261778 Q9C0B7.139 UPI00001FF4A8 8 NA NA PASS SITE 6,30|1,11 NA NA 1 30 40,38 200,237 60,60 10 1.06 NA 2.96 NA FALSE 6.00 74 NA NA NA FALSE NA NA 36.52 8 69085210 HCC1395_HCC1395T 26 0.344 38 13,4 8,6 22,11 NA 0/1 NA NA NA NA 5,21,1,11 C/G PANCANCER NA FALSE TANGO6 chr16:69085210:69085211:C:G SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 69167789 69167790 T C 85 124 0.685483870967742 MODIFIER UTP4 ENSG00000141076 C intron_variant Transcript ENST00000314423 protein_coding 16/16 ENST00000314423.12:c.1944+604T>C NA rs80161903 1 SNV HGNC HGNC:1983 YES NM_032830.3 1 P1 CCDS10872.1 ENSP00000327179 Q969X6.187 UPI0000037300 Q969X6-1 1 0.0258 0.0038 0.0317 0.0179 0.0616 0.0225 0.05046 0.01357 0.08791 0.04805 0.04121 0.01317 0.09603 0.01899 0.07135 0.0462 0.02338 0.09603 gnomADg_FIN 8 NA NA PASS SITE 16,67|25,60 NA NA 1 49 36,20 176,161 60,60 15 1.54 NA 9.93 NA FALSE 1.25 54 NA NA NA FALSE NA NA 238.98 8 69167789 HCC1395_HCC1395T 39 0.639 124 3,7 17,33 34,61 NA 0/1 NA NA NA NA 5,34,25,60 T/C PANCANCER NA FALSE UTP4 chr16:69167789:69167790:T:C SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 69464650 69464651 G T 87 129 0.674418604651163 MODIFIER CYB5B ENSG00000103018 T 3_prime_UTR_variant Transcript ENST00000307892 protein_coding 5/5 ENST00000307892.13:c.*2130G>T NA 2648 rs112630491 1 SNV HGNC HGNC:24374 YES NM_030579.3 1 P2 CCDS10880.2 ENSP00000308430 O43169.188 UPI00000710AB 0.0010 0 0 0 0.005 0 0.005539 0.0004343 0.04057 0.0007199 0.0005764 0.0001921 0.02778 0 0.006821 0.00239 0.002068 0.04057 gnomADg_AMI 8 NA NA PASS SITE 32,68|35,52 NA NA 1 93 39,35 194,221 60,60 27 1.71 NA 15.05 NA FALSE 2.09 93 NA NA NA FALSE NA NA 286.52 8 69464650 HCC1395_HCC1395T 42 0.674 129 13,33 22,44 39,82 NA 0/1 NA NA NA NA 10,32,35,52 G/T PANCANCER NA FALSE CYB5B chr16:69464650:69464651:G:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 69707001 69707002 C G 51 147 0.346938775510204 MODIFIER NQO1 ENSG00000181019 G downstream_gene_variant Transcript ENST00000320623 protein_coding NA 2400 -1 SNV HGNC HGNC:2874 YES NM_000903.3 1 P1 CCDS10883.1 ENSP00000319788 P15559.226 UPI0000000C86 P15559-1 1 8 NA NA PASS SITE 80,81|25,26 NA NA 1 93 20,20 161,177 60,60 37 1.66 NA 13.24 NA FALSE 6.00 92 NA NA NA FALSE NA NA 131.16 8 69707001 HCC1395_HCC1395T 96 0.367 147 24,10 32,20 62,36 NA 0/1 NA NA NA NA 50,46,25,26 C/G PANCANCER NA FALSE NQO1 chr16:69707001:69707002:C:G SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 69748750 69748751 C T 42 58 0.724137931034483 MODIFIER NOB1 ENSG00000141101 T intron_variant Transcript ENST00000268802 protein_coding 6/8 ENST00000268802.10:c.726+168G>A NA rs118190723 -1 SNV HGNC HGNC:29540 YES NM_014062.3 1 P1 CCDS10884.1 ENSP00000268802 Q9ULX3.177 UPI0000034E10 0.0010 0 0.0014 0 0.003 0.001 0.003212 0.001013 0 0.001308 0.000288 0 0.0009411 0 0.005952 0.00191 0.001449 0.005952 gnomADg_NFE 8 NA NA PASS SITE 30,10|31,11 NA NA 1 24 34,35 170,178 60,60 29 1.31 NA 5.72 NA FALSE 2.56 93 NA NA NA FALSE NA NA 128.90 8 69748750 HCC1395_HCC1395T 16 0.711 58 2,14 10,17 12,31 NA 0/1 NA NA NA NA 12,4,31,11 C/T PANCANCER NA FALSE NOB1 chr16:69748750:69748751:C:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 70532416 70532417 A G 25 50 0.5 MODIFIER SF3B3 ENSG00000189091 G intron_variant Transcript ENST00000302516 protein_coding 4/25 ENST00000302516.10:c.571-63A>G NA rs56313425 1 SNV HGNC HGNC:10770 YES NM_012426.5 1 P1 CCDS10894.1 ENSP00000305790 Q15393.210 UPI0000167878 Q15393-1 0.0078 0.0008 0.0202 0 0.0239 0 0.01636 0.004785 0.08443 0.01592 0.011 0 0.01283 0.003289 0.02541 0.02006 0.0004292 0.08443 gnomADg_AMI 8 NA NA PASS SITE 31,14|21,4 NA NA 1 3 20,37 167,194 60,60 33 1.15 NA 3.91 NA FALSE 1.80 89 NA NA NA FALSE NA NA 74.08 8 70532416 HCC1395_HCC1395T 25 0.537 50 8,8 8,10 18,21 NA 0/1 NA NA NA NA 18,7,21,4 A/G PANCANCER NA FALSE SF3B3 chr16:70532416:70532417:A:G SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 71806623 71806624 C T 43 98 0.438775510204082 MODIFIER AP1G1 ENSG00000166747 T intron_variant Transcript ENST00000299980 protein_coding 1/22 ENST00000299980.9:c.-4+2140G>A NA rs113946669 -1 SNV HGNC HGNC:555 YES NM_001128.6 1 P4 CCDS32480.1 ENSP00000299980 O43747.210 UPI000013E60C O43747-1 1 0.0060 0.0023 0.0058 0 0.0179 0.0051 0.01231 0.003716 0.04057 0.005111 0.004608 0 0.02659 0.006329 0.01841 0.005742 0.008271 0.04057 gnomADg_AMI 8 NA NA PASS SITE 75,41|32,11 NA NA 1 82 20,37 160,186 60,60 30 1.61 NA 12.04 NA FALSE 1.82 89 NA NA NA FALSE NA NA 126.13 8 71806623 HCC1395_HCC1395T 55 0.466 98 10,11 28,22 38,33 NA 0/1 NA NA NA NA 36,19,32,11 C/T PANCANCER NA FALSE AP1G1 chr16:71806623:71806624:C:T SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 71999986 71999987 G A 6 21 0.285714285714286 MODIFIER ENSG00000263311 A downstream_gene_variant Transcript ENST00000570531 unprocessed_pseudogene NA 4253 -1 SNV YES 8 NA NA PASS SITE 4,21|1,5 NA NA 1 25 33,36 177,167 60,60 23 0.954 NA 2.41 NA FALSE 6.00 43 NA NA NA FALSE NA NA 16.21 8 71999986 HCC1395_HCC1395T 15 0.302 21 4,3 7,2 13,5 NA 0/1 NA NA NA NA 2,13,1,5 G/A PANCANCER NA FALSE chr16:71999986:71999987:G:A SNV 6:0 chr16:46608374:72014433:6:0:1 NA NA 0.96 +chr16 73093455 73093456 G A 5 29 0.172413793103448 LOW HCCAT5 ENSG00000260880 A splice_polypyrimidine_tract_variant&intron_variant&non_coding_transcript_variant Transcript ENST00000569990 lncRNA 2/2 ENST00000569990.2:n.769-9G>A NA 1 SNV HGNC HGNC:48612 1 8 NA NA PASS SITE 30,9|4,1 NA NA 1 35 26,34 193,135 60,60 35 1.04 NA 3.01 NA FALSE 6.00 21 NA NA NA FALSE NA NA 11.24 8 73093455 HCC1395_HCC1395T 24 0.192 29 5,1 15,3 20,4 NA 0/1 NA NA NA NA 20,4,4,1 G/A PANCANCER NA FALSE HCCAT5 chr16:73093455:73093456:G:A SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 74622462 74622463 CA C 84 133 0.631578947368421 MODIFIER RFWD3 ENSG00000168411 - 3_prime_UTR_variant Transcript ENST00000361070 protein_coding 13/13 ENST00000361070.9:c.*1465del NA 3884 rs11327273 -1 deletion HGNC HGNC:25539 YES NM_018124.4 1 P1 CCDS32486.1 ENSP00000354361 Q6PCD5.164 UPI0000366B66 1 0.7620 0.8396 0.7003 0.8333 0.6292 0.7638 0.7041 0.8183 0.7412 0.7281 0.5294 0.8081 0.6117 0.6242 0.641 0.6891 0.7592 0.8396 AFR 8 NA NA PASS SITE 62,36|52,32 NA NA 1 22 20,20 173,173 60,60 27 1.57 NA 10.44 NA FALSE 0.161 93 7,6 A NA TRUE NA 93 129.05 8 74622462 HCC1395_HCC1395T 49 0.619 133 12,16 20,38 35,57 NA 0/1 NA NA NA NA 33,16,52,32 CA/C PANCANCER NA FALSE RFWD3 chr16:74622462:74622463:CA:C indel 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 74660907 74660908 C G 39 119 0.327731092436975 MODIFIER RFWD3 ENSG00000168411 G intron_variant Transcript ENST00000361070 protein_coding 2/12 ENST00000361070.9:c.518+25G>C NA -1 SNV HGNC HGNC:25539 YES NM_018124.4 1 P1 CCDS32486.1 ENSP00000354361 Q6PCD5.164 UPI0000366B66 1 8 NA NA PASS SITE 78,34|25,14 NA NA 1 69 20,20 158,162 60,60 34 1.40 NA 6.92 NA FALSE 6.00 92 NA NA NA FALSE NA NA 96.42 8 74660907 HCC1395_HCC1395T 80 0.314 119 20,9 37,16 58,26 NA 0/1 NA NA NA NA 55,25,25,14 C/G PANCANCER NA FALSE RFWD3 chr16:74660907:74660908:C:G SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 74666843 74666845 T TC 39 75 0.52 MODIFIER RFWD3 ENSG00000168411 C 5_prime_UTR_variant Transcript ENST00000361070 protein_coding 1/13 ENST00000361070.9:c.-61_-60insG NA 34-35 rs561883735 -1 insertion HGNC HGNC:25539 YES NM_018124.4 1 P1 CCDS32486.1 ENSP00000354361 Q6PCD5.164 UPI0000366B66 1 0.5595 0.7312 0.4447 0.4734 0.4638 0.7725 0.4356 0.5192 0.4839 0.5564 0.5707 0.7725 gnomADg_EAS 8 NA NA PASS SITE 44,41|21,18 NA NA 2 32 20,37 157,141 60,60 31 1.54 NA 10.23 NA FALSE 0.268 93 1,2 C NA TRUE NA 93 162.99 8 74666843 HCC1395_HCC1395T 36 0.547 75 9,13 8,9 23,28 NA 0|1 0|1 74666843_T_TC NA 74666843 19,17,21,18 T|TC PANCANCER NA FALSE RFWD3 chr16:74666843:74666845:T:TC indel 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 74666845 74666869 G GCCGAAGACTCGGTAGTTACCTCC 52 88 0.590909090909091 MODIFIER RFWD3 ENSG00000168411 CCGAAGACTCGGTAGTTACCTCC 5_prime_UTR_variant Transcript ENST00000361070 protein_coding 1/13 ENST00000361070.9:c.-63_-62insGGAGGTAACTACCGAGTCTTCGG NA 32-33 rs56890104 -1 insertion HGNC HGNC:25539 YES NM_018124.4 1 P1 CCDS32486.1 ENSP00000354361 Q6PCD5.164 UPI0000366B66 1 0.4126 0.6303 0.3819 0.2875 0.3151 0.385 0.3415 0.3726 0.3376 0.3998 0.2664 0.6303 gnomADg_AFR 8 NA NA PASS SITE 44,41|27,25 NA NA 2 84 20,20 157,141 60,60 32 1.26 NA 10.29 NA FALSE 6.00 93 NA NA NA FALSE NA NA 137.00 8 74666845 HCC1395_HCC1395T 36 0.589 88 9,13 10,9 26,34 NA 0|1 0|1 74666843_T_TC NA 74666843 19,17,27,25 G|GCCGAAGACTCGGTAGTTACCTCC PANCANCER NA FALSE RFWD3 chr16:74666845:74666869:G:GCCGAAGACTCGGTAGTTACCTCC indel 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 74774370 74774371 G T 22 99 0.222222222222222 MODIFIER FA2H ENSG00000103089 T intron_variant Transcript ENST00000219368 protein_coding 1/6 ENST00000219368.8:c.270+116C>A NA -1 SNV HGNC HGNC:21197 YES NM_024306.5 1 P1 CCDS10911.1 ENSP00000219368 Q7L5A8.162 UPI000013C77C Q7L5A8-1 1 8 NA NA PASS SITE 83,30|16,6 NA NA 1 93 20,34 177,172 60,60 25 1.47 NA 8.38 NA FALSE 6.00 76 NA NA NA FALSE NA NA 53.43 8 74774370 HCC1395_HCC1395T 77 0.247 99 23,7 30,10 57,18 NA 0/1 NA NA NA NA 56,21,16,6 G/T PANCANCER NA FALSE FA2H chr16:74774370:74774371:G:T SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 74774839 74774840 C G 90 165 0.545454545454545 MODIFIER FA2H ENSG00000103089 G upstream_gene_variant Transcript ENST00000219368 protein_coding NA rs8056865 19 -1 SNV HGNC HGNC:21197 YES NM_024306.5 1 P1 CCDS10911.1 ENSP00000219368 Q7L5A8.162 UPI000013C77C Q7L5A8-1 1 0.6851 0.8018 0.5187 0.62 0.7704 0.6247 0.7494 0.8143 0.7319 0.593 0.788 0.6229 0.7948 0.828 0.7532 0.7536 0.6382 0.828 gnomADg_MID benign 1 8 NA NA PASS SITE 92,102|42,48 NA NA 1 93 20,20 149,154 60,60 39 1.85 NA 21.06 NA FALSE 0.121 93 NA NA NA FALSE NA NA 219.79 8 74774839 HCC1395_HCC1395T 75 0.557 165 17,27 28,26 45,57 NA 0/1 NA NA NA NA 35,40,42,48 C/G PANCANCER NA FALSE FA2H chr16:74774839:74774840:C:G SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 75148456 75148457 G C 32 51 0.627450980392157 MODIFIER ZFP1 ENSG00000184517 C upstream_gene_variant Transcript ENST00000332307 protein_coding NA rs8058619 78 1 SNV HGNC HGNC:23328 1 CCDS82013.1 ENSP00000333192 J3KNQ1.76 UPI00005A9025 0.1881 0.2088 0.1412 0.0704 0.2982 0.2014 0.2539 0.2092 0.2248 0.1901 0.2695 0.07944 0.3258 0.2025 0.3017 0.2342 0.2017 0.3258 gnomADg_FIN 8 NA NA PASS SITE 41,12|21,11 NA NA 1 22 29,29 183,185 60,60 27 1.45 NA 8.08 NA FALSE 0.569 93 NA NA NA FALSE NA NA 96.05 8 75148456 HCC1395_HCC1395T 19 0.610 51 6,8 8,16 15,24 NA 0/1 NA NA NA NA 15,4,21,11 G/C PANCANCER NA FALSE ZFP1 chr16:75148456:75148457:G:C SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 75171315 75171316 A G 86 140 0.614285714285714 MODIFIER ZFP1 ENSG00000184517 G downstream_gene_variant Transcript ENST00000332307 protein_coding NA rs17673793 798 1 SNV HGNC HGNC:23328 1 CCDS82013.1 ENSP00000333192 J3KNQ1.76 UPI00005A9025 0.1643 0.1172 0.1311 0.0665 0.3082 0.2045 0.2386 0.1513 0.2154 0.1827 0.2843 0.07357 0.3259 0.2025 0.3047 0.2177 0.2013 0.3259 gnomADg_FIN 1 31669095&32888493&34887591 8 NA NA PASS SITE 55,48|51,35 NA NA 1 64 34,40 206,206 60,60 34 1.63 NA 12.34 NA FALSE 0.590 93 NA NA NA FALSE NA NA 285.67 8 75171315 HCC1395_HCC1395T 54 0.586 140 17,28 33,42 51,73 NA 0/1 NA NA NA NA 30,24,51,35 A/G PANCANCER NA FALSE ZFP1 chr16:75171315:75171316:A:G SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 75235679 75235680 C G 261 458 0.569868995633188 MODERATE BCAR1 ENSG00000050820 G missense_variant Transcript ENST00000162330 protein_coding 5/7 ENST00000162330.10:c.1220G>C ENSP00000162330.5:p.S407T ENSP00000162330.5 p.S407T 1362 1220 407 S/T aGt/aCt rs144989936&COSV50809790 -1 SNV HGNC HGNC:971 YES NM_014567.5 1 P4 CCDS10915.1 ENSP00000162330 P56945.212 UPI00001FFC1B P56945-1 tolerated(0.21) PANTHER:PTHR10654&AlphaFold_DB_import:AF-P56945-F1 1.662e-05 0 0 0 0 0 3.771e-05 0 0 3.771e-05 gnomADe_NFE 0&1 0&1 8 NA NA PASS SITE 268,215|147,114 NA NA 1 93 20,20 151,164 60,60 37 2.27 NA 54.48 NA FALSE 6.00 93 NA NA NA FALSE NA NA 697.60 8 75235679 HCC1395_HCC1395T 197 0.559 458 61,73 70,93 135,172 NA 0/1 NA NA NA NA 111,86,147,114 C/G PANCANCER NA FALSE BCAR1_p.S407T chr16:75235679:75235680:C:G SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 75444549 75444550 A G 133 202 0.658415841584158 MODIFIER TMEM170A ENSG00000166822 G 3_prime_UTR_variant Transcript ENST00000357613 protein_coding 3/3 ENST00000357613.8:c.*3009T>C NA 3464 rs4888427 -1 SNV HGNC HGNC:29577 1 CCDS76901.1 ENSP00000350230 Q8WVE7.126 UPI00001A994B Q8WVE7-2 0.4718 0.2496 0.6599 0.5556 0.5577 0.4642 0.4955 0.2838 0.348 0.6226 0.5709 0.5594 0.5315 0.5222 0.5802 0.5307 0.5235 0.6599 AMR 8 NA NA PASS SITE 91,62|69,64 NA NA 1 93 20,20 179,183 60,60 35 1.80 NA 18.06 NA FALSE 0.298 93 NA NA NA FALSE NA NA 362.74 8 75444549 HCC1395_HCC1395T 69 0.657 202 9,28 37,57 47,91 NA 0/1 NA NA NA NA 39,30,69,64 A/G PANCANCER NA FALSE TMEM170A chr16:75444549:75444550:A:G SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 75445255 75445256 T C 190 272 0.698529411764706 MODIFIER TMEM170A ENSG00000166822 C 3_prime_UTR_variant Transcript ENST00000357613 protein_coding 3/3 ENST00000357613.8:c.*2303A>G NA 2758 rs2161684 -1 SNV HGNC HGNC:29577 1 CCDS76901.1 ENSP00000350230 Q8WVE7.126 UPI00001A994B Q8WVE7-2 0.5050 0.3419 0.6758 0.5585 0.5696 0.4826 0.5226 0.3543 0.375 0.636 0.5979 0.5607 0.5497 0.5506 0.5883 0.556 0.5394 0.6758 AMR 8 NA NA PASS SITE 106,115|93,99 NA NA 1 93 20,20 176,173 60,60 33 -9.149e-01 NA 23.72 NA FALSE 0.277 61 NA NA NA FALSE NA NA 543.84 8 75445255 HCC1395_HCC1395T 82 0.690 272 7,21 47,104 58,130 NA 0/1 NA NA NA NA 43,39,92,98 T/C PANCANCER NA FALSE TMEM170A chr16:75445255:75445256:T:C SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 75477075 75477076 A C 321 572 0.561188811188811 MODIFIER CHST6 ENSG00000183196 C 3_prime_UTR_variant Transcript ENST00000332272 protein_coding 3/3 ENST00000332272.9:c.*1566T>G NA 3347 rs4888432 -1 SNV HGNC HGNC:6938 YES NM_021615.5 3 P1 CCDS10918.1 ENSP00000328983 Q9GZX3.165 UPI00000467C8 1 0.5080 0.3941 0.6427 0.5466 0.5457 0.4877 0.512 0.3966 0.3681 0.6386 0.5539 0.5487 0.5531 0.538 0.5404 0.5576 0.5455 0.6427 AMR benign 1 8 NA NA PASS SITE 239,235|166,156 NA NA 1 93 20,20 160,158 60,60 36 2.12 NA 41.54 NA FALSE 0.292 93 NA NA NA FALSE NA NA 810.34 8 75477075 HCC1395_HCC1395T 251 0.553 572 52,84 99,111 163,202 NA 0/1 NA NA NA NA 122,129,166,155 A/C PANCANCER NA FALSE CHST6 chr16:75477075:75477076:A:C SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 75477368 75477369 AG A 77 118 0.652542372881356 MODIFIER CHST6 ENSG00000183196 - 3_prime_UTR_variant Transcript ENST00000332272 protein_coding 3/3 ENST00000332272.9:c.*1272del NA 3053 rs200888552 -1 deletion HGNC HGNC:6938 YES NM_021615.5 3 P1 CCDS10918.1 ENSP00000328983 Q9GZX3.165 UPI00000467C8 1 0.0032 0.0008 0 0 0.0149 0 0.01006 0.003933 0.04396 0.002487 0.004323 0 0.001225 0.003165 0.01832 0.006208 0.0002068 0.04396 gnomADg_AMI 8 NA NA PASS SITE 43,42|42,35 NA NA 1 29 20,20 163,165 60,60 31 1.48 NA 8.72 NA FALSE 2.00 93 2,1 G NA TRUE NA 93 160.14 8 75477368 HCC1395_HCC1395T 41 0.622 118 8,14 17,29 30,50 NA 0/1 NA NA NA NA 23,18,42,35 AG/A PANCANCER NA FALSE CHST6 chr16:75477368:75477369:AG:A indel 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 75647522 75647523 T C 34 69 0.492753623188406 MODIFIER TERF2IP ENSG00000166848 C upstream_gene_variant Transcript ENST00000300086 protein_coding NA rs117457640 251 1 SNV HGNC HGNC:19246 YES NM_018975.4 1 P1 CCDS32491.1 ENSP00000300086 Q9NYB0.204 UPI0000136B77 1 0.0040 0.0008 0.0029 0 0.0169 0 0.011 0.003889 0.04496 0.003796 0.01037 0 0.002358 0.003165 0.01963 0.00622 0.0006209 0.04496 gnomADg_AMI likely_benign 1 8 NA NA PASS SITE 49,30|22,12 NA NA 1 55 20,20 165,156 60,60 26 1.50 NA 9.03 NA FALSE 1.92 93 NA NA NA FALSE NA NA 90.83 8 75647522 HCC1395_HCC1395T 35 0.490 69 7,13 16,10 24,23 NA 0/1 NA NA NA NA 22,13,22,12 T/C PANCANCER NA FALSE TERF2IP chr16:75647522:75647523:T:C SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 76309915 76309917 GG AA 27 52 0.519230769230769 MODIFIER CNTNAP4 ENSG00000152910 AA intron_variant Transcript ENST00000307431 protein_coding 1/23 ENST00000307431.12:c.86-6498_86-6497delinsAA NA rs35939460 1 substitution HGNC HGNC:18747 5 A1 ENSP00000306893 A0A0A0MR20.59 UPI0004E4CB06 8 NA NA PASS SITE 38,25|17,10 NA NA 2 78 20,20 150,151 60,60 24 1.41 NA 7.53 NA FALSE 6.00 93 NA NA NA FALSE NA NA 110.10 8 76309915 HCC1395_HCC1395T 25 0.529 52 8,9 7,8 15,17 NA 0/1 NA NA NA NA 15,10,17,10 GG/AA PANCANCER NA FALSE CNTNAP4 chr16:76309915:76309917:GG:AA indel 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 77193354 77193355 G T 37 83 0.44578313253012 MODIFIER MON1B ENSG00000103111 T intron_variant Transcript ENST00000248248 protein_coding 2/5 ENST00000248248.8:c.149-97G>T NA 1 SNV HGNC HGNC:25020 YES NM_014940.4 1 P1 CCDS10925.1 ENSP00000248248 Q7L1V2.139 UPI0000072AD7 Q7L1V2-1 8 NA NA PASS SITE 57,40|18,19 NA NA 1 93 25,21 172,178 60,60 32 1.60 NA 11.44 NA FALSE 6.00 93 NA NA NA FALSE NA NA 97.39 8 77193354 HCC1395_HCC1395T 46 0.446 83 14,11 18,15 35,28 NA 0/1 NA NA NA NA 26,20,18,19 G/T PANCANCER NA FALSE MON1B chr16:77193354:77193355:G:T SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 77979314 77979315 A G 75 136 0.551470588235294 MODIFIER VAT1L ENSG00000171724 G 3_prime_UTR_variant Transcript ENST00000302536 protein_coding 9/9 ENST00000302536.3:c.*1619A>G NA 2998 rs429536 1 SNV HGNC HGNC:29315 YES NM_020927.3 1 P1 CCDS32492.1 ENSP00000303129 Q9HCJ6.150 UPI00000741CE 0.3405 0.2799 0.366 0.3105 0.4006 0.3732 0.3725 0.3035 0.4418 0.4081 0.4265 0.3042 0.3648 0.443 0.4083 0.411 0.3627 0.443 gnomADg_MID 8 NA NA PASS SITE 27,72|20,55 NA NA 1 47 36,39 184,206 60,60 28 1.55 NA 9.93 NA FALSE 0.435 93 NA NA NA FALSE NA NA 258.80 8 77979314 HCC1395_HCC1395T 61 0.574 136 13,22 33,40 50,68 NA 0/1 NA NA NA NA 19,42,20,55 A/G PANCANCER NA FALSE VAT1L chr16:77979314:77979315:A:G SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 78029167 78029168 G T 60 98 0.612244897959184 MODIFIER CLEC3A ENSG00000166509 T intron_variant Transcript ENST00000299642 protein_coding 2/2 ENST00000299642.10:c.199+977G>T NA rs7190832&COSV55223329 1 SNV HGNC HGNC:2052 YES NM_005752.6 1 P1 CCDS10927.3 ENSP00000299642 O75596.153 UPI000004A9A6 0.3602 0.1415 0.4207 0.506 0.3658 0.4571 0.3834 0.1769 0.4443 0.3148 0.4822 0.2894 0.3539 0.3776 0.4389 0.3143 0.1767 0.5022 0.414 0.3089 0.4764 0.2841 0.3987 0.3541 0.371 0.4474 0.506 EAS 0&1 0&1 8 NA NA PASS SITE 39,35|31,29 NA NA 1 24 20,20 173,168 60,60 41 1.47 NA 8.43 NA FALSE 0.520 93 NA NA NA FALSE NA NA 162.14 8 78029167 HCC1395_HCC1395T 38 0.609 98 6,17 20,22 26,41 NA 0/1 NA NA NA NA 20,18,31,29 G/T PANCANCER NA FALSE CLEC3A chr16:78029167:78029168:G:T SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 78031591 78031592 T C 199 295 0.674576271186441 MODIFIER CLEC3A ENSG00000166509 C 3_prime_UTR_variant Transcript ENST00000299642 protein_coding 3/3 ENST00000299642.10:c.*750T>C NA 1423 rs2072665 1 SNV HGNC HGNC:2052 YES NM_005752.6 1 P1 CCDS10927.3 ENSP00000299642 O75596.153 UPI000004A9A6 0.3874 0.1793 0.438 0.5079 0.4046 0.4908 0.3517 0.2138 0.5022 0.4452 0.3447 0.4778 0.3162 0.4335 0.3984 0.409 0.4695 0.5079 EAS 8 NA NA PASS SITE 90,149|78,121 NA NA 1 93 20,20 170,165 60,60 28 1.98 NA 28.30 NA FALSE 0.471 93 NA NA NA FALSE NA NA 545.49 8 78031591 HCC1395_HCC1395T 96 0.660 295 24,41 35,78 67,131 NA 0/1 NA NA NA NA 35,61,78,121 T/C PANCANCER NA FALSE CLEC3A chr16:78031591:78031592:T:C SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 78031776 78031777 A T 67 113 0.592920353982301 MODIFIER CLEC3A ENSG00000166509 T 3_prime_UTR_variant Transcript ENST00000299642 protein_coding 3/3 ENST00000299642.10:c.*935A>T NA 1608 rs7188702 1 SNV HGNC HGNC:2052 YES NM_005752.6 1 P1 CCDS10927.3 ENSP00000299642 O75596.153 UPI000004A9A6 0.3876 0.1785 0.4395 0.5079 0.4056 0.4908 0.3507 0.2096 0.5011 0.4449 0.3445 0.4786 0.3163 0.4335 0.3986 0.4092 0.4703 0.5079 EAS 8 NA NA PASS SITE 57,37|43,24 NA NA 1 43 35,20 170,181 60,60 36 1.54 NA 10.23 NA FALSE 0.474 93 NA NA NA FALSE NA NA 176.93 8 78031776 HCC1395_HCC1395T 46 0.547 113 11,13 26,33 38,46 NA 0/1 NA NA NA NA 32,14,43,24 A/T PANCANCER NA FALSE CLEC3A chr16:78031776:78031777:A:T SNV 3:1 chr16:72014733:79212426:3:1:1 NA NA 0.96 +chr16 79595226 79595227 G A 137 386 0.354922279792746 MODIFIER MAF ENSG00000178573 A intron_variant Transcript ENST00000326043 protein_coding 1/1 ENST00000326043.5:c.1119-673C>T NA rs40965 -1 SNV HGNC HGNC:6776 YES NM_005360.5 1 P4 CCDS10928.1 ENSP00000327048 O75444.184 UPI000012EB25 O75444-1 1 0.0982 0.0098 0.1542 0.0149 0.1779 0.182 0.1323 0.03509 0.2467 0.1501 0.1079 0.01351 0.1861 0.09236 0.1843 0.1333 0.1842 0.2467 gnomADg_AMI 8 NA NA PASS SITE 185,166|76,61 NA NA 1 93 20,20 157,166 60,60 42 1.82 NA 19.22 NA FALSE 0.866 93 NA NA NA FALSE NA NA 333.63 8 79595226 HCC1395_HCC1395T 249 0.369 386 55,35 98,54 154,90 NA 0/1 NA NA NA NA 131,118,76,61 G/A PANCANCER TRUE FALSE MAF chr16:79595226:79595227:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 80550475 80550476 T G 59 166 0.355421686746988 MODIFIER DYNLRB2 ENSG00000168589 G intron_variant Transcript ENST00000305904 protein_coding 3/3 ENST00000305904.11:c.248-40T>G NA rs1042022436 1 SNV HGNC HGNC:15467 YES NM_130897.3 1 P1 CCDS10929.1 ENSP00000302936 Q8TF09.143 A0A140VJH9.33 UPI00000437D9 2.001e-05 6.243e-05 0 0 0 0 3.544e-05 0 0 3.942e-05 2.413e-05 0 6.541e-05 0 0 0 0 5.879e-05 0 0 6.541e-05 gnomADg_AMR 8 NA NA PASS SITE 114,35|47,12 NA NA 2 76 35,39 199,210 60,60 31 1.50 NA 8.98 NA FALSE 4.61 93 NA NA NA FALSE NA NA 187.32 8 80550475 HCC1395_HCC1395T 107 0.374 166 23,22 63,26 86,51 NA 0/1 NA NA NA NA 85,22,47,12 T/G PANCANCER NA FALSE DYNLRB2 chr16:80550475:80550476:T:G SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 81006950 81006951 G T 52 142 0.366197183098592 MODIFIER CMC2 ENSG00000103121 T upstream_gene_variant Transcript ENST00000219400 protein_coding NA rs2287991 65 -1 SNV HGNC HGNC:24447 YES NM_020188.5 1 P1 CCDS10930.1 ENSP00000219400 Q9NRP2.122 UPI000006E3AA 0.2458 0.1831 0.3271 0.369 0.2187 0.1738 0.2199 0.1734 0.1465 0.2902 0.1524 0.3615 0.2827 0.1646 0.219 0.2199 0.186 0.369 EAS 1 34594039 8 NA NA PASS SITE 68,69|27,25 NA NA 1 60 29,36 176,178 60,60 36 1.61 NA 11.39 NA FALSE 0.648 93 NA NA NA FALSE NA NA 151.81 8 81006950 HCC1395_HCC1395T 90 0.379 142 25,20 40,19 70,42 NA 0/1 NA NA NA NA 47,43,27,25 G/T PANCANCER NA FALSE CMC2 chr16:81006950:81006951:G:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 81036086 81036087 G C 87 275 0.316363636363636 LOW ATMIN ENSG00000166454 C synonymous_variant Transcript ENST00000299575 protein_coding 1/4 ENST00000299575.5:c.216G>C ENSP00000299575.3:p.S72= ENSP00000299575.3 p.S72= 245 216 72 S tcG/tcC rs200817365&COSV55147628 1 SNV HGNC HGNC:29034 YES NM_015251.3 1 P1 CCDS32494.1 ENSP00000299575 O43313.176 UPI00001B2485 O43313-1 AlphaFold_DB_import:AF-O43313-F1&PANTHER:PTHR46664 0.0192 0.0083 0.0303 0.002 0.0308 0.0317 0.0288 0.01093 0.01767 0.02067 0.002523 0.03372 0.03405 0.0291 0.03809 0.02808 0.01226 0.001099 0.02874 0.01995 0.003118 0.03921 0.0129 0.03807 0.03174 0.03808 0.03921 gnomADg_FIN 0&1 0&1 8 NA NA PASS SITE 174,130|53,34 NA NA 1 93 20,20 153,163 60,60 41 1.87 NA 21.97 NA FALSE 1.55 93 NA NA NA FALSE NA NA 214.80 8 81036086 HCC1395_HCC1395T 188 0.323 275 50,22 70,32 127,60 NA 0/1 NA NA NA NA 107,81,53,34 G/C PANCANCER NA FALSE ATMIN_p.S72= chr16:81036086:81036087:G:C SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 81533949 81533950 A G 54 178 0.303370786516854 MODIFIER CMIP ENSG00000153815 G intron_variant Transcript ENST00000537098 protein_coding 1/20 ENST00000537098.8:c.301-73618A>G NA rs2925980 1 SNV HGNC HGNC:24319 YES NM_198390.3 1 P1 CCDS54044.1 ENSP00000446100 Q8IY22.153 UPI00001FFCBD Q8IY22-1 0.3786 0.3888 0.3746 0.4613 0.3191 0.3436 0.325 0.125 0.3333 0.3846 0.3426 0.3788 0.4637 0.3566 0.4189 0.4509 0.232 0.3924 0.3195 0.3739 0.3463 0.4637 gnomADg_AMI 34149802&34135841&35250545 8 NA NA PASS SITE 95,87|29,25 NA NA 1 52 20,20 164,169 60,60 37 1.57 NA 10.84 NA FALSE 0.480 91 NA NA NA FALSE NA NA 122.71 8 81533949 HCC1395_HCC1395T 124 0.302 178 29,13 49,20 79,34 NA 0/1 NA NA NA NA 62,62,29,25 A/G PANCANCER NA FALSE CMIP chr16:81533949:81533950:A:G SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 81711382 81711383 GA G 464 1170 0.396581196581197 MODIFIER CMIP ENSG00000153815 - downstream_gene_variant Transcript ENST00000398040 protein_coding NA rs889821470 845 1 deletion HGNC HGNC:24319 1 ENSP00000381120 Q8IY22.153 UPI00000742EA Q8IY22-3 0.0001581 0.0002017 0 0.0002055 0.0002943 0 0.0003302 0 0.0001062 0 0.00022 0.0003302 gnomADg_FIN 8 NA NA PASS SITE 468,496|237,233 NA NA 1 93 20,20 159,162 60,60 38 1.12 NA 44.13 NA FALSE 2.71 93 10,9 A NA TRUE NA 93 469.21 8 81711382 HCC1395_HCC1395T 706 0.393 1170 151,85 220,159 465,303 NA 0/1 NA NA NA NA 347,359,233,231 GA/G PANCANCER NA FALSE CMIP chr16:81711382:81711383:GA:G indel 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 81896036 81896037 G A 51 134 0.380597014925373 MODIFIER PLCG2 ENSG00000197943 A intron_variant&non_coding_transcript_variant Transcript ENST00000562605 protein_coding_CDS_not_defined 4/4 ENST00000562605.5:n.387+109G>A NA rs9928597 1 SNV HGNC HGNC:9066 4 1 0.0433 0.0703 0.0389 0.002 0.0696 0.0256 0.06276 0.07359 0.08571 0.04291 0.0389 0.0003857 0.048 0.02215 0.07191 0.04703 0.02549 0.08571 gnomADg_AMI benign 1 8 NA NA PASS SITE 34,87|16,35 NA NA 1 43 34,20 171,175 60,60 23 1.50 NA 9.03 NA FALSE 1.21 82 NA NA NA FALSE NA NA 132.89 8 81896036 HCC1395_HCC1395T 83 0.366 134 25,11 31,19 63,36 NA 0/1 NA NA NA NA 22,61,16,35 G/A PANCANCER NA FALSE PLCG2 chr16:81896036:81896037:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 81908329 81908330 G C 81 194 0.417525773195876 MODIFIER PLCG2 ENSG00000197943 C downstream_gene_variant Transcript ENST00000563375 nonsense_mediated_decay NA rs62044874 1406 1 cds_start_NF SNV HGNC HGNC:9066 3 ENSP00000454536 H3BMT7.43 UPI000246730D 1 0.0419 0.0507 0.0432 0.002 0.0944 0.0164 0.07167 0.05391 0.09101 0.0519 0.08727 0.000578 0.06556 0.03797 0.0962 0.06781 0.01988 0.0962 gnomADg_NFE benign 1 8 NA NA PASS SITE 113,57|51,30 NA NA 1 78 20,20 168,177 60,60 28 1.63 NA 12.34 NA FALSE 1.14 80 NA NA NA FALSE NA NA 212.31 8 81908329 HCC1395_HCC1395T 113 0.410 194 24,11 54,44 81,56 NA 0/1 NA NA NA NA 73,40,51,30 G/C PANCANCER NA FALSE PLCG2 chr16:81908329:81908330:G:C SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 82035758 82035759 T C 43 111 0.387387387387387 MODIFIER HSD17B2 ENSG00000086696 C intron_variant Transcript ENST00000199936 protein_coding 1/4 ENST00000199936.9:c.265+69T>C NA rs1012392749 1 SNV HGNC HGNC:5211 YES NM_002153.3 1 P1 CCDS10936.1 ENSP00000199936 P37059.197 UPI000004C78E 2.628e-05 2.412e-05 0 0 0 0 0 0 4.409e-05 0 0 4.409e-05 gnomADg_NFE 8 NA NA PASS SITE 28,74|12,31 NA NA 1 62 34,20 185,164 60,60 39 1.41 NA 7.53 NA FALSE 4.61 93 NA NA NA FALSE NA NA 106.82 8 82035758 HCC1395_HCC1395T 68 0.379 111 20,12 28,17 53,32 NA 0/1 NA NA NA NA 17,51,12,31 T/C PANCANCER NA FALSE HSD17B2 chr16:82035758:82035759:T:C SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 82848812 82848813 C G 20 53 0.377358490566038 MODIFIER CDH13 ENSG00000140945 G intron_variant Transcript ENST00000268613 protein_coding 2/14 ENST00000268613.14:c.187-9550C>G NA rs35862345 1 SNV HGNC HGNC:1753 2 CCDS58485.1 ENSP00000268613 P55290.202 UPI00020E71A6 P55290-4 0.0819 0.0703 0.0893 0.001 0.1869 0.0675 0.119 0.08681 0.09121 0.1105 0.1326 0.0009638 0.07299 0.1392 0.1591 0.1291 0.07632 0.1869 EUR 8 NA NA PASS SITE 7,47|2,18 NA NA 1 3 37,39 203,210 60,60 33 1.26 NA 5.07 NA FALSE 0.939 93 NA NA NA FALSE NA NA 66.57 8 82848812 HCC1395_HCC1395T 33 0.392 53 15,12 13,7 30,19 NA 0/1 NA NA NA NA 3,30,2,18 C/G PANCANCER NA FALSE CDH13 chr16:82848812:82848813:C:G SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 83796186 83796187 AG A 14 599 0.0233722871452421 MODIFIER CDH13 ENSG00000140945 - downstream_gene_variant Transcript ENST00000268613 protein_coding NA 811 1 deletion HGNC HGNC:1753 2 CCDS58485.1 ENSP00000268613 P55290.202 UPI00020E71A6 P55290-4 8 NA NA PASS SITE 359,363|5,9 NA NA 1 93 20,20 180,184 60,60 28 2.00 NA 29.18 NA FALSE 6.00 93 NA NA NA FALSE NA NA 17.84 8 83796186 HCC1395_HCC1395T 585 0.024 599 141,3 194,3 441,10 NA 0/1 NA NA NA NA 298,287,5,9 AG/A PANCANCER NA FALSE CDH13 chr16:83796186:83796187:AG:A indel 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 83796694 83796695 T G 66 162 0.407407407407407 MODIFIER CDH13 ENSG00000140945 G downstream_gene_variant Transcript ENST00000268613 protein_coding NA rs460796 1318 1 SNV HGNC HGNC:1753 2 CCDS58485.1 ENSP00000268613 P55290.202 UPI00020E71A6 P55290-4 0.1771 0.1906 0.1844 0.0278 0.2416 0.2413 0.2003 0.1981 0.3033 0.1558 0.2369 0.02103 0.2257 0.2092 0.2159 0.1949 0.2482 0.3033 gnomADg_AMI 8 NA NA PASS SITE 22,112|18,48 NA NA 1 53 38,34 197,175 60,60 19 1.56 NA 10.49 NA FALSE 0.721 93 NA NA NA FALSE NA NA 187.39 8 83796694 HCC1395_HCC1395T 96 0.388 162 33,18 41,25 81,51 NA 0/1 NA NA NA NA 16,80,18,48 T/G PANCANCER NA FALSE CDH13 chr16:83796694:83796695:T:G SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 83812311 83812312 C T 147 461 0.318872017353579 MODIFIER HSBP1 ENSG00000230989 T 3_prime_UTR_variant Transcript ENST00000433866 protein_coding 4/4 ENST00000433866.7:c.*893C>T NA 1223 rs769814291 1 SNV HGNC HGNC:5203 YES NM_001537.4 1 P2 CCDS45534.1 ENSP00000392896 O75506.176 UPI000004B12F 2.628e-05 4.826e-05 0 6.545e-05 0 0 0 0 1.47e-05 0 0 6.545e-05 gnomADg_AMR 8 NA NA PASS SITE 190,235|58,89 NA NA 1 93 20,32 183,183 60,60 29 1.90 NA 23.43 NA FALSE 4.31 93 NA NA NA FALSE NA NA 398.25 8 83812311 HCC1395_HCC1395T 314 0.323 461 95,49 126,56 230,109 NA 0/1 NA NA NA NA 139,175,58,89 C/T PANCANCER NA FALSE HSBP1 chr16:83812311:83812312:C:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 83812593 83812594 G A 50 152 0.328947368421053 MODIFIER HSBP1 ENSG00000230989 A 3_prime_UTR_variant Transcript ENST00000433866 protein_coding 4/4 ENST00000433866.7:c.*1175G>A NA 1505 rs4522&COSV105353391 1 SNV HGNC HGNC:5203 YES NM_001537.4 1 P2 CCDS45534.1 ENSP00000392896 O75506.176 UPI000004B12F 0.3079 0.2436 0.3401 0.1677 0.4185 0.4029 0.3617 0.2671 0.4009 0.3403 0.3939 0.1528 0.4218 0.3671 0.4263 0.375 0.3876 0.4263 gnomADg_NFE 0&1 0&1 8 NA NA PASS SITE 71,70|25,25 NA NA 1 50 38,35 203,210 60,60 29 1.58 NA 10.84 NA FALSE 0.429 93 NA NA NA FALSE NA NA 150.83 8 83812593 HCC1395_HCC1395T 102 0.355 152 30,16 52,29 88,48 NA 0/1 NA NA NA NA 47,55,25,25 G/A PANCANCER NA FALSE HSBP1 chr16:83812593:83812594:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 83915949 83915950 A C 188 518 0.362934362934363 MODIFIER MLYCD ENSG00000103150 C 3_prime_UTR_variant Transcript ENST00000262430 protein_coding 5/5 ENST00000262430.6:c.*460A>C NA 1972 rs1127387&COSV105103749 1 SNV HGNC HGNC:7150 YES NM_012213.3 1 P1 CCDS42206.1 ENSP00000262430 O95822.186 UPI0000128FD5 O95822-1 1 0.0767 0.0756 0.0648 0.0387 0.1302 0.0706 0.1008 0.08093 0.3564 0.07583 0.09447 0.0413 0.0749 0.1044 0.1251 0.09943 0.08444 0.3564 gnomADg_AMI benign 0&1 1&1 8 NA NA PASS SITE 307,164|124,64 NA NA 1 93 20,20 172,158 60,60 32 2.00 NA 29.15 NA FALSE 1.01 93 NA NA NA FALSE NA NA 490.67 8 83915949 HCC1395_HCC1395T 330 0.358 518 89,42 145,84 239,133 NA 0/1 NA NA NA NA 218,112,124,64 A/C PANCANCER NA FALSE MLYCD chr16:83915949:83915950:A:C SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 84054238 84054239 A C 26 175 0.148571428571429 MODIFIER MBTPS1 ENSG00000140943 C 3_prime_UTR_variant Transcript ENST00000343411 protein_coding 23/23 ENST00000343411.8:c.*211T>G NA 3902 -1 SNV HGNC HGNC:15456 YES NM_003791.4 1 P1 CCDS10941.1 ENSP00000344223 Q14703.202 UPI0000033348 1 8 NA NA PASS SITE 102,114|12,14 NA NA 1 93 20,20 164,179 60,60 36 1.68 NA 13.85 NA FALSE 6.00 93 NA NA NA FALSE NA NA 59.89 8 84054238 HCC1395_HCC1395T 149 0.154 175 39,8 59,7 103,18 NA 0/1 NA NA NA NA 67,82,12,14 A/C PANCANCER NA FALSE MBTPS1 chr16:84054238:84054239:A:C SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 84116685 84116686 G A 39 97 0.402061855670103 MODIFIER MBTPS1 ENSG00000140943 A intron_variant Transcript ENST00000343411 protein_coding 1/22 ENST00000343411.8:c.-325+50C>T NA rs7205646 -1 SNV HGNC HGNC:15456 YES NM_003791.4 1 P1 CCDS10941.1 ENSP00000344223 Q14703.202 UPI0000033348 1 0.4403 0.3313 0.4063 0.6865 0.4095 0.3896 0.3993 0.3462 0.5428 0.4042 0.442 0.6733 0.4433 0.3949 0.4 0.4114 0.379 0.6865 EAS 8 NA NA PASS SITE 87,8|34,5 NA NA 1 51 32,37 192,171 60,60 20 1.57 NA 10.83 NA FALSE 0.393 58 NA NA NA FALSE NA NA 122.26 8 84116685 HCC1395_HCC1395T 58 0.398 97 23,9 26,24 52,34 NA 0/1 NA NA NA NA 51,7,34,5 G/A PANCANCER NA FALSE MBTPS1 chr16:84116685:84116686:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 84116773 84116774 A G 185 475 0.389473684210526 MODIFIER MBTPS1 ENSG00000140943 G 5_prime_UTR_variant Transcript ENST00000343411 protein_coding 1/23 ENST00000343411.8:c.-363T>C NA 170 rs7205363 -1 SNV HGNC HGNC:15456 YES NM_003791.4 1 P1 CCDS10941.1 ENSP00000344223 Q14703.202 UPI0000033348 1 0.4471 0.3525 0.4078 0.6895 0.4115 0.3896 0.4057 0.3663 0.5428 0.4069 0.4424 0.675 0.4435 0.4038 0.401 0.4172 0.3806 0.6895 EAS 8 NA NA PASS SITE 260,218|100,85 NA NA 2 93 20,20 158,154 60,60 40 2.07 NA 34.91 NA FALSE 0.387 93 NA NA NA FALSE NA NA 444.70 8 84116773 HCC1395_HCC1395T 290 0.388 475 83,41 89,68 174,110 NA 0/1 NA NA NA NA 160,130,100,85 A/G PANCANCER NA FALSE MBTPS1 chr16:84116773:84116774:A:G SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 84116849 84116850 A G 129 358 0.360335195530726 MODIFIER MBTPS1 ENSG00000140943 G 5_prime_UTR_variant Transcript ENST00000343411 protein_coding 1/23 ENST00000343411.8:c.-439T>C NA 94 rs7205403 -1 SNV HGNC HGNC:15456 YES NM_003791.4 1 P1 CCDS10941.1 ENSP00000344223 Q14703.202 UPI0000033348 1 0.4938 0.4622 0.4308 0.6925 0.4274 0.4448 0.4503 0.4678 0.5505 0.4367 0.4706 0.6751 0.4469 0.4808 0.4239 0.4515 0.447 0.6925 EAS 8 NA NA PASS SITE 162,233|49,80 NA NA 2 93 20,20 159,164 60,60 22 2.04 NA 32.51 NA FALSE 0.350 93 NA NA NA FALSE NA NA 317.80 8 84116849 HCC1395_HCC1395T 229 0.364 358 47,26 49,24 150,86 NA 0/1 NA NA NA NA 94,135,49,80 A/G PANCANCER NA FALSE MBTPS1 chr16:84116849:84116850:A:G SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 84318346 84318347 G A 31 97 0.319587628865979 MODERATE WFDC1 ENSG00000103175 A missense_variant Transcript ENST00000219454 protein_coding 3/7 ENST00000219454.10:c.412G>A ENSP00000219454.5:p.V138M ENSP00000219454.5 p.V138M 506 412 138 V/M Gtg/Atg rs11643870&COSV54744190 1 SNV HGNC HGNC:15466 YES NM_021197.4 1 P1 CCDS10946.1 ENSP00000219454 Q9HC57.153 UPI0000138EFA deleterious(0) benign(0.291) PANTHER:PTHR14308&AlphaFold_DB_import:AF-Q9HC57-F1 0.0048 0 0.0058 0.0069 0.0109 0.002 0.008803 0.002155 0.00668 0.02581 0 0.002496 0.01331 0.01174 0.001568 0.008306 0.00263 0 0.009029 0.0222 0 0.003577 0.01266 0.01266 0.01148 0.002689 0.02581 gnomADe_ASJ benign 0&1 1&1 8 NA NA PASS SITE 42,55|15,16 NA NA 1 20 20,20 154,144 60,60 30 1.33 NA 5.97 NA FALSE 2.07 84 NA NA NA FALSE NA NA 68.10 8 84318346 HCC1395_HCC1395T 66 0.308 97 19,8 22,10 44,19 NA 0/1 NA NA NA NA 29,37,15,16 G/A PANCANCER NA FALSE WFDC1_p.V138M chr16:84318346:84318347:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 84319331 84319332 G A 71 251 0.282868525896414 MODIFIER WFDC1 ENSG00000103175 A intron_variant Transcript ENST00000219454 protein_coding 3/6 ENST00000219454.10:c.422-100G>A NA rs118176311 1 SNV HGNC HGNC:15466 YES NM_021197.4 1 P1 CCDS10946.1 ENSP00000219454 Q9HC57.153 UPI0000138EFA 0.0032 0 0.0058 0 0.0109 0.001 0.008459 0.002538 0 0.009564 0.02483 0 0.003203 0.01582 0.01278 0.0139 0.002486 0.02483 gnomADg_ASJ 8 NA NA PASS SITE 191,77|52,19 NA NA 1 93 20,33 162,162 60,60 25 1.78 NA 17.76 NA FALSE 2.07 93 NA NA NA FALSE NA NA 189.71 8 84319331 HCC1395_HCC1395T 180 0.285 251 50,20 82,33 137,54 NA 0/1 NA NA NA NA 133,47,52,19 G/A PANCANCER NA FALSE WFDC1 chr16:84319331:84319332:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 84462044 84462045 C T 81 230 0.352173913043478 LOW ATP2C2 ENSG00000064270 T synonymous_variant Transcript ENST00000262429 protein_coding 26/27 ENST00000262429.9:c.2637C>T ENSP00000262429.4:p.V879= ENSP00000262429.4 p.V879= 2715 2637 879 V gtC/gtT rs376362270&COSV52294724 1 SNV HGNC HGNC:29103 YES NM_014861.4 1 P1 CCDS42207.1 ENSP00000262429 O75185.186 UPI0000425C6A O75185-1 CDD:cd02085&Pfam:PF00689&Gene3D:1.20.1110.10&TIGRFAM:TIGR01522&Superfamily:SSF81665&PANTHER:PTHR42861&Transmembrane_helices:TMhelix&AlphaFold_DB_import:AF-O75185-F1 0.0001763 0 0 0 0 0 0.0003796 0.0001651 0 0.0001577 2.413e-05 0 0.0001309 0 0 0 0 0.0003087 0 0 0.0003796 gnomADe_NFE 0&1 0&1 8 NA NA PASS SITE 87,123|30,51 NA NA 1 93 20,20 158,157 60,60 38 1.63 NA 12.64 NA FALSE 3.76 93 NA NA NA FALSE NA NA 198.04 8 84462044 HCC1395_HCC1395T 149 0.379 230 28,21 57,28 91,55 NA 0/1 NA NA NA NA 64,85,30,51 C/T PANCANCER NA FALSE ATP2C2_p.V879= chr16:84462044:84462045:C:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 85088809 85088810 G T 60 149 0.402684563758389 MODIFIER KIAA0513 ENSG00000135709 T 3_prime_UTR_variant Transcript ENST00000538274 protein_coding 12/12 ENST00000538274.6:c.*484G>T NA 1939 rs3751755 1 SNV HGNC HGNC:29058 2 P4 CCDS67091.1 ENSP00000446439 O60268.142 UPI00001FFD3C O60268-3 0.1500 0.1672 0.2161 0.2183 0.0606 0.1012 0.09709 0.1473 0.159 0.2007 0.01615 0.1974 0.0615 0.04747 0.04413 0.09943 0.1035 0.2183 EAS 1 35857289 8 NA NA PASS SITE 41,87|18,42 NA NA 1 45 38,34 179,182 60,60 27 1.51 NA 9.33 NA FALSE 1.08 93 NA NA NA FALSE NA NA 167.78 8 85088809 HCC1395_HCC1395T 89 0.397 149 23,19 37,24 75,49 NA 0/1 NA NA NA NA 27,62,18,42 G/T PANCANCER NA FALSE KIAA0513 chr16:85088809:85088810:G:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 85089542 85089543 G C 108 250 0.432 MODIFIER KIAA0513 ENSG00000135709 C 3_prime_UTR_variant Transcript ENST00000538274 protein_coding 12/12 ENST00000538274.6:c.*1217G>C NA 2672 rs4783124 1 SNV HGNC HGNC:29058 2 P4 CCDS67091.1 ENSP00000446439 O60268.142 UPI00001FFD3C O60268-3 0.1508 0.1672 0.2176 0.2192 0.0606 0.1033 0.0984 0.1488 0.159 0.2023 0.01787 0.2006 0.06149 0.04747 0.04524 0.1008 0.1062 0.2192 EAS 8 NA NA PASS SITE 114,132|46,62 NA NA 1 93 20,20 153,171 60,60 28 1.82 NA 19.52 NA FALSE 1.07 93 NA NA NA FALSE NA NA 293.06 8 85089542 HCC1395_HCC1395T 142 0.450 250 40,29 48,42 92,75 NA 0/1 NA NA NA NA 66,76,46,62 G/C PANCANCER NA FALSE KIAA0513 chr16:85089542:85089543:G:C SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 85092569 85092570 A C 77 193 0.398963730569948 MODIFIER KIAA0513 ENSG00000135709 C 3_prime_UTR_variant Transcript ENST00000538274 protein_coding 12/12 ENST00000538274.6:c.*4244A>C NA 5699 rs28499180 1 SNV HGNC HGNC:29058 2 P4 CCDS67091.1 ENSP00000446439 O60268.142 UPI00001FFD3C O60268-3 0.1518 0.1778 0.2176 0.2173 0.0596 0.0971 0.09896 0.1541 0.1571 0.2024 0.01815 0.1967 0.06131 0.05063 0.04401 0.09875 0.1015 0.2176 AMR 8 NA NA PASS SITE 99,71|43,34 NA NA 2 69 20,20 169,166 60,60 25 1.61 NA 11.74 NA FALSE 1.07 93 NA NA NA FALSE NA NA 298.11 8 85092569 HCC1395_HCC1395T 116 0.392 193 36,26 50,27 89,57 NA 0|1 0|1 85092569_A_C NA 85092569 68,48,43,34 A|C PANCANCER NA FALSE KIAA0513 chr16:85092569:85092570:A:C SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 85092573 85092574 C T 78 198 0.393939393939394 MODIFIER KIAA0513 ENSG00000135709 T 3_prime_UTR_variant Transcript ENST00000538274 protein_coding 12/12 ENST00000538274.6:c.*4248C>T NA 5703 rs28677468 1 SNV HGNC HGNC:29058 2 P4 CCDS67091.1 ENSP00000446439 O60268.142 UPI00001FFD3C O60268-3 0.1462 0.1581 0.2161 0.2173 0.0586 0.0971 0.0946 0.1389 0.1571 0.2011 0.01815 0.1966 0.06099 0.05063 0.04398 0.09684 0.1012 0.2173 EAS 8 NA NA PASS SITE 101,73|43,35 NA NA 2 69 20,20 169,164 60,60 28 1.60 NA 11.74 NA FALSE 1.09 93 NA NA NA FALSE NA NA 299.54 8 85092573 HCC1395_HCC1395T 120 0.391 198 35,26 50,26 91,58 NA 0|1 0|1 85092569_A_C NA 85092569 70,50,43,35 C|T PANCANCER NA FALSE KIAA0513 chr16:85092573:85092574:C:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 85092935 85092936 A G 59 149 0.395973154362416 MODIFIER KIAA0513 ENSG00000135709 G 3_prime_UTR_variant Transcript ENST00000538274 protein_coding 12/12 ENST00000538274.6:c.*4610A>G NA 6065 rs3794687 1 SNV HGNC HGNC:29058 2 P4 CCDS67091.1 ENSP00000446439 O60268.142 UPI00001FFD3C O60268-3 0.1066 0.0779 0.1009 0.1706 0.0676 0.1237 0.07775 0.08329 0.2015 0.09852 0.08271 0.1555 0.03984 0.05696 0.06496 0.0819 0.1176 0.2015 gnomADg_AMI 8 NA NA PASS SITE 91,59|34,25 NA NA 1 85 20,32 164,168 60,60 27 1.66 NA 13.24 NA FALSE 1.15 93 NA NA NA FALSE NA NA 161.38 8 85092935 HCC1395_HCC1395T 90 0.417 149 27,26 33,20 65,46 NA 0/1 NA NA NA NA 53,37,34,25 A/G PANCANCER NA FALSE KIAA0513 chr16:85092935:85092936:A:G SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 85688972 85688973 C A 101 215 0.469767441860465 MODIFIER GINS2 ENSG00000131153 A upstream_gene_variant Transcript ENST00000253462 protein_coding NA rs943515493 18 -1 SNV HGNC HGNC:24575 YES NM_016095.3 1 P1 CCDS10953.1 ENSP00000253462 Q9Y248.165 UPI000006D930 7.89e-05 4.825e-05 0 6.543e-05 0 0 0.0001883 0 0.0001031 0 0 0.0001883 gnomADg_FIN 8 NA NA PASS SITE 33,147|23,78 NA NA 1 93 31,38 183,180 60,60 23 1.76 NA 16.46 NA FALSE 3.76 93 NA NA NA FALSE NA NA 313.73 8 85688972 HCC1395_HCC1395T 114 0.469 215 40,24 38,48 97,85 NA 0/1 NA NA NA NA 20,94,23,78 C/A PANCANCER NA FALSE GINS2 chr16:85688972:85688973:C:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 85922065 85922066 C T 47 129 0.364341085271318 MODIFIER IRF8 ENSG00000140968 T 3_prime_UTR_variant Transcript ENST00000268638 protein_coding 9/9 ENST00000268638.10:c.*783C>T NA 2127 rs1044873 1 SNV HGNC HGNC:5358 YES NM_002163.4 1 P1 CCDS10956.1 ENSP00000268638 Q02556.191 UPI000012D188 1 0.3548 0.4433 0.2824 0.372 0.3986 0.2239 0.3969 0.4495 0.2599 0.315 0.3443 0.3891 0.4798 0.3956 0.3867 0.386 0.2452 0.4798 gnomADg_FIN 1 25114582&25075970&25541970&21859832&24292274&22879909&23307532&23926461&33374413&33751038&35632621 8 NA NA PASS SITE 39,80|11,36 NA NA 1 29 32,38 195,197 60,60 24 1.48 NA 8.73 NA FALSE 0.387 93 NA NA NA FALSE NA NA 150.30 8 85922065 HCC1395_HCC1395T 82 0.383 129 26,18 42,24 70,43 NA 0/1 NA NA NA NA 26,56,11,36 C/T PANCANCER NA FALSE IRF8 chr16:85922065:85922066:C:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 86546722 86546723 G A 126 346 0.364161849710983 MODIFIER MTHFSD ENSG00000103248 A intron_variant Transcript ENST00000360900 protein_coding 4/7 ENST00000360900.11:c.352-73C>T NA -1 SNV HGNC HGNC:25778 YES NM_001159377.2 1 A2 CCDS54047.1 ENSP00000354152 Q2M296.138 UPI000059D3CD Q2M296-1 8 NA NA PASS SITE 134,200|44,82 NA NA 1 93 20,20 162,169 60,60 35 1.86 NA 20.98 NA FALSE 6.00 93 NA NA NA FALSE NA NA 313.85 8 86546722 HCC1395_HCC1395T 220 0.383 346 65,31 68,50 144,89 NA 0/1 NA NA NA NA 86,134,44,82 G/A PANCANCER NA FALSE MTHFSD chr16:86546722:86546723:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 87305844 87305845 C T 109 368 0.296195652173913 MODERATE C16orf95 ENSG00000260456 T missense_variant Transcript ENST00000253461 protein_coding 4/5 ENST00000253461.8:c.392G>A ENSP00000253461.4:p.C131Y ENSP00000253461.4 p.C131Y 566 392 131 C/Y tGt/tAt rs141912735&COSV106089970 -1 SNV HGNC HGNC:40033 1 CCDS54049.1 ENSP00000253461 Q9H693.108 UPI0000052205 deleterious_low_confidence(0.01) probably_damaging(0.922) AlphaFold_DB_import:AF-Q9H693-F1 0.0052 0.0008 0.0086 0 0.0159 0.0031 0.008094 0.002563 0.003127 0.000997 0 0.009634 0.01607 0.005271 0.004613 0.01038 0.003112 0.006579 0.005889 0.0002885 0 0.00791 0 0.01814 0.007648 0.003932 0.01814 gnomADg_NFE 0&1 0&1 8 NA NA PASS SITE 194,223|56,53 NA NA 1 93 20,20 160,167 60,60 31 1.99 NA 28.60 NA FALSE 2.00 93 NA NA NA FALSE NA NA 242.51 8 87305844 HCC1395_HCC1395T 259 0.299 368 56,27 88,37 164,70 NA 0/1 NA NA NA NA 124,135,56,53 C/T PANCANCER NA FALSE C16orf95_p.C131Y chr16:87305844:87305845:C:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 87417564 87417565 G C 125 445 0.280898876404494 MODERATE ZCCHC14 ENSG00000140948 C missense_variant Transcript ENST00000268616 protein_coding 8/13 ENST00000268616.9:c.868C>G ENSP00000268616.4:p.L290V ENSP00000268616.4 p.L290V 895 868 290 L/V Ctg/Gtg COSV51891120 -1 SNV HGNC HGNC:24134 1 ENSP00000268616 Q8WYQ9.152 UPI00000705C4 Q8WYQ9-1 tolerated(0.57) benign(0.031) AlphaFold_DB_import:AF-Q8WYQ9-F1&PANTHER:PTHR16195 1 1 8 NA NA PASS SITE 201,253|62,63 NA NA 1 93 20,20 167,166 60,60 30 1.96 NA 27.09 NA FALSE 6.00 93 NA NA NA FALSE NA NA 298.91 8 87417564 HCC1395_HCC1395T 320 0.271 445 97,44 104,32 220,81 NA 0/1 NA NA NA NA 138,182,62,63 G/C PANCANCER NA FALSE ZCCHC14_p.L290V chr16:87417564:87417565:G:C SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 87695791 87695792 C T 217 563 0.385435168738899 MODIFIER JPH3 ENSG00000154118 T intron_variant Transcript ENST00000284262 protein_coding 4/4 ENST00000284262.3:c.2167-789C>T NA rs117376372 1 SNV HGNC HGNC:14203 YES NM_020655.4 1 P1 CCDS10962.1 ENSP00000284262 Q8WXH2.178 UPI000012DAC4 Q8WXH2-1 1 0.0096 0.0023 0.0144 0.001 0.0229 0.0112 0.01593 0.003451 0.007883 0.003706 9.582e-05 0.02152 0.02718 0.01403 0.0151 0.01693 0.005166 0.08991 0.01119 0.004035 0.0001925 0.01453 0.006329 0.02725 0.01052 0.01306 0.08991 gnomADg_AMI 8 NA NA PASS SITE 240,249|113,104 NA NA 1 93 20,20 163,164 60,60 29 2.01 NA 29.80 NA FALSE 1.72 93 NA NA NA FALSE NA NA 534.49 8 87695791 HCC1395_HCC1395T 346 0.381 563 104,57 118,81 240,147 NA 0/1 NA NA NA NA 165,181,113,104 C/T PANCANCER NA FALSE JPH3 chr16:87695791:87695792:C:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 87701921 87701922 G A 91 260 0.35 MODIFIER JPH3 ENSG00000154118 A downstream_gene_variant Transcript ENST00000284262 protein_coding NA rs7199037&COSV52469588 3765 1 SNV HGNC HGNC:14203 YES NM_020655.4 1 P1 CCDS10962.1 ENSP00000284262 Q8WXH2.178 UPI000012DAC4 Q8WXH2-1 1 0.1783 0.2141 0.1427 0.1319 0.1889 0.1922 0.1792 0.1857 0.1585 0.135 0.1378 0.2492 0.1861 0.1686 0.205 0.1889 0.1986 0.25 0.1487 0.1421 0.1412 0.2463 0.1994 0.1882 0.1558 0.2049 0.25 gnomADg_AMI 0&1 0&1 8 NA NA PASS SITE 109,150|41,51 NA NA 1 93 20,20 153,158 60,60 35 1.82 NA 18.64 NA FALSE 0.688 93 NA NA NA FALSE NA NA 224.55 8 87701921 HCC1395_HCC1395T 169 0.372 260 43,24 48,33 104,61 NA 0/1 NA NA NA NA 72,97,40,51 G/A PANCANCER NA FALSE JPH3 chr16:87701921:87701922:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 87851696 87851697 G A 96 214 0.448598130841121 MODIFIER SLC7A5 ENSG00000103257 A intron_variant Transcript ENST00000261622 protein_coding 2/9 ENST00000261622.5:c.664+28C>T NA rs33975475 -1 SNV HGNC HGNC:11063 YES NM_003486.7 1 P1 CCDS10964.1 ENSP00000261622 Q01650.215 UPI000000D9ED 0.0114 0.0023 0.0101 0 0.0417 0.0051 0.02578 0.00433 0.009294 0.002235 0 0.106 0.0299 0.02641 0.007229 0.0258 0.005378 0.02961 0.01118 0.002592 0 0.1134 0.003165 0.03265 0.01528 0.008065 0.1134 gnomADg_FIN 32874918 8 NA NA PASS SITE 133,58|62,34 NA NA 1 93 20,20 170,170 60,60 22 1.72 NA 15.05 NA FALSE 1.47 93 NA NA NA FALSE NA NA 244.71 8 87851696 HCC1395_HCC1395T 118 0.426 214 31,32 54,30 88,65 NA 0/1 NA NA NA NA 85,33,62,34 G/A PANCANCER NA FALSE SLC7A5 chr16:87851696:87851697:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 88072242 88072243 G A 28 88 0.318181818181818 MODIFIER BANP ENSG00000172530 A intron_variant Transcript ENST00000286122 protein_coding 13/13 ENST00000286122.11:c.1488+30G>A NA rs764645448 1 SNV HGNC HGNC:13450 5 CCDS54054.1 ENSP00000286122 Q8N9N5.157 UPI0000E59DA3 Q8N9N5-1 3.328e-05 0 0 0 0 0.000109 4.337e-05 0 3.709e-05 1.97e-05 0 0 0 0 0 0 0 4.409e-05 0 0 0.000109 gnomADe_FIN 8 NA NA PASS SITE 23,62|7,21 NA NA 1 40 34,30 173,166 60,60 19 1.30 NA 5.72 NA FALSE 4.31 71 NA NA NA FALSE NA NA 74.01 8 88072242 HCC1395_HCC1395T 60 0.319 88 20,8 24,6 46,21 NA 0/1 NA NA NA NA 17,43,7,21 G/A PANCANCER NA FALSE BANP chr16:88072242:88072243:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 88435610 88435611 C T 96 343 0.279883381924198 LOW ZNF469 ENSG00000225614 T synonymous_variant Transcript ENST00000437464 protein_coding 2/2 ENST00000437464.1:c.8056C>T ENSP00000402343.1:p.L2686= ENSP00000402343.1 p.L2686= 8056 8056 2686 L Ctg/Ttg 1 SNV HGNC HGNC:23216 5 A2 ENSP00000402343 Q96JG9.153 UPI0004E4C937 1 PANTHER:PTHR21465&MobiDB_lite:mobidb-lite 8 NA NA PASS SITE 215,142|62,34 NA NA 1 93 20,34 173,181 60,60 29 1.89 NA 22.87 NA FALSE 6.00 93 NA NA NA FALSE NA NA 253.31 8 88435610 HCC1395_HCC1395T 247 0.291 343 65,39 109,34 182,74 NA 0/1 NA NA NA NA 151,96,62,34 C/T PANCANCER NA FALSE ZNF469_p.L2686= chr16:88435610:88435611:C:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 88440191 88440192 AT A 109 274 0.397810218978102 MODIFIER ZNF469 ENSG00000225614 - 3_prime_UTR_variant Transcript ENST00000437464 protein_coding 2/2 ENST00000437464.1:c.*870del NA 12638 rs35684712 1 deletion HGNC HGNC:23216 5 A2 ENSP00000402343 Q96JG9.153 UPI0004E4C937 1 10 0.5501 0.3116 0.6095 0.5615 0.6262 0.7403 0.5519 0.358 0.5991 0.6348 0.6151 0.5385 0.5672 0.6859 0.6304 0.6093 0.7148 0.7403 SAS benign 1 8 NA NA PASS SITE 127,126|57,54 NA NA 1 77 20,20 154,153 60,60 35 1.41 NA 15.00 NA FALSE 0.269 93 11,10 T NA TRUE NA 93 102.91 8 88440191 HCC1395_HCC1395T 165 0.395 274 42,27 48,34 107,70 NA 0/1 NA NA NA NA 82,83,56,53 AT/A PANCANCER NA FALSE ZNF469 chr16:88440191:88440192:AT:A indel 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 88486234 88486235 G A 26 50 0.52 MODIFIER ZFPM1 ENSG00000179588 A intron_variant Transcript ENST00000319555 protein_coding 2/9 ENST00000319555.8:c.145+191G>A NA rs1000030630 1 SNV HGNC HGNC:19762 YES NM_153813.3 1 P1 CCDS32502.1 ENSP00000326630 Q8IX07.165 UPI000049DE26 1.971e-05 0 0 0 0 0 0 0 4.41e-05 0 0 4.41e-05 gnomADg_NFE 8 NA NA PASS SITE 4,33|3,23 NA NA 1 28 40,39 194,212 60,60 25 1.15 NA 3.91 NA FALSE 4.61 93 NA NA NA FALSE NA NA 91.72 8 88486234 HCC1395_HCC1395T 24 0.553 50 9,14 8,10 20,25 NA 0/1 NA NA NA NA 4,20,3,23 G/A PANCANCER NA FALSE ZFPM1 chr16:88486234:88486235:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 88586510 88586511 A C 100 323 0.309597523219814 MODIFIER ZC3H18 ENSG00000158545 C intron_variant Transcript ENST00000301011 protein_coding 2/17 ENST00000301011.10:c.604-90A>C NA 1 SNV HGNC HGNC:25091 YES NM_144604.4 1 P1 CCDS10967.1 ENSP00000301011 Q86VM9.153 UPI00001FF676 8 NA NA PASS SITE 210,100|67,33 NA NA 1 93 20,20 168,162 60,60 33 1.78 NA 17.46 NA FALSE 6.00 93 NA NA NA FALSE NA NA 251.45 8 88586510 HCC1395_HCC1395T 223 0.305 323 56,24 102,44 160,70 NA 0/1 NA NA NA NA 154,69,67,33 A/C PANCANCER NA FALSE ZC3H18 chr16:88586510:88586511:A:C SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 88643362 88643363 C T 33 288 0.114583333333333 MODIFIER IL17C ENSG00000124391 T downstream_gene_variant Transcript ENST00000244241 protein_coding NA 2894 1 SNV HGNC HGNC:5983 YES NM_013278.4 1 P1 CCDS42217.1 ENSP00000244241 Q9P0M4.146 UPI000003E87C 8 NA NA PASS SITE 181,186|16,17 NA NA 1 93 20,20 151,155 60,60 36 1.86 NA 21.07 NA FALSE 6.00 65 NA NA NA FALSE NA NA 61.52 8 88643362 HCC1395_HCC1395T 255 0.113 288 69,7 77,12 156,19 NA 0/1 NA NA NA NA 126,129,16,17 C/T PANCANCER NA FALSE IL17C chr16:88643362:88643363:C:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 88651945 88651946 C T 46 138 0.333333333333333 MODIFIER CYBA ENSG00000051523 T upstream_gene_variant Transcript ENST00000261623 protein_coding NA rs9932581&CR033688 892 -1 SNV HGNC HGNC:2577 YES NM_000101.4 1 P1 CCDS32504.1 ENSP00000261623 P13498.214 UPI000013D1BE 1 0.4165 0.2352 0.4986 0.5952 0.4026 0.4335 0.3909 0.2831 0.5429 0.4817 0.4315 0.5876 0.4274 0.481 0.4067 0.4242 0.4367 0.5952 EAS benign 1&1 31231424&24895604&24562334&32185238&29342889&21902598&25787042&23725037&22470385&27901128&30654669&27607450&24477591&25862415&30723314&24349292&31527397&20080081&30310735&27048830&32961879&34308116&32423015&22550613&34970365&36675214 8 NA NA PASS SITE 87,60|30,16 NA NA 1 47 20,34 164,183 60,60 35 1.56 NA 10.53 NA FALSE 0.401 93 NA NA NA FALSE NA NA 124.62 8 88651945 HCC1395_HCC1395T 92 0.362 138 28,18 34,18 66,37 NA 0/1 NA NA NA NA 56,36,30,16 C/T PANCANCER NA FALSE CYBA chr16:88651945:88651946:C:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 88652056 88652057 G A 37 176 0.210227272727273 MODIFIER CYBA ENSG00000051523 A upstream_gene_variant Transcript ENST00000261623 protein_coding NA 1003 -1 SNV HGNC HGNC:2577 YES NM_000101.4 1 P1 CCDS32504.1 ENSP00000261623 P13498.214 UPI000013D1BE 1 8 NA NA PASS SITE 96,105|16,21 NA NA 1 93 20,33 163,153 60,60 30 1.65 NA 12.90 NA FALSE 6.00 64 NA NA NA FALSE NA NA 92.70 8 88652056 HCC1395_HCC1395T 139 0.214 176 37,8 59,16 102,27 NA 0/1 NA NA NA NA 67,72,16,21 G/A PANCANCER NA FALSE CYBA chr16:88652056:88652057:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 88697159 88697160 C G 257 842 0.305225653206651 MODIFIER RNF166 ENSG00000158717 G 3_prime_UTR_variant Transcript ENST00000312838 protein_coding 6/6 ENST00000312838.9:c.*409G>C NA 1206 rs117229196 -1 SNV HGNC HGNC:28856 YES NM_178841.4 1 P1 CCDS10969.1 ENSP00000326095 Q96A37.157 UPI0000071276 Q96A37-1 0.0403 0.0068 0.0735 0.002 0.0855 0.0552 0.06357 0.01708 0.1451 0.08921 0.04553 0.0009626 0.0719 0.02532 0.08977 0.05849 0.06395 0.1451 gnomADg_AMI 8 NA NA PASS SITE 434,436|128,129 NA NA 1 93 20,20 159,161 60,60 41 2.24 NA 52.07 NA FALSE 1.20 93 NA NA NA FALSE NA NA 550.82 8 88697159 HCC1395_HCC1395T 585 0.294 842 132,61 210,80 377,157 NA 0/1 NA NA NA NA 290,295,128,129 C/G PANCANCER NA FALSE RNF166 chr16:88697159:88697160:C:G SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 88706407 88706408 C T 116 285 0.407017543859649 MODIFIER CTU2 ENSG00000174177 T upstream_gene_variant Transcript ENST00000312060 protein_coding NA rs880233 76 1 SNV HGNC HGNC:28005 5 A2 CCDS32506.1 ENSP00000308617 Q2VPK5.131 UPI00004EC06A Q2VPK5-5 1 0.3448 0.1944 0.3429 0.7222 0.1918 0.318 0.2254 0.1984 0.1385 0.316 0.1924 0.7128 0.2636 0.1943 0.1763 0.2244 0.3014 0.7222 EAS 8 NA NA PASS SITE 146,133|65,51 NA NA 1 93 20,20 160,160 60,60 31 1.90 NA 23.18 NA FALSE 0.652 93 NA NA NA FALSE NA NA 288.91 8 88706407 HCC1395_HCC1395T 169 0.391 285 61,38 57,38 123,79 NA 0/1 NA NA NA NA 91,78,65,51 C/T PANCANCER NA FALSE CTU2 chr16:88706407:88706408:C:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 88738168 88738169 C T 187 506 0.369565217391304 MODIFIER PIEZO1 ENSG00000103335 T intron_variant Transcript ENST00000301015 protein_coding 7/50 ENST00000301015.14:c.848+59G>A NA rs72813506 -1 SNV HGNC HGNC:28993 YES NM_001142864.4 1 P1 CCDS54058.1 ENSP00000301015 Q92508.175 UPI0001B300F3 1 0.0096 0.0015 0.0115 0.001 0.0318 0.0051 0.02189 0.006972 0.1099 0.007717 0.004896 0 0.03331 0 0.03529 0.01438 0.004762 0.1099 gnomADg_AMI likely_benign 1 8 NA NA PASS SITE 225,258|86,101 NA NA 1 93 20,20 161,166 60,60 28 2.07 NA 34.01 NA FALSE 1.62 93 NA NA NA FALSE NA NA 479.98 8 88738168 HCC1395_HCC1395T 319 0.374 506 86,51 119,72 220,131 NA 0/1 NA NA NA NA 151,168,86,101 C/T PANCANCER NA FALSE PIEZO1 chr16:88738168:88738169:C:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 88817961 88817962 C T 87 199 0.437185929648241 MODIFIER GALNS ENSG00000141012 T intron_variant Transcript ENST00000268695 protein_coding 13/13 ENST00000268695.10:c.1482+46G>A NA rs190672441 -1 SNV HGNC HGNC:4122 YES NM_000512.5 1 P1 CCDS10970.1 ENSP00000268695 P34059.206 UPI000012AF92 1 0.0018 0.0008 0.0014 0 0.007 0 0.002986 0.001292 0.0005632 0 0 0.003096 0.005869 0.002829 0.0007623 0.003022 0.001133 0.002193 0.0007851 0 0 0.0048 0 0.005042 0.001912 0.000207 0.007 EUR 8 NA NA PASS SITE 128,58|59,28 NA NA 1 93 20,20 174,167 60,60 28 1.73 NA 15.04 NA FALSE 2.39 93 NA NA NA FALSE NA NA 220.50 8 88817961 HCC1395_HCC1395T 112 0.435 199 29,27 50,35 82,63 NA 0/1 NA NA NA NA 78,34,59,28 C/T PANCANCER NA FALSE GALNS chr16:88817961:88817962:C:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 89093921 89093922 C G 141 456 0.309210526315789 MODIFIER ACSF3 ENSG00000176715 G 5_prime_UTR_variant Transcript ENST00000317447 protein_coding 1/11 ENST00000317447.9:c.-265C>G NA 70 rs145228567&COSV104615700 1 SNV HGNC HGNC:27288 2 P1 CCDS10974.1 ENSP00000320646 Q4G176.136 UPI00001AF19E 1 0.1635 0.0144 0.3718 0.1875 0.1153 0.2423 0.2276 0.03169 0.5088 0.1302 0.2204 0.1044 0.1513 0.1697 0.2036 0.136 0.03344 0.06908 0.3157 0.1197 0.1923 0.1139 0.07962 0.1547 0.1347 0.2031 0.5088 gnomADe_AMR benign 0&1 1&1 8 NA NA PASS SITE 281,255|73,68 NA NA 1 93 20,20 153,156 60,60 42 2.13 NA 40.02 NA FALSE 0.910 93 NA NA NA FALSE NA NA 292.20 8 89093921 HCC1395_HCC1395T 315 0.307 456 96,41 91,37 194,86 NA 0/1 NA NA NA NA 166,149,73,68 C/G PANCANCER NA FALSE ACSF3 chr16:89093921:89093922:C:G SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 89196023 89196024 G A 106 303 0.34983498349835 MODIFIER CDH15 ENSG00000129910 A downstream_gene_variant Transcript ENST00000289746 protein_coding NA rs2287353&COSV57023910 531 1 SNV HGNC HGNC:1754 YES NM_004933.3 1 P1 CCDS10976.1 ENSP00000289746 P55291.187 UPI0000126DAF 1 0.1326 0.0144 0.2853 0.1508 0.0895 0.2096 0.1761 0.02663 0.3726 0.09559 0.2 0.0774 0.1191 0.1334 0.1776 0.1072 0.02972 0.03947 0.2439 0.09418 0.1845 0.08291 0.06329 0.1185 0.09904 0.1797 0.3726 gnomADe_AMR benign 0&1 1&1 8 NA NA PASS SITE 135,172|47,59 NA NA 1 93 20,20 159,155 60,60 36 1.87 NA 21.67 NA FALSE 0.991 93 NA NA NA FALSE NA NA 274.75 8 89196023 HCC1395_HCC1395T 197 0.355 303 49,34 77,35 135,74 NA 0/1 NA NA NA NA 88,109,47,59 G/A PANCANCER NA FALSE CDH15 chr16:89196023:89196024:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 89201529 89201530 G A 158 334 0.473053892215569 MODIFIER SLC22A31 ENSG00000259803 A 5_prime_UTR_variant Transcript ENST00000562855 protein_coding 1/9 ENST00000562855.7:c.-568C>T NA 123 rs112083449 -1 SNV HGNC HGNC:27091 5 CCDS73927.1 ENSP00000474621 A6NKX4.103 UPI00006C16D6 0.0152 0.0015 0.0187 0.002 0.0427 0.0164 0.05462 0 0 0 0.05882 0 0.04189 0.01148 0.01319 0.03247 0.05245 0.0001928 0.02901 0.006369 0.06978 0.035 0.01633 0.06978 gnomADg_NFE 8 NA NA PASS SITE 180,140|85,73 NA NA 1 93 20,20 155,164 60,60 32 1.98 NA 28.20 NA FALSE 1.33 93 NA NA NA FALSE NA NA 393.98 8 89201529 HCC1395_HCC1395T 176 0.480 334 55,41 52,57 115,106 NA 0/1 NA NA NA NA 100,76,85,73 G/A PANCANCER NA FALSE SLC22A31 chr16:89201529:89201530:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 89226952 89226953 G A 8 444 0.018018018018018 MODERATE ZNF778 ENSG00000170100 A missense_variant Transcript ENST00000306502 protein_coding 5/5 ENST00000306502.6:c.454G>A ENSP00000305203.6:p.D152N ENSP00000305203.6 p.D152N 624 454 152 D/N Gac/Aac 1 SNV HGNC HGNC:26479 2 ENSP00000305203 Q96MU6.160 UPI0001AE6853 Q96MU6-2 tolerated(0.21) possibly_damaging(0.737) Gene3D:3.30.160.60&AlphaFold_DB_import:AF-Q96MU6-F1 8 NA NA PASS SITE 278,275|5,3 NA NA 1 93 20,30 157,179 60,60 32 1.90 NA 23.48 NA FALSE 6.00 25 NA NA NA FALSE NA NA 9.66 8 89226952 HCC1395_HCC1395T 436 0.023 444 96,2 163,3 286,6 NA 0/1 NA NA NA NA 218,218,5,3 G/A PANCANCER NA FALSE ZNF778_p.D152N chr16:89226952:89226953:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 89329030 89329031 G A 103 293 0.351535836177474 MODIFIER ANKRD11 ENSG00000167522 A intron_variant Transcript ENST00000301030 protein_coding 2/12 ENST00000301030.10:c.-59-11952C>T NA rs113955902 -1 SNV HGNC HGNC:21316 YES NM_013275.6 5 P1 CCDS32513.1 ENSP00000301030 Q6UB99.155 UPI00004569E1 1 0.0138 0.003 0.0159 0.001 0.0507 0.002 0.04035 0.0138 0.04084 0.0152 0.05927 0 0.05586 0 0.06199 0.02302 0.002731 0.06199 gnomADg_NFE 8 NA NA PASS SITE 141,162|51,52 NA NA 1 93 20,20 154,156 60,60 33 1.87 NA 21.97 NA FALSE 1.40 93 NA NA NA FALSE NA NA 236.70 8 89329030 HCC1395_HCC1395T 190 0.359 293 57,29 50,30 125,70 NA 0/1 NA NA NA NA 88,102,51,52 G/A PANCANCER NA FALSE ANKRD11 chr16:89329030:89329031:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 89544491 89544492 G T 41 141 0.290780141843972 MODIFIER SPG7 ENSG00000197912 T intron_variant Transcript ENST00000268704 protein_coding 9/16 ENST00000268704.7:c.1304-157G>T NA rs1049965561 1 SNV HGNC HGNC:11237 1 A2 ENSP00000268704 A0A2U3TZH1.25 UPI000D1973D3 1 1.972e-05 4.829e-05 0 0 0 0 0 0 1.47e-05 0 0 4.829e-05 gnomADg_AFR 8 NA NA PASS SITE 89,79|23,18 NA NA 1 93 20,20 164,155 60,60 45 1.65 NA 13.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 90.80 8 89544491 HCC1395_HCC1395T 100 0.295 141 30,12 33,14 66,27 NA 0/1 NA NA NA NA 53,47,23,18 G/T PANCANCER NA FALSE SPG7 chr16:89544491:89544492:G:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 89549174 89549175 G C 79 248 0.318548387096774 MODIFIER SPG7 ENSG00000197912 C intron_variant Transcript ENST00000268704 protein_coding 12/16 ENST00000268704.7:c.1642+1061G>C NA rs916064113 1 SNV HGNC HGNC:11237 1 A2 ENSP00000268704 A0A2U3TZH1.25 UPI000D1973D3 1 8 NA NA PASS SITE 113,126|38,41 NA NA 1 93 20,20 167,165 60,60 30 1.73 NA 15.65 NA FALSE 6.00 93 NA NA NA FALSE NA NA 210.07 8 89549174 HCC1395_HCC1395T 169 0.330 248 41,21 74,32 118,58 NA 0/1 NA NA NA NA 81,88,38,41 G/C PANCANCER NA FALSE SPG7 chr16:89549174:89549175:G:C SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 89596975 89596976 G T 63 338 0.186390532544379 MODIFIER CPNE7 ENSG00000178773 T 3_prime_UTR_variant Transcript ENST00000268720 protein_coding 17/17 ENST00000268720.9:c.*354G>T NA 2386 1 SNV HGNC HGNC:2320 1 CCDS10980.1 ENSP00000268720 Q9UBL6.166 UPI0000127C17 Q9UBL6-1 8 NA NA PASS SITE 176,210|30,33 NA NA 1 93 20,20 161,159 60,60 29 1.87 NA 21.38 NA FALSE 6.00 93 NA NA NA FALSE NA NA 126.24 8 89596975 HCC1395_HCC1395T 275 0.181 338 68,15 101,21 187,41 NA 0/1 NA NA NA NA 124,151,30,33 G/T PANCANCER NA FALSE CPNE7 chr16:89596975:89596976:G:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 89752324 89752325 C G 34 125 0.272 MODIFIER FANCA ENSG00000187741 G intron_variant&non_coding_transcript_variant Transcript ENST00000305699 retained_intron 2/10 ENST00000305699.15:n.225-102G>C NA rs12931267 -1 SNV HGNC HGNC:3582 2 1 0.0212 0.003 0.0144 0.0179 0.0686 0.0051 0.04571 0.01504 0.05066 0.01684 0.07435 0.0183 0.05655 0.003165 0.07341 0.02682 0.005176 0.07435 gnomADg_ASJ benign 1 20585627&29895819&28510302&30657907&23021409&30166351&25963972&23843775&27089180&34290314&34737440&36536295&36378845 8 NA NA PASS SITE 43,87|13,21 NA NA 1 36 20,20 160,183 60,60 30 1.45 NA 8.13 NA FALSE 1.31 93 NA NA NA FALSE NA NA 82.69 8 89752324 HCC1395_HCC1395T 91 0.278 125 19,11 37,9 64,24 NA 0/1 NA NA NA NA 31,60,13,21 C/G PANCANCER NA FALSE FANCA chr16:89752324:89752325:C:G SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 89846998 89846999 CAA C 115 300 0.383333333333333 MODIFIER SPIRE2 ENSG00000204991 - intron_variant Transcript ENST00000378247 protein_coding 2/14 ENST00000378247.8:c.288+1634_288+1635del NA rs36100920 1 deletion HGNC HGNC:30623 YES NM_032451.2 1 P1 CCDS32516.1 ENSP00000367494 Q8WWL2.144 UPI00001C1FA8 Q8WWL2-1 0.0176 0.003 0.0144 0 0.0716 0.002 0.04581 0.01482 0.04967 0.0161 0.07384 0 0.06749 0.006452 0.07388 0.02644 0.00273 0.07388 gnomADg_NFE 8 NA NA PASS SITE 147,101|65,50 NA NA 2 93 20,20 174,168 60,60 27 1.19 NA 12.90 NA FALSE 1.35 93 NA NA NA FALSE NA NA 111.69 8 89846998 HCC1395_HCC1395T 185 0.386 300 23,11 43,35 125,78 NA 0/1 NA NA NA NA 109,76,65,50 CAA/C PANCANCER NA FALSE SPIRE2 chr16:89846998:89846999:CAA:C indel 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 89859116 89859117 G A 83 193 0.430051813471503 MODIFIER SPIRE2 ENSG00000204991 A intron_variant Transcript ENST00000378247 protein_coding 8/14 ENST00000378247.8:c.1273-49G>A NA 1 SNV HGNC HGNC:30623 YES NM_032451.2 1 P1 CCDS32516.1 ENSP00000367494 Q8WWL2.144 UPI00001C1FA8 Q8WWL2-1 8 NA NA PASS SITE 121,60|60,23 NA NA 1 93 20,36 169,183 60,60 29 1.70 NA 14.40 NA FALSE 6.00 93 NA NA NA FALSE NA NA 242.92 8 89859116 HCC1395_HCC1395T 110 0.452 193 37,26 41,39 79,65 NA 0/1 NA NA NA NA 75,35,60,23 G/A PANCANCER NA FALSE SPIRE2 chr16:89859116:89859117:G:A SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr16 89919709 89919710 C T 270 755 0.357615894039735 MODIFIER TUBB3 ENSG00000258947 T upstream_gene_variant Transcript ENST00000315491 protein_coding NA rs1805007&CM981238 3633 1 SNV HGNC HGNC:20772 YES NM_006086.4 1 P1 CCDS10988.1 ENSP00000320295 Q13509.210 UPI00001369F9 Q13509-1 1 0.0186 0.003 0.0159 0.001 0.0716 0.0051 0.04416 0.01317 0.009367 0.06563 0.0006132 0.07055 0.0718 0.04121 0.003632 0.04627 0.01483 0.05044 0.01674 0.0746 0.0009626 0.06991 0.006329 0.07407 0.02725 0.004549 0.0746 gnomADg_ASJ benign&association&affects&risk_factor 1&1 25741868&16595073&27539887&27716216&20585627&20546537&20876667&29895819&24086514&20158590&21926416&24274136&20393453&21445957&19812545&23548203&27459457&26547235&24642353&25945350&17999355&21700618&20042077&23927501&20691402&22629401&27424798&19884608&21197618&20457063&24809478&24473444&17952075&28242083&19710684&26848990&29109912&31612033&30980179&29518100&24924479&26286644&32121219&24436253&12876664&28510302&25159867&30760877&29054604&30520188&24439955&27047535&21829225&22140526&17616515&21052032&27488084&30657907&31834199&16601669&20670983&9571181&15994880&16463023&19194882&23393597&25631192&28081215&29771307&29662168&31220071&26103569&24392023&25058410&28212542&24179397&23360207&27555332&23149900&28602423&31238981&26829030&30531825&29774366&30323283&30205563&23441100&25762173&28701907&26908436&25154630&30166351&29317335&28030571&26030184&21693730&24278778&25963972&27766958&30278967&23843775&31174203&22486937&27755135&23317428&28819144&32041948&29846678&28500464&19615406&20598278&16472919&15579207&30595370 8 NA NA PASS SITE 399,338|147,123 NA NA 1 93 20,20 157,161 60,60 30 2.21 NA 48.07 NA FALSE 1.29 93 NA NA NA FALSE NA NA 632.70 8 89919709 HCC1395_HCC1395T 485 0.351 755 143,89 153,78 318,172 NA 0/1 NA NA NA NA 270,215,147,123 C/T PANCANCER NA FALSE TUBB3 chr16:89919709:89919710:C:T SNV 8:0 chr16:79585938:90075679:8:0:1 NA NA 0.96 +chr17 2364457 2364458 T G 50 78 0.641025641025641 MODIFIER SGSM2 ENSG00000141258 G intron_variant Transcript ENST00000268989 protein_coding 8/23 ENST00000268989.8:c.933-139T>G NA 1 SNV HGNC HGNC:29026 YES NM_014853.3 1 P4 CCDS32526.1 ENSP00000268989 O43147.146 UPI0000160300 O43147-2 9 NA NA PASS SITE 71,19|37,13 NA NA 1 93 34,31 176,182 60,60 24 1.73 NA 15.61 NA FALSE 6.00 93 NA NA NA FALSE NA NA 153.80 9 2364457 HCC1395_HCC1395T 28 0.632 78 6,13 13,25 22,38 NA 0/1 NA NA NA NA 20,8,37,13 T/G PANCANCER NA FALSE SGSM2 chr17:2364457:2364458:T:G SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 3033336 3033337 C G 5 28 0.178571428571429 MODIFIER RAP1GAP2 ENSG00000132359 G intron_variant Transcript ENST00000254695 protein_coding 24/24 ENST00000254695.13:c.*31-56C>G NA 1 SNV HGNC HGNC:29176 YES NM_015085.5 1 P4 CCDS45573.1 ENSP00000254695 Q684P5.130 UPI0000D622A3 Q684P5-1 9 NA NA PASS SITE 35,16|3,2 NA NA 1 79 20,35 161,191 60,60 14 1.33 NA 6.02 NA FALSE 6.00 47 NA NA NA FALSE NA NA 12.52 9 3033336 HCC1395_HCC1395T 23 0.218 28 7,3 9,1 17,4 NA 0/1 NA NA NA NA 15,8,3,2 C/G PANCANCER NA FALSE RAP1GAP2 chr17:3033336:3033337:C:G SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 4189200 4189201 A G 9 24 0.375 MODIFIER ANKFY1 ENSG00000185722 G intron_variant Transcript ENST00000341657 protein_coding 11/24 ENST00000341657.9:c.1470+182T>C NA -1 SNV HGNC HGNC:20763 YES NM_001330063.2 5 P3 CCDS82038.1 ENSP00000343362 Q9P2R3.179 UPI0000038C5D Q9P2R3-1 1 9 NA NA PASS SITE 38,1|9,0 NA NA 1 71 38,41 213,235 60,60 24 1.40 NA 6.92 NA FALSE 6.00 37 NA NA NA FALSE NA NA 28.35 9 4189200 HCC1395_HCC1395T 15 0.386 24 6,2 8,6 15,9 NA 0/1 NA NA NA NA 15,0,9,0 A/G PANCANCER NA FALSE ANKFY1 chr17:4189200:4189201:A:G SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 4545725 4545726 T C 73 221 0.330316742081448 MODERATE MYBBP1A ENSG00000132382 C missense_variant Transcript ENST00000254718 protein_coding 15/26 ENST00000254718.9:c.1958A>G ENSP00000254718.4:p.E653G ENSP00000254718.4 p.E653G 2018 1958 653 E/G gAg/gGg -1 SNV HGNC HGNC:7546 YES NM_014520.4 1 A2 CCDS11046.1 ENSP00000254718 Q9BQG0.187 UPI000013CE54 Q9BQG0-1 deleterious(0.01) probably_damaging(0.993) Gene3D:1.25.10.10&AlphaFold_DB_import:AF-Q9BQG0-F1&Pfam:PF04931&PANTHER:PTHR13213&Superfamily:SSF48371&Low_complexity_(Seg):seg 9 NA NA PASS SITE 216,167|41,32 NA NA 1 93 20,20 161,157 60,60 25 2.22 NA 48.70 NA FALSE 6.00 93 NA NA NA FALSE NA NA 175.80 9 4545725 HCC1395_HCC1395T 148 0.323 221 48,26 52,19 103,49 NA 0/1 NA NA NA NA 89,59,41,32 T/C PANCANCER NA FALSE MYBBP1A_p.E653G chr17:4545725:4545726:T:C SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 4818361 4818362 TGGACAGAATCCTGAA T 78 288 0.270833333333333 MODERATE PLD2 ENSG00000129219 - inframe_deletion Transcript ENST00000263088 protein_coding 19/25 ENST00000263088.11:c.1988_2002del ENSP00000263088.5:p.D663_K667del ENSP00000263088.5 p.D663_K667del 2061-2075 1986-2000 662-667 VDRILK/V gtGGACAGAATCCTGAAg/gtg 1 deletion HGNC HGNC:9068 YES NM_002663.5 1 P1 CCDS11057.1 ENSP00000263088 O14939.201 UPI0000131BDE O14939-1 PDB-ENSP_mappings:6ohm.A&PDB-ENSP_mappings:6ohm.B&PDB-ENSP_mappings:6oho.A&PDB-ENSP_mappings:6oho.B&PDB-ENSP_mappings:6ohp.A&PDB-ENSP_mappings:6ohp.B&PDB-ENSP_mappings:6ohp.C&PDB-ENSP_mappings:6ohp.D&PDB-ENSP_mappings:6ohq.A&PDB-ENSP_mappings:6ohq.B&PDB-ENSP_mappings:6ohs.A&PDB-ENSP_mappings:6ohs.B&PDB-ENSP_mappings:6ohs.C&PDB-ENSP_mappings:6ohs.D&CDD:cd09845&PANTHER:PTHR18896&Gene3D:3.30.870.10&PIRSF:PIRSF009376&Pfam:PF13091&Superfamily:SSF56024&AlphaFold_DB_import:AF-O14939-F1 2 9 NA NA PASS SITE 309,194|46,32 NA NA 1 93 20,32 165,193 60,60 34 2.30 NA 58.27 NA FALSE 6.00 93 NA NA NA FALSE NA NA 295.83 9 4818361 HCC1395_HCC1395T 210 0.286 288 38,22 79,27 152,60 NA 0/1 NA NA NA NA 132,78,46,32 TGGACAGAATCCTGAA/T PANCANCER NA FALSE PLD2_p.D663_K667del chr17:4818361:4818362:TGGACAGAATCCTGAA:T indel 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 5007047 5007048 C T 12 38 0.315789473684211 MODERATE KIF1C ENSG00000129250 T missense_variant Transcript ENST00000320785 protein_coding 14/23 ENST00000320785.10:c.1298C>T ENSP00000320821.5:p.S433F ENSP00000320821.5 p.S433F 1653 1298 433 S/F tCc/tTc 1 SNV HGNC HGNC:6317 YES NM_006612.6 1 P1 CCDS11065.1 ENSP00000320821 O43896.196 UPI0000001C26 1 deleterious_low_confidence(0.02) benign(0.081) Gene3D:6.10.250.2520&AlphaFold_DB_import:AF-O43896-F1&Pfam:PF16183&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite 9 NA NA PASS SITE 25,53|4,8 NA NA 1 93 20,36 175,180 60,60 31 1.61 NA 11.74 NA FALSE 6.00 49 NA NA NA FALSE NA NA 34.44 9 5007047 HCC1395_HCC1395T 26 0.344 38 3,3 15,6 18,9 NA 0/1 NA NA NA NA 10,16,4,8 C/T PANCANCER NA FALSE KIF1C_p.S433F chr17:5007047:5007048:C:T SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 5413902 5413903 A G 107 107 1 MODIFIER NUP88 ENSG00000108559 G intron_variant Transcript ENST00000225696 protein_coding 3/16 ENST00000225696.9:c.593+107T>C NA -1 SNV HGNC HGNC:8067 5 CCDS92236.1 ENSP00000225696 J3KMX1.62 UPI000387D3F0 1 9 NA NA PASS SITE 59,38|68,39 NA NA 1 93 20,20 161,172 60,60 32 1.82 NA 18.96 NA FALSE 6.00 93 NA NA NA FALSE NA NA 334.28 9 5413902 HCC1395_HCC1395T 0 0.988 107 0,23 0,52 0,78 NA 0/1 NA NA NA NA 0,0,68,39 A/G PANCANCER NA FALSE NUP88 chr17:5413902:5413903:A:G SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 7588500 7588501 G C 67 88 0.761363636363636 MODERATE SOX15 ENSG00000129194 C missense_variant Transcript ENST00000250055 protein_coding 2/2 ENST00000250055.3:c.580C>G ENSP00000355354.2:p.Q194E ENSP00000355354.2 p.Q194E 998 580 194 Q/E Cag/Gag COSV51468093&COSV51468733 -1 SNV HGNC HGNC:11196 YES NM_006942.2 1 P1 CCDS32549.1 ENSP00000355354 O60248.185 UPI00001362B5 O60248-1 tolerated_low_confidence(0.12) benign(0.036) AlphaFold_DB_import:AF-O60248-F1&PANTHER:PTHR10270 1&1 1&1 9 NA NA PASS SITE 45,62|24,43 NA NA 1 93 20,20 161,166 60,60 24 1.78 NA 17.76 NA FALSE 6.00 93 NA NA NA FALSE NA NA 203.77 9 7588500 HCC1395_HCC1395T 21 0.754 88 6,19 8,24 15,48 NA 0/1 NA NA NA NA 9,12,24,43 G/C PANCANCER NA FALSE SOX15_p.Q194E chr17:7588500:7588501:G:C SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 7675088 7675089 C T 279 280 0.996428571428571 MODERATE TP53 ENSG00000141510 T missense_variant Transcript ENST00000269305 protein_coding 5/11 ENST00000269305.9:c.524G>A ENSP00000269305.4:p.R175H ENSP00000269305.4 p.R175H 666 524 175 R/H cGc/cAc rs28934578&CM062017&CM951224&COSV52661038&COSV52677601&COSV52731306&COSV53801286 -1 SNV HGNC HGNC:11998 YES NM_000546.6 1 P1 CCDS11118.1 ENSP00000269305 P04637.298 K7PPA8.83 UPI000002ED67 P04637-1 1 tolerated(0.08) PDB-ENSP_mappings:1gzh.A&PDB-ENSP_mappings:1gzh.C&PDB-ENSP_mappings:1kzy.A&PDB-ENSP_mappings:1kzy.B&PDB-ENSP_mappings:1tsr.A&PDB-ENSP_mappings:1tsr.B&PDB-ENSP_mappings:1tsr.C&PDB-ENSP_mappings:1tup.A&PDB-ENSP_mappings:1tup.B&PDB-ENSP_mappings:1tup.C&PDB-ENSP_mappings:1uol.A&PDB-ENSP_mappings:1uol.B&PDB-ENSP_mappings:1ycs.A&PDB-ENSP_mappings:2ac0.A&PDB-ENSP_mappings:2ac0.B&PDB-ENSP_mappings:2ac0.C&PDB-ENSP_mappings:2ac0.D&PDB-ENSP_mappings:2ady.A&PDB-ENSP_mappings:2ady.B&PDB-ENSP_mappings:2ahi.A&PDB-ENSP_mappings:2ahi.B&PDB-ENSP_mappings:2ahi.C&PDB-ENSP_mappings:2ahi.D&PDB-ENSP_mappings:2ata.A&PDB-ENSP_mappings:2ata.B&PDB-ENSP_mappings:2ata.C&PDB-ENSP_mappings:2ata.D&PDB-ENSP_mappings:2bim.A&PDB-ENSP_mappings:2bim.B&PDB-ENSP_mappings:2bin.A&PDB-ENSP_mappings:2bio.A&PDB-ENSP_mappings:2bip.A&PDB-ENSP_mappings:2biq.A&PDB-ENSP_mappings:2fej.A&PDB-ENSP_mappings:2h1l.M&PDB-ENSP_mappings:2h1l.N&PDB-ENSP_mappings:2h1l.O&PDB-ENSP_mappings:2h1l.P&PDB-ENSP_mappings:2h1l.Q&PDB-ENSP_mappings:2h1l.R&PDB-ENSP_mappings:2h1l.S&PDB-ENSP_mappings:2h1l.T&PDB-ENSP_mappings:2h1l.U&PDB-ENSP_mappings:2h1l.V&PDB-ENSP_mappings:2h1l.W&PDB-ENSP_mappings:2h1l.X&PDB-ENSP_mappings:2j1w.A&PDB-ENSP_mappings:2j1w.B&PDB-ENSP_mappings:2j1x.A&PDB-ENSP_mappings:2j1x.B&PDB-ENSP_mappings:2j1y.A&PDB-ENSP_mappings:2j1y.B&PDB-ENSP_mappings:2j1y.C&PDB-ENSP_mappings:2j1y.D&PDB-ENSP_mappings:2j1z.A&PDB-ENSP_mappings:2j1z.B&PDB-ENSP_mappings:2j20.A&PDB-ENSP_mappings:2j20.B&PDB-ENSP_mappings:2j21.A&PDB-ENSP_mappings:2j21.B&PDB-ENSP_mappings:2mej.B&PDB-ENSP_mappings:2ocj.A&PDB-ENSP_mappings:2ocj.B&PDB-ENSP_mappings:2ocj.C&PDB-ENSP_mappings:2ocj.D&PDB-ENSP_mappings:2pcx.A&PDB-ENSP_mappings:2vuk.A&PDB-ENSP_mappings:2vuk.B&PDB-ENSP_mappings:2wgx.A&PDB-ENSP_mappings:2wgx.B&PDB-ENSP_mappings:2x0u.A&PDB-ENSP_mappings:2x0u.B&PDB-ENSP_mappings:2x0v.A&PDB-ENSP_mappings:2x0v.B&PDB-ENSP_mappings:2x0w.A&PDB-ENSP_mappings:2x0w.B&PDB-ENSP_mappings:2xwr.A&PDB-ENSP_mappings:2xwr.B&PDB-ENSP_mappings:2ybg.A&PDB-ENSP_mappings:2ybg.B&PDB-ENSP_mappings:2ybg.C&PDB-ENSP_mappings:2ybg.D&PDB-ENSP_mappings:3d05.A&PDB-ENSP_mappings:3d06.A&PDB-ENSP_mappings:3d07.A&PDB-ENSP_mappings:3d07.B&PDB-ENSP_mappings:3d08.A&PDB-ENSP_mappings:3d09.A&PDB-ENSP_mappings:3d0a.A&PDB-ENSP_mappings:3d0a.B&PDB-ENSP_mappings:3d0a.C&PDB-ENSP_mappings:3d0a.D&PDB-ENSP_mappings:3igk.A&PDB-ENSP_mappings:3igl.A&PDB-ENSP_mappings:3kmd.A&PDB-ENSP_mappings:3kmd.B&PDB-ENSP_mappings:3kmd.C&PDB-ENSP_mappings:3kmd.D&PDB-ENSP_mappings:3kz8.A&PDB-ENSP_mappings:3kz8.B&PDB-ENSP_mappings:3q01.A&PDB-ENSP_mappings:3q01.B&PDB-ENSP_mappings:3q05.A&PDB-ENSP_mappings:3q05.B&PDB-ENSP_mappings:3q05.C&PDB-ENSP_mappings:3q05.D&PDB-ENSP_mappings:3q06.A&PDB-ENSP_mappings:3q06.B&PDB-ENSP_mappings:3q06.C&PDB-ENSP_mappings:3q06.D&PDB-ENSP_mappings:3ts8.A&PDB-ENSP_mappings:3ts8.B&PDB-ENSP_mappings:3ts8.C&PDB-ENSP_mappings:3ts8.D&PDB-ENSP_mappings:3zme.A&PDB-ENSP_mappings:3zme.B&PDB-ENSP_mappings:4agl.A&PDB-ENSP_mappings:4agl.B&PDB-ENSP_mappings:4agm.A&PDB-ENSP_mappings:4agm.B&PDB-ENSP_mappings:4agn.A&PDB-ENSP_mappings:4agn.B&PDB-ENSP_mappings:4ago.A&PDB-ENSP_mappings:4ago.B&PDB-ENSP_mappings:4agp.A&PDB-ENSP_mappings:4agp.B&PDB-ENSP_mappings:4agq.A&PDB-ENSP_mappings:4agq.B&PDB-ENSP_mappings:4hje.A&PDB-ENSP_mappings:4hje.B&PDB-ENSP_mappings:4hje.C&PDB-ENSP_mappings:4hje.D&PDB-ENSP_mappings:4ibq.A&PDB-ENSP_mappings:4ibq.B&PDB-ENSP_mappings:4ibq.C&PDB-ENSP_mappings:4ibq.D&PDB-ENSP_mappings:4ibs.A&PDB-ENSP_mappings:4ibs.B&PDB-ENSP_mappings:4ibs.C&PDB-ENSP_mappings:4ibs.D&PDB-ENSP_mappings:4ibt.A&PDB-ENSP_mappings:4ibt.B&PDB-ENSP_mappings:4ibt.C&PDB-ENSP_mappings:4ibt.D&PDB-ENSP_mappings:4ibu.A&PDB-ENSP_mappings:4ibu.B&PDB-ENSP_mappings:4ibu.C&PDB-ENSP_mappings:4ibu.D&PDB-ENSP_mappings:4ibv.A&PDB-ENSP_mappings:4ibw.A&PDB-ENSP_mappings:4iby.A&PDB-ENSP_mappings:4iby.B&PDB-ENSP_mappings:4ibz.A&PDB-ENSP_mappings:4ibz.B&PDB-ENSP_mappings:4ibz.C&PDB-ENSP_mappings:4ibz.D&PDB-ENSP_mappings:4ijt.A&PDB-ENSP_mappings:4kvp.A&PDB-ENSP_mappings:4kvp.B&PDB-ENSP_mappings:4kvp.C&PDB-ENSP_mappings:4kvp.D&PDB-ENSP_mappings:4lo9.A&PDB-ENSP_mappings:4lo9.B&PDB-ENSP_mappings:4lo9.C&PDB-ENSP_mappings:4lo9.D&PDB-ENSP_mappings:4loe.A&PDB-ENSP_mappings:4loe.B&PDB-ENSP_mappings:4loe.C&PDB-ENSP_mappings:4loe.D&PDB-ENSP_mappings:4lof.A&PDB-ENSP_mappings:4mzi.A&PDB-ENSP_mappings:4mzr.A&PDB-ENSP_mappings:4mzr.B&PDB-ENSP_mappings:4mzr.C&PDB-ENSP_mappings:4mzr.D&PDB-ENSP_mappings:4qo1.B&PDB-ENSP_mappings:4xr8.C&PDB-ENSP_mappings:4xr8.D&PDB-ENSP_mappings:5a7b.A&PDB-ENSP_mappings:5a7b.B&PDB-ENSP_mappings:5ab9.A&PDB-ENSP_mappings:5ab9.B&PDB-ENSP_mappings:5aba.A&PDB-ENSP_mappings:5aba.B&PDB-ENSP_mappings:5aoi.A&PDB-ENSP_mappings:5aoi.B&PDB-ENSP_mappings:5aoj.A&PDB-ENSP_mappings:5aoj.B&PDB-ENSP_mappings:5aok.A&PDB-ENSP_mappings:5aok.B&PDB-ENSP_mappings:5aol.A&PDB-ENSP_mappings:5aol.B&PDB-ENSP_mappings:5aom.A&PDB-ENSP_mappings:5aom.B&PDB-ENSP_mappings:5bua.A&PDB-ENSP_mappings:5ecg.A&PDB-ENSP_mappings:5ecg.B&PDB-ENSP_mappings:5g4m.A&PDB-ENSP_mappings:5g4m.B&PDB-ENSP_mappings:5g4n.A&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3.98e-06 0 0 0 0 0 8.803e-06 0 0 6.57e-06 0 0 0 0 0 0 0 1.47e-05 0 0 1.47e-05 gnomADg_NFE pathogenic&likely_pathogenic¬_provided 0&0&0&1&1&1&1 1&1&1&1&1&1&1 26900293&27153395&25157968&22006311&21264207&25105660&16489069&17606709&18511570&23161690&24929325&11370630&21305319&21761402&16401470&8649785&9047394&11101847&15977174&18391940&19881536&20128691&20689556&21343334&22233476&22698404&23792586&24573247&12826609&14559903&16861262&20407015&27374712&28163917&12619118&30224644&30709875&29979965&28873162&19127115&27516001&23263379&16707427&32000721&15607981&8164043&28349240&23639312&15607980&25927356&9242456&30816478&8825920&20516128&12007217&34203389&33076847&31907277&31371350&32467344&25404506&34514028&34771529&34964846&33174010&35328276&36077746&36531003&35867400 9 NA NA PASS SITE 110,124|135,145 NA NA 1 93 20,21 161,168 60,60 29 0.978 NA 47.59 NA FALSE 6.00 93 NA NA NA FALSE NA NA 899.20 9 7675088 HCC1395_HCC1395T 1 0.991 280 1,89 0,97 1,207 NA 0/1 NA NA NA NA 0,1,135,144 C/T PANCANCER TRUE TRUE TP53_p.R175H chr17:7675088:7675089:C:T SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 7807669 7807670 C G 88 88 1 MODIFIER DNAH2 ENSG00000183914 G intron_variant Transcript ENST00000389173 protein_coding 62/84 ENST00000389173.6:c.9729+83C>G NA 1 SNV HGNC HGNC:2948 2 P1 CCDS32551.1 ENSP00000373825 Q9P225.148 UPI00005B2F0D Q9P225-1 1 9 NA NA PASS SITE 30,54|31,57 NA NA 1 93 20,20 162,158 60,60 34 1.77 NA 17.16 NA FALSE 6.00 93 NA NA NA FALSE NA NA 264.05 9 7807669 HCC1395_HCC1395T 0 0.984 88 0,24 0,31 0,59 NA 0/1 NA NA NA NA 0,0,31,57 C/G PANCANCER NA FALSE DNAH2 chr17:7807669:7807670:C:G SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 9959188 9959189 C G 33 109 0.302752293577982 MODIFIER GAS7 ENSG00000007237 G intron_variant Transcript ENST00000323816 protein_coding 6/14 ENST00000323816.8:c.345+14G>C NA -1 SNV HGNC HGNC:4169 1 ENSP00000322608 O60861.199 UPI000023C3D6 O60861-4 1 9 NA NA PASS SITE 104,43|24,9 NA NA 1 93 20,20 168,162 60,60 33 1.75 NA 15.95 NA FALSE 6.00 93 NA NA NA FALSE NA NA 87.45 9 9959188 HCC1395_HCC1395T 76 0.305 109 21,9 33,15 56,24 NA 0/1 NA NA NA NA 55,21,24,9 C/G PANCANCER NA FALSE GAS7 chr17:9959188:9959189:C:G SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 10499041 10499042 G A 219 219 1 MODERATE MYH1 ENSG00000109061 A missense_variant Transcript ENST00000226207 protein_coding 29/40 ENST00000226207.6:c.3917C>T ENSP00000226207.5:p.S1306L ENSP00000226207.5 p.S1306L 4011 3917 1306 S/L tCg/tTg rs752643679&COSV106051765&COSV56851278&COSV56855512 -1 SNV HGNC HGNC:7567 YES NM_005963.4 5 P1 CCDS11155.1 ENSP00000226207 P12882.210 UPI000013C891 deleterious_low_confidence(0.01) benign(0.005) PANTHER:PTHR45615&Pfam:PF01576&Gene3D:1.20.5.340&Superfamily:SSF90257&Coiled-coils_(Ncoils):Coil&AlphaFold_DB_import:AF-P12882-F1 3.579e-05 0 0 0 0 0 6.154e-05 0 6.533e-05 1.972e-05 0 0 0 0 0 0 0 2.94e-05 0 0.0002071 0.0002071 gnomADg_SAS 0&1&1&1 0&1&1&1 9 NA NA PASS SITE 80,86|109,110 NA NA 1 93 20,20 151,161 60,60 36 2.04 NA 32.21 NA FALSE 4.61 93 NA NA NA FALSE NA NA 624.67 9 10499041 HCC1395_HCC1395T 0 0.993 219 0,42 0,87 0,137 NA 0/1 NA NA NA NA 0,0,109,110 G/A PANCANCER NA FALSE MYH1_p.S1306L chr17:10499041:10499042:G:A SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 11784435 11784436 G C 49 203 0.241379310344828 MODERATE DNAH9 ENSG00000007174 C missense_variant Transcript ENST00000262442 protein_coding 41/69 ENST00000262442.9:c.7957G>C ENSP00000262442.3:p.D2653H ENSP00000262442.3 p.D2653H 7986 7957 2653 D/H Gat/Cat COSV52375013&COSV52381788 1 SNV HGNC HGNC:2953 YES NM_001372.4 1 P1 CCDS11160.1 ENSP00000262442 Q9NYC9.176 UPI0000141BA2 Q9NYC9-1 1 tolerated_low_confidence(0.18) benign(0.005) Gene3D:3.40.50.300&Pfam:PF17857&Gene3D:1.20.920.30&Superfamily:SSF52540 1&1 1&1 9 NA NA PASS SITE 158,154|22,27 NA NA 1 93 20,20 162,151 60,60 24 2.03 NA 32.16 NA FALSE 6.00 93 NA NA NA FALSE NA NA 118.48 9 11784435 HCC1395_HCC1395T 154 0.235 203 46,9 57,18 110,33 NA 0/1 NA NA NA NA 77,77,22,27 G/C PANCANCER NA FALSE DNAH9_p.D2653H chr17:11784435:11784436:G:C SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 18119985 18119986 C T 393 393 1 MODIFIER MYO15A ENSG00000091536 T non_coding_transcript_exon_variant Transcript ENST00000583079 retained_intron 1/1 ENST00000583079.1:n.818C>T NA 818 COSV52752493&COSV52753787 1 SNV HGNC HGNC:7594 1 1&1 1&1 9 NA NA PASS SITE 191,155|236,157 NA NA 1 93 20,20 163,159 60,60 32 2.39 NA 72.08 NA FALSE 6.00 93 NA NA NA FALSE NA NA 1212.00 9 18119985 HCC1395_HCC1395T 0 0.996 393 0,116 0,146 0,275 NA 0/1 NA NA NA NA 0,0,236,157 C/T PANCANCER NA FALSE MYO15A chr17:18119985:18119986:C:T SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 18143814 18143815 G A 184 279 0.659498207885305 MODIFIER MYO15A ENSG00000091536 A downstream_gene_variant Transcript ENST00000412324 protein_coding_CDS_not_defined NA rs369719467 1677 1 SNV HGNC HGNC:7594 5 1 1.663e-05 0 3.708e-05 0 0 0 1.321e-05 0 4.044e-05 3.285e-05 2.413e-05 0 0 0 0 0 0.003165 4.411e-05 0 0 0.003165 gnomADg_MID likely_benign 1 25741868 9 NA NA PASS SITE 168,182|88,96 NA NA 1 93 20,20 164,171 60,60 32 2.24 NA 51.12 NA FALSE 4.61 93 NA NA NA FALSE NA NA 521.80 9 18143814 HCC1395_HCC1395T 95 0.668 279 29,55 29,68 65,132 NA 0/1 NA NA NA NA 42,53,88,96 G/A PANCANCER NA FALSE MYO15A chr17:18143814:18143815:G:A SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 18988513 18988514 C T 14 40 0.35 MODIFIER SLC5A10 ENSG00000154025 T intron_variant Transcript ENST00000317977 protein_coding 8/14 ENST00000317977.10:c.733+11524C>T NA 1 SNV HGNC HGNC:23155 1 CCDS74008.1 ENSP00000324346 A0PJK1.131 UPI000007437A A0PJK1-3 9 NA NA PASS SITE 22,44|3,11 NA NA 1 93 20,29 172,173 60,60 37 1.47 NA 8.43 NA FALSE 6.00 50 NA NA NA FALSE NA NA 34.67 9 18988513 HCC1395_HCC1395T 26 0.389 40 6,3 8,6 18,11 NA 0/1 NA NA NA NA 10,16,3,11 C/T PANCANCER NA FALSE SLC5A10 chr17:18988513:18988514:C:T SNV 3:0 chr17:161952:22299650:3:0:1 NA NA 0.96 +chr17 29120930 29120931 G C 16 16 1 MODIFIER MYO18A ENSG00000196535 C intron_variant Transcript ENST00000527372 protein_coding 6/41 ENST00000527372.7:c.1585+68C>G NA rs1457537621 -1 SNV HGNC HGNC:31104 YES NM_078471.4 1 P4 CCDS45642.1 ENSP00000437073 Q92614.214 UPI0000167F32 Q92614-1 9 NA NA PASS SITE 14,7|10,6 NA NA 1 51 20,20 161,152 60,60 29 1.18 NA 4.21 NA FALSE 6.00 93 NA NA NA FALSE NA NA 45.82 9 29120930 HCC1395_HCC1395T 0 0.917 16 0,6 0,4 0,10 NA 0/1 NA NA NA NA 0,0,10,6 G/C PANCANCER NA FALSE MYO18A chr17:29120930:29120931:G:C SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 29286060 29286061 C G 131 131 1 MODERATE NUFIP2 ENSG00000108256 G missense_variant Transcript ENST00000225388 protein_coding 2/4 ENST00000225388.9:c.1934G>C ENSP00000225388.3:p.R645T ENSP00000225388.3 p.R645T 2023 1934 645 R/T aGa/aCa COSV56603056 -1 SNV HGNC HGNC:17634 YES NM_020772.3 1 P1 CCDS32600.1 ENSP00000225388 Q7Z417.157 UPI00001B078D Q7Z417-1 deleterious(0.03) benign(0.412) AlphaFold_DB_import:AF-Q7Z417-F1&Pfam:PF15293&PANTHER:PTHR28333 1 1 9 NA NA PASS SITE 69,53|75,56 NA NA 1 93 20,20 158,160 60,60 36 1.89 NA 22.23 NA FALSE 6.00 93 NA NA NA FALSE NA NA 393.99 9 29286060 HCC1395_HCC1395T 0 0.989 131 0,31 0,50 0,86 NA 0/1 NA NA NA NA 0,0,75,56 C/G PANCANCER NA FALSE NUFIP2_p.R645T chr17:29286060:29286061:C:G SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 35132507 35132508 C G 54 54 1 MODIFIER FNDC8 ENSG00000073598 G downstream_gene_variant Transcript ENST00000158009 protein_coding NA 1775 1 SNV HGNC HGNC:25286 YES NM_017559.4 1 P1 CCDS11290.1 ENSP00000158009 Q8TC99.132 UPI000006D671 9 NA NA PASS SITE 28,47|20,34 NA NA 1 93 20,20 139,174 60,60 30 1.71 NA 14.75 NA FALSE 6.00 93 NA NA NA FALSE NA NA 165.92 9 35132507 HCC1395_HCC1395T 0 0.975 54 0,18 0,17 0,37 NA 0/1 NA NA NA NA 0,0,20,34 C/G PANCANCER NA FALSE FNDC8 chr17:35132507:35132508:C:G SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 35447309 35447310 G A 127 127 1 MODIFIER SLFN13 ENSG00000154760 A 5_prime_UTR_variant Transcript ENST00000285013 protein_coding 2/6 ENST00000285013.11:c.-55C>T NA 151 -1 SNV HGNC HGNC:26481 YES NM_144682.6 1 P1 CCDS32620.1 ENSP00000285013 Q68D06.131 UPI000004E65A Q68D06-1 9 NA NA PASS SITE 77,55|84,43 NA NA 1 93 20,20 170,163 60,60 32 1.95 NA 26.19 NA FALSE 6.00 93 NA NA NA FALSE NA NA 392.56 9 35447309 HCC1395_HCC1395T 0 0.989 127 0,30 0,55 0,87 NA 0/1 NA NA NA NA 0,0,84,43 G/A PANCANCER NA FALSE SLFN13 chr17:35447309:35447310:G:A SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 35522730 35522731 G C 75 171 0.43859649122807 MODIFIER SLFN12L ENSG00000205045 C 5_prime_UTR_variant Transcript ENST00000628453 protein_coding 2/5 ENST00000628453.4:c.-366C>G NA 346 -1 SNV HGNC HGNC:33920 YES NM_001363830.2 5 A2 CCDS86591.2 ENSP00000487397 A0A8I5QCZ1.3 UPI001B887394 9 NA NA PASS SITE 116,190|28,47 NA NA 1 93 20,20 173,178 60,60 30 2.18 NA 44.25 NA FALSE 6.00 93 NA NA NA FALSE NA NA 198.10 9 35522730 HCC1395_HCC1395T 96 0.446 171 26,17 34,27 65,52 NA 0/1 NA NA NA NA 41,55,28,47 G/C PANCANCER NA FALSE SLFN12L chr17:35522730:35522731:G:C SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 36071227 36071228 C G 197 197 1 MODIFIER CCL3-AS1 ENSG00000277089 G upstream_gene_variant Transcript ENST00000610845 lncRNA NA 1651 1 SNV HGNC HGNC:55229 5 9 NA NA PASS SITE 99,107|104,93 NA NA 1 93 20,38 183,185 60,60 24 2.18 NA 44.84 NA FALSE 6.00 93 NA NA NA FALSE NA NA 696.96 9 36071227 HCC1395_HCC1395T 0 0.994 197 0,48 0,94 0,159 NA 0/1 NA NA NA NA 0,0,104,93 C/G PANCANCER NA FALSE CCL3-AS1 chr17:36071227:36071228:C:G SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 37517436 37517437 ACGGTATCATCGGGAG A 35 35 1 MODIFIER SYNRG ENSG00000275066 - 3_prime_UTR_variant Transcript ENST00000612223 protein_coding 22/22 ENST00000612223.5:c.*1489_*1503del NA 5497-5511 -1 deletion HGNC HGNC:557 YES NM_007247.6 1 P4 CCDS11321.1 ENSP00000483453 Q9UMZ2.174 UPI000013C4EA Q9UMZ2-1 9 NA NA PASS SITE 31,23|18,17 NA NA 1 93 20,34 173,188 60,60 24 1.60 NA 11.40 NA FALSE 6.00 93 NA NA NA FALSE NA NA 153.58 9 37517436 HCC1395_HCC1395T 0 0.969 35 0,6 0,18 0,29 NA 0/1 NA NA NA NA 0,0,18,17 ACGGTATCATCGGGAG/A PANCANCER NA FALSE SYNRG chr17:37517436:37517437:ACGGTATCATCGGGAG:A indel 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 37612591 37612592 T A 18 141 0.127659574468085 MODIFIER MIR378J ENSG00000274620 A downstream_gene_variant Transcript ENST00000611988 miRNA NA 2340 -1 SNV HGNC HGNC:49979 YES 9 NA NA PASS SITE 164,71|13,5 NA NA 1 93 20,31 173,198 60,60 19 1.93 NA 24.98 NA FALSE 6.00 26 NA NA NA FALSE NA NA 41.72 9 37612591 HCC1395_HCC1395T 123 0.135 141 16,2 73,11 89,13 NA 0/1 NA NA NA NA 86,37,13,5 T/A PANCANCER NA FALSE MIR378J chr17:37612591:37612592:T:A SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 40294636 40294637 G A 16 16 1 MODIFIER CDC6 ENSG00000094804 A intron_variant Transcript ENST00000209728 protein_coding 7/11 ENST00000209728.9:c.1083+133G>A NA 1 SNV HGNC HGNC:1744 YES NM_001254.4 1 P1 CCDS11365.1 ENSP00000209728 Q99741.192 A0A024R1S2.67 UPI0000073C6C 1 9 NA NA PASS SITE 0,19|0,16 NA NA 1 66 40,38 238,244 60,60 25 1.31 NA 5.72 NA FALSE 6.00 93 NA NA NA FALSE NA NA 60.36 9 40294636 HCC1395_HCC1395T 0 0.945 16 0,6 0,9 0,16 NA 0/1 NA NA NA NA 0,0,0,16 G/A PANCANCER NA FALSE CDC6 chr17:40294636:40294637:G:A SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 41025937 41025938 T G 14 28 0.5 MODIFIER KRTAP1-5 ENSG00000221852 G downstream_gene_variant Transcript ENST00000361883 protein_coding NA 89 -1 SNV HGNC HGNC:16777 YES NM_031957.2 P1 CCDS42321.1 ENSP00000355302 Q9BYS1.138 UPI00000707CB 9 NA NA PASS SITE 32,10|11,3 NA NA 1 93 31,33 152,192 60,60 17 1.38 NA 6.62 NA FALSE 6.00 61 NA NA NA FALSE NA NA 39.61 9 41025937 HCC1395_HCC1395T 14 0.480 28 0,3 12,7 12,11 NA 0/1 NA NA NA NA 10,4,11,3 T/G PANCANCER NA FALSE KRTAP1-5 chr17:41025937:41025938:T:G SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 41516976 41516977 G A 166 166 1 LOW KRT15 ENSG00000171346 A splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000254043 protein_coding 2/7 ENST00000254043.8:c.582-12C>T NA -1 SNV HGNC HGNC:6421 YES NM_002275.4 1 P1 CCDS11398.1 ENSP00000254043 P19012.196 UPI000013CE0E P19012-1 9 NA NA PASS SITE 120,118|76,90 NA NA 1 93 20,20 157,157 60,60 33 2.18 NA 45.05 NA FALSE 6.00 93 NA NA NA FALSE NA NA 477.52 9 41516976 HCC1395_HCC1395T 0 0.991 166 0,56 0,44 0,108 NA 0/1 NA NA NA NA 0,0,76,90 G/A PANCANCER NA FALSE KRT15 chr17:41516976:41516977:G:A SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 41771694 41771695 GTGTACTGGCGCCCGCAGGCCTCATCCTCCTCCATGATGCCCT G 95 96 0.989583333333333 MODERATE JUP ENSG00000173801 - inframe_deletion Transcript ENST00000310706 protein_coding 2/15 ENST00000310706.9:c.119_160del ENSP00000311113.5:p.K40_Y53del ENSP00000311113.5 p.K40_Y53del 238-279 119-160 40-54 KGIMEEDEACGRQYT/T aAGGGCATCATGGAGGAGGATGAGGCCTGCGGGCGCCAGTACAcg/acg -1 deletion HGNC HGNC:6207 1 P1 CCDS11407.1 ENSP00000311113 P14923.221 A0A0S2Z487.38 UPI0000073ED4 1 AlphaFold_DB_import:AF-P14923-F1&PANTHER:PTHR45976&Low_complexity_(Seg):seg 9 NA NA PASS SITE 138,115|60,35 NA NA 1 93 20,31 148,199 60,60 40 2.15 NA 41.90 NA FALSE 6.00 93 NA NA NA FALSE NA NA 422.22 9 41771694 HCC1395_HCC1395T 1 0.974 96 0,26 0,37 1,70 NA 0/1 NA NA NA NA 0,1,60,35 GTGTACTGGCGCCCGCAGGCCTCATCCTCCTCCATGATGCCCT/G PANCANCER NA FALSE JUP_p.K40_Y53del chr17:41771694:41771695:GTGTACTGGCGCCCGCAGGCCTCATCCTCCTCCATGATGCCCT:G indel 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 42609399 42609400 T C 107 107 1 MODIFIER TUBG1 ENSG00000131462 C upstream_gene_variant Transcript ENST00000251413 protein_coding NA 284 1 SNV HGNC HGNC:12417 YES NM_001070.5 1 P1 CCDS11433.1 ENSP00000251413 P23258.220 UPI0000136A56 1 9 NA NA PASS SITE 71,126|36,71 NA NA 1 93 20,20 151,158 60,60 22 2.15 NA 40.93 NA FALSE 6.00 93 NA NA NA FALSE NA NA 353.00 9 42609399 HCC1395_HCC1395T 0 0.988 107 0,35 0,35 0,78 NA 0/1 NA NA NA NA 0,0,36,71 T/C PANCANCER NA FALSE TUBG1 chr17:42609399:42609400:T:C SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 44777930 44777931 C G 224 226 0.991150442477876 MODIFIER ADAM11 ENSG00000073670 G intron_variant Transcript ENST00000200557 protein_coding 23/26 ENST00000200557.11:c.2071-22C>G NA 1 SNV HGNC HGNC:189 YES NM_002390.6 1 P1 CCDS11486.1 ENSP00000200557 O75078.187 UPI000013C629 O75078-1 9 NA NA PASS SITE 147,134|120,104 NA NA 1 93 20,20 162,164 60,60 31 2.29 NA 57.19 NA FALSE 6.00 93 NA NA NA FALSE NA NA 707.33 9 44777930 HCC1395_HCC1395T 2 0.988 226 0,55 1,96 1,156 NA 0/1 NA NA NA NA 1,1,120,104 C/G PANCANCER NA FALSE ADAM11 chr17:44777930:44777931:C:G SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 44929040 44929041 G A 41 69 0.594202898550725 MODIFIER KIF18B ENSG00000186185 A downstream_gene_variant Transcript ENST00000585687 retained_intron NA 3282 -1 SNV HGNC HGNC:27102 3 9 NA NA PASS SITE 38,83|18,23 NA NA 1 93 20,20 153,155 60,60 25 1.83 NA 19.52 NA FALSE 6.00 84 NA NA NA FALSE NA NA 97.93 9 44929040 HCC1395_HCC1395T 28 0.565 69 3,8 12,15 19,25 NA 0/1 NA NA NA NA 9,19,18,23 G/A PANCANCER NA FALSE KIF18B chr17:44929040:44929041:G:A SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 45119014 45119015 TAGACGGTCGTTGTTG T 107 107 1 MODIFIER PLCD3 ENSG00000161714 - downstream_gene_variant Transcript ENST00000538093 protein_coding NA COSV59560012 1407 -1 cds_end_NF deletion HGNC HGNC:9061 4 ENSP00000440378 F5GXC1.77 UPI000204A8F1 1 1 9 NA NA PASS SITE 166,175|47,60 NA NA 1 93 20,20 149,174 60,60 37 2.32 NA 61.71 NA FALSE 6.00 93 NA NA NA FALSE NA NA 478.16 9 45119014 HCC1395_HCC1395T 0 0.986 107 0,23 0,39 0,70 NA 0/1 NA NA NA NA 0,0,47,60 TAGACGGTCGTTGTTG/T PANCANCER NA FALSE PLCD3 chr17:45119014:45119015:TAGACGGTCGTTGTTG:T indel 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 45222039 45222040 C T 15 15 1 MODIFIER FMNL1 ENSG00000184922 T 5_prime_UTR_variant Transcript ENST00000331495 protein_coding 1/27 ENST00000331495.8:c.-86C>T NA 155 rs989047572 1 SNV HGNC HGNC:1212 YES NM_005892.4 1 P3 CCDS11497.1 ENSP00000329219 O95466.190 UPI0000246EE9 O95466-1 1.338e-05 4.863e-05 0 0 0 0 0 0 0 0 0 4.863e-05 gnomADg_AFR 9 NA NA PASS SITE 15,20|3,12 NA NA 1 84 20,38 185,211 60,60 31 1.42 NA 7.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 59.68 9 45222039 HCC1395_HCC1395T 0 0.937 15 0,4 0,10 0,14 NA 0/1 NA NA NA NA 0,0,3,12 C/T PANCANCER NA FALSE FMNL1 chr17:45222039:45222040:C:T SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 45845905 45845906 C T 195 195 1 LOW SPPL2C ENSG00000185294 T synonymous_variant Transcript ENST00000329196 protein_coding 1/1 ENST00000329196.7:c.999C>T ENSP00000332488.5:p.T333= ENSP00000332488.5 p.T333= 1025 999 333 T acC/acT rs754600209&COSV61292740 1 SNV HGNC HGNC:28902 YES NM_175882.3 P1 CCDS32673.1 ENSP00000332488 Q8IUH8.125 UPI0000EE80B4 AlphaFold_DB_import:AF-Q8IUH8-F1&Pfam:PF04258&PANTHER:PTHR12174&SMART:SM00730&Transmembrane_helices:TMhelix 5.683e-05 0 0 0 5.438e-05 0 0 0 0.0004246 3.942e-05 4.825e-05 0 0 0 0.0001927 0 0 2.939e-05 0 0.0002069 0.0004246 gnomADe_SAS 0&1 0&1 9 NA NA PASS SITE 175,160|103,94 NA NA 1 93 20,20 152,159 60,60 33 1.22 NA 59.75 NA FALSE 4.31 93 NA NA NA FALSE NA NA 595.87 9 45845905 HCC1395_HCC1395T 0 0.992 195 0,53 0,68 0,129 NA 0/1 NA NA NA NA 0,0,102,93 C/T PANCANCER NA FALSE SPPL2C_p.T333= chr17:45845905:45845906:C:T SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 46751428 46751429 A G 3 8 0.375 MODIFIER NSF ENSG00000073969 G intron_variant Transcript ENST00000398238 protein_coding 18/20 ENST00000398238.8:c.2044-75A>G NA 1 SNV HGNC HGNC:8016 YES NM_006178.4 1 P3 CCDS42354.1 ENSP00000381293 P46459.213 A0A384MTI6.20 UPI000006D238 P46459-1 1 9 NA NA PASS SITE 15,0|3,0 NA NA 1 40 34,41 258,178 60,60 35 1.06 NA 3.01 NA FALSE 6.00 15 NA NA NA FALSE NA NA 7.30 9 46751428 HCC1395_HCC1395T 5 0.383 8 0,0 5,2 5,3 NA 0/1 NA NA NA NA 5,0,3,0 A/G PANCANCER NA FALSE NSF chr17:46751428:46751429:A:G SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 46938480 46938481 G C 56 56 1 MODIFIER GOSR2 ENSG00000108433 C intron_variant Transcript ENST00000225567 protein_coding 5/6 ENST00000225567.9:c.478-119G>C NA 1 SNV HGNC HGNC:4431 1 CCDS11507.1 ENSP00000225567 O14653.188 UPI000002AACF O14653-2 1 9 NA NA PASS SITE 37,22|42,14 NA NA 1 93 20,28 154,185 60,60 28 1.59 NA 11.44 NA FALSE 6.00 93 NA NA NA FALSE NA NA 187.14 9 46938480 HCC1395_HCC1395T 0 0.979 56 0,15 0,28 0,43 NA 0/1 NA NA NA NA 0,0,42,14 G/C PANCANCER NA FALSE GOSR2 chr17:46938480:46938481:G:C SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 53822975 53822976 G T 44 87 0.505747126436782 MODIFIER KIF2B ENSG00000141200 T 5_prime_UTR_variant Transcript ENST00000268919 protein_coding 1/1 ENST00000268919.6:c.-59G>T NA 49 1 SNV HGNC HGNC:29443 YES NM_032559.5 P1 CCDS32685.1 ENSP00000268919 Q8N4N8.165 A0A140VKG5.44 UPI000013D7E6 9 NA NA PASS SITE 94,86|20,24 NA NA 1 93 20,32 156,173 60,60 25 2.01 NA 29.75 NA FALSE 6.00 93 NA NA NA FALSE NA NA 124.73 9 53822975 HCC1395_HCC1395T 43 0.507 87 16,15 13,17 33,34 NA 0/1 NA NA NA NA 22,21,20,24 G/T PANCANCER NA FALSE KIF2B chr17:53822975:53822976:G:T SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 55720816 55720817 G A 213 215 0.990697674418605 LOW TMEM100 ENSG00000166292 A synonymous_variant Transcript ENST00000424486 protein_coding 2/2 ENST00000424486.3:c.255C>T ENSP00000395328.2:p.I85= ENSP00000395328.2 p.I85= 566 255 85 I atC/atT -1 SNV HGNC HGNC:25607 YES NM_018286.3 1 P1 CCDS11587.1 ENSP00000395328 Q9NV29.126 UPI000004A0C2 AlphaFold_DB_import:AF-Q9NV29-F1&Pfam:PF16311&PANTHER:PTHR16100&Transmembrane_helices:TMhelix 9 NA NA PASS SITE 109,123|102,111 NA NA 1 93 20,20 164,161 60,60 33 2.19 NA 45.45 NA FALSE 6.00 93 NA NA NA FALSE NA NA 623.15 9 55720816 HCC1395_HCC1395T 2 0.986 215 0,55 1,74 1,138 NA 0/1 NA NA NA NA 1,1,102,111 G/A PANCANCER NA FALSE TMEM100_p.I85= chr17:55720816:55720817:G:A SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 58249650 58249651 C T 101 103 0.980582524271845 LOW LPO ENSG00000167419 T synonymous_variant Transcript ENST00000262290 protein_coding 6/13 ENST00000262290.9:c.528C>T ENSP00000262290.4:p.F176= ENSP00000262290.4 p.F176= 686 528 176 F ttC/ttT COSV51858221&COSV51861894 1 SNV HGNC HGNC:6678 YES NM_006151.3 1 P1 CCDS32689.1 ENSP00000262290 P22079.200 UPI0000131631 P22079-1 Gene3D:1.10.640.10&AlphaFold_DB_import:AF-P22079-F1&Pfam:PF03098&PROSITE_profiles:PS50292&PANTHER:PTHR11475&Superfamily:SSF48113 1&1 1&1 9 NA NA PASS SITE 76,84|45,56 NA NA 1 93 20,20 159,162 60,60 26 2.06 NA 33.09 NA FALSE 6.00 93 NA NA NA FALSE NA NA 307.54 9 58249650 HCC1395_HCC1395T 2 0.973 103 0,24 1,38 1,70 NA 0/1 NA NA NA NA 1,1,45,56 C/T PANCANCER NA FALSE LPO_p.F176= chr17:58249650:58249651:C:T SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 63494542 63494543 G A 53 53 1 MODIFIER ACE ENSG00000159640 A intron_variant Transcript ENST00000290863 protein_coding 11/13 ENST00000290863.10:c.1658+72G>A NA rs910245918 1 SNV HGNC HGNC:2707 1 CCDS45755.1 ENSP00000290863 P12821.254 UPI000002DB19 P12821-3 1 1.971e-05 7.236e-05 0 0 0 0 0 0 0 0 0 7.236e-05 gnomADg_AFR 9 NA NA PASS SITE 11,23|19,34 NA NA 1 93 35,20 186,159 60,60 38 1.45 NA 8.13 NA FALSE 6.00 93 NA NA NA FALSE NA NA 142.15 9 63494542 HCC1395_HCC1395T 0 0.973 53 0,9 0,11 0,34 NA 0/1 NA NA NA NA 0,0,19,34 G/A PANCANCER NA FALSE ACE chr17:63494542:63494543:G:A SNV 2:0 chr17:27301794:67344504:2:0:1 TRUE NA 0.96 +chr17 68529082 68529083 A G 7 22 0.318181818181818 MODIFIER PRKAR1A ENSG00000108946 G intron_variant Transcript ENST00000358598 protein_coding 9/10 ENST00000358598.6:c.891+91A>G NA 1 SNV HGNC HGNC:9388 1 P1 CCDS11678.1 ENSP00000351410 P10644.243 B2R5T5.121 UPI0000001C57 P10644-1 1 9 NA NA PASS SITE 0,28|0,7 NA NA 1 54 38,40 221,185 60,60 26 1.16 NA 3.91 NA FALSE 6.00 15 NA NA NA FALSE NA NA 24.64 9 68529082 HCC1395_HCC1395T 15 0.333 22 5,1 9,5 15,7 NA 0/1 NA NA NA NA 0,15,0,7 A/G PANCANCER NA FALSE PRKAR1A chr17:68529082:68529083:A:G SNV 5:0 chr17:67578321:73169179:5:0:1 NA NA 0.96 +chr17 73206481 73206482 T C 6 19 0.315789473684211 MODIFIER COG1 ENSG00000166685 C intron_variant Transcript ENST00000299886 protein_coding 11/13 ENST00000299886.9:c.2619+219T>C NA 1 SNV HGNC HGNC:6545 YES NM_018714.3 1 P1 CCDS11692.1 ENSP00000299886 Q8WTW3.169 UPI0000127E34 1 9 NA NA PASS SITE 1,21|0,6 NA NA 1 39 37,40 223,199 60,60 18 0.997 NA 2.66 NA FALSE 6.00 42 NA NA NA FALSE NA NA 20.38 9 73206481 HCC1395_HCC1395T 13 0.350 19 4,3 8,2 12,6 NA 0/1 NA NA NA NA 1,12,0,6 T/C PANCANCER NA FALSE COG1 chr17:73206481:73206482:T:C SNV 4:0 chr17:73170562:80208843:4:0:1 NA NA 0.96 +chr17 73336206 73336207 G A 12 21 0.571428571428571 MODIFIER SDK2 ENSG00000069188 A 3_prime_UTR_variant Transcript ENST00000392650 protein_coding 45/45 ENST00000392650.8:c.*2381C>T NA 9257 -1 SNV HGNC HGNC:19308 YES NM_001144952.2 5 P1 CCDS45769.1 ENSP00000376421 Q58EX2.159 UPI0000E5A088 Q58EX2-1 9 NA NA PASS SITE 11,10|9,3 NA NA 1 64 37,35 180,171 60,60 15 1.11 NA 3.61 NA FALSE 6.00 41 NA NA NA FALSE NA NA 36.19 9 73336206 HCC1395_HCC1395T 9 0.579 21 1,2 3,8 7,10 NA 0/1 NA NA NA NA 4,5,9,3 G/A PANCANCER NA FALSE SDK2 chr17:73336206:73336207:G:A SNV 4:0 chr17:73170562:80208843:4:0:1 NA NA 0.96 +chr17 74299542 74299543 C G 9 15 0.6 MODIFIER DNAI2 ENSG00000171595 G intron_variant Transcript ENST00000311014 protein_coding 6/13 ENST00000311014.11:c.725-176C>G NA rs1598312613 1 SNV HGNC HGNC:18744 YES NM_023036.6 1 P2 CCDS11697.1 ENSP00000308312 Q9GZS0.177 UPI000013EC1D Q9GZS0-1 1 9 NA NA PASS SITE 14,2|7,2 NA NA 1 41 38,34 199,189 60,60 29 0.954 NA 2.41 NA FALSE 6.00 19 NA NA NA FALSE NA NA 26.64 9 74299542 HCC1395_HCC1395T 6 0.534 15 3,0 3,7 6,7 NA 0/1 NA NA NA NA 6,0,7,2 C/G PANCANCER NA FALSE DNAI2 chr17:74299542:74299543:C:G SNV 4:0 chr17:73170562:80208843:4:0:1 NA NA 0.96 +chr17 74748666 74748667 C G 220 426 0.516431924882629 MODIFIER NHERF1 ENSG00000109062 G 5_prime_UTR_variant Transcript ENST00000262613 protein_coding 1/6 ENST00000262613.10:c.-181C>G NA 39 rs112977728 1 SNV HGNC HGNC:11075 YES NM_004252.5 1 P1 CCDS11705.1 ENSP00000262613 O14745.222 UPI0000072521 O14745-1 1 6.57e-06 0 0 0 0 0 0 0 1.47e-05 0 0 1.47e-05 gnomADg_NFE 23032637 9 NA NA PASS SITE 318,227|137,83 NA NA 1 93 20,20 154,162 60,60 31 2.34 NA 64.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 585.63 9 74748666 HCC1395_HCC1395T 206 0.518 426 61,63 70,78 135,145 NA 0/1 NA NA NA NA 121,85,137,83 C/G PANCANCER NA FALSE NHERF1 chr17:74748666:74748667:C:G SNV 4:0 chr17:73170562:80208843:4:0:1 NA NA 0.96 +chr17 74771706 74771707 G A 70 129 0.542635658914729 MODIFIER NHERF1 ENSG00000109062 A downstream_gene_variant Transcript ENST00000262613 protein_coding NA rs779259903 2353 1 SNV HGNC HGNC:11075 YES NM_004252.5 1 P1 CCDS11705.1 ENSP00000262613 O14745.222 UPI0000072521 O14745-1 1 4.042e-06 0 0 0 0 0 8.987e-06 0 0 8.987e-06 gnomADe_NFE 9 NA NA PASS SITE 85,63|40,30 NA NA 1 93 20,20 166,178 60,60 32 1.84 NA 19.87 NA FALSE 6.00 93 NA NA NA FALSE NA NA 188.81 9 74771706 HCC1395_HCC1395T 59 0.543 129 15,20 24,29 41,49 NA 0/1 NA NA NA NA 34,25,40,30 G/A PANCANCER NA FALSE NHERF1 chr17:74771706:74771707:G:A SNV 4:0 chr17:73170562:80208843:4:0:1 NA NA 0.96 +chr17 74795641 74795642 C T 41 158 0.259493670886076 MODIFIER TMEM104 ENSG00000109066 T intron_variant Transcript ENST00000335464 protein_coding 8/9 ENST00000335464.10:c.636+9C>T NA 1 SNV HGNC HGNC:25984 YES NM_017728.4 1 P1 CCDS32723.1 ENSP00000334849 Q8NE00.137 A0A024R8L3.56 UPI00002001C9 Q8NE00-1 9 NA NA PASS SITE 113,93|20,21 NA NA 1 93 20,20 171,174 60,60 30 1.80 NA 18.36 NA FALSE 6.00 93 NA NA NA FALSE NA NA 96.35 9 74795641 HCC1395_HCC1395T 117 0.262 158 31,13 44,11 78,27 NA 0/1 NA NA NA NA 63,54,20,21 C/T PANCANCER NA FALSE TMEM104 chr17:74795641:74795642:C:T SNV 4:0 chr17:73170562:80208843:4:0:1 NA NA 0.96 +chr17 74844321 74844322 C T 165 297 0.555555555555556 LOW GRIN2C ENSG00000161509 T synonymous_variant Transcript ENST00000293190 protein_coding 12/13 ENST00000293190.10:c.2538G>A ENSP00000293190.5:p.S846= ENSP00000293190.5 p.S846= 2695 2538 846 S tcG/tcA COSV53111533 -1 SNV HGNC HGNC:4587 YES NM_000835.6 1 P1 CCDS32724.1 ENSP00000293190 Q14957.197 A0A8D9PH81.5 UPI00001AEBA4 PDB-ENSP_mappings:8e92.B&PDB-ENSP_mappings:8e92.D&PDB-ENSP_mappings:8e93.B&PDB-ENSP_mappings:8e93.D&PDB-ENSP_mappings:8e94.B&PDB-ENSP_mappings:8e94.D&PDB-ENSP_mappings:8e97.B&PDB-ENSP_mappings:8e97.D&PDB-ENSP_mappings:8e98.B&PDB-ENSP_mappings:8e98.D&PDB-ENSP_mappings:8e99.D&AlphaFold_DB_import:AF-Q14957-F1&Pfam:PF10565&PANTHER:PTHR18966 1 1 9 NA NA PASS SITE 194,147|96,69 NA NA 1 93 20,20 166,155 60,60 27 2.15 NA 41.54 NA FALSE 6.00 93 NA NA NA FALSE NA NA 432.20 9 74844321 HCC1395_HCC1395T 132 0.542 297 38,52 49,53 91,108 NA 0/1 NA NA NA NA 77,55,96,69 C/T PANCANCER NA FALSE GRIN2C_p.S846= chr17:74844321:74844322:C:T SNV 4:0 chr17:73170562:80208843:4:0:1 NA NA 0.96 +chr17 74951140 74951141 T A 16 99 0.161616161616162 MODIFIER OTOP3 ENSG00000182938 A downstream_gene_variant Transcript ENST00000328801 protein_coding NA 1148 1 SNV HGNC HGNC:19658 YES NM_001272005.2 2 P1 CCDS86637.1 ENSP00000328090 A0A2U3TZI1.22 UPI0002ADBBCE 9 NA NA PASS SITE 76,64|10,6 NA NA 1 93 20,37 180,170 60,60 32 1.61 NA 12.04 NA FALSE 6.00 65 NA NA NA FALSE NA NA 41.43 9 74951140 HCC1395_HCC1395T 83 0.180 99 23,7 35,5 63,13 NA 0/1 NA NA NA NA 44,39,10,6 T/A PANCANCER NA FALSE OTOP3 chr17:74951140:74951141:T:A SNV 4:0 chr17:73170562:80208843:4:0:1 NA NA 0.96 +chr17 75501507 75501508 C G 10 415 0.0240963855421687 MODIFIER TMEM94 ENSG00000177728 G downstream_gene_variant Transcript ENST00000314256 protein_coding NA 1055 1 SNV HGNC HGNC:28983 YES NM_014738.6 1 P3 CCDS32732.1 ENSP00000313885 Q12767.153 A0A024R8S6.57 UPI0000139439 Q12767-1 1 9 NA NA PASS SITE 373,328|6,4 NA NA 1 93 20,20 159,157 60,60 19 2.28 NA 55.39 NA FALSE 6.00 18 NA NA NA FALSE NA NA 16.76 9 75501507 HCC1395_HCC1395T 405 0.028 415 137,1 118,6 274,7 NA 0/1 NA NA NA NA 212,193,6,4 C/G PANCANCER NA FALSE TMEM94 chr17:75501507:75501508:C:G SNV 4:0 chr17:73170562:80208843:4:0:1 NA NA 0.96 +chr17 75614937 75614938 G C 118 225 0.524444444444444 MODIFIER MYO15B ENSG00000266714 C upstream_gene_variant Transcript ENST00000577342 nonsense_mediated_decay NA 1753 1 cds_start_NF SNV HGNC HGNC:14083 5 ENSP00000488316 A0A0J9YXA6.25 UPI00064546B6 9 NA NA PASS SITE 145,136|61,57 NA NA 1 93 20,34 162,163 60,60 31 2.08 NA 35.22 NA FALSE 6.00 93 NA NA NA FALSE NA NA 360.36 9 75614937 HCC1395_HCC1395T 107 0.548 225 32,32 36,52 75,91 NA 0/1 NA NA NA NA 58,49,61,57 G/C PANCANCER NA FALSE MYO15B chr17:75614937:75614938:G:C SNV 4:0 chr17:73170562:80208843:4:0:1 NA NA 0.96 +chr17 76565610 76565611 C G 278 585 0.475213675213675 MODIFIER ST6GALNAC2 ENSG00000070731 G 3_prime_UTR_variant Transcript ENST00000225276 protein_coding 9/9 ENST00000225276.10:c.*494G>C NA 1671 rs943912117 -1 SNV HGNC HGNC:10867 YES NM_006456.3 1 P1 CCDS11747.1 ENSP00000225276 Q9UJ37.169 A0A024R8M1.61 UPI000000D98B 6.593e-06 2.423e-05 0 0 0 0 0 0 0 0 0 2.423e-05 gnomADg_AFR 9 NA NA PASS SITE 226,357|98,180 NA NA 2 93 20,20 171,176 60,60 38 2.30 NA 59.58 NA FALSE 6.00 93 NA NA NA FALSE NA NA 706.63 9 76565610 HCC1395_HCC1395T 307 0.487 585 45,36 48,56 215,204 NA 0/1 NA NA NA NA 118,189,98,180 C/G PANCANCER NA FALSE ST6GALNAC2 chr17:76565610:76565611:C:G SNV 4:0 chr17:73170562:80208843:4:0:1 NA NA 0.96 +chr17 78414747 78414748 C T 29 59 0.491525423728814 MODIFIER PGS1 ENSG00000087157 T intron_variant Transcript ENST00000262764 protein_coding 7/9 ENST00000262764.11:c.1403-132C>T NA rs1036425720 1 SNV HGNC HGNC:30029 YES NM_024419.5 1 P1 CCDS42391.1 ENSP00000262764 Q32NB8.128 A0A024R8V5.45 UPI00000435E5 Q32NB8-1 1.972e-05 7.243e-05 0 0 0 0 0 0 0 0 0 7.243e-05 gnomADg_AFR 9 NA NA PASS SITE 44,14|22,7 NA NA 1 93 34,38 175,208 60,60 28 1.40 NA 6.92 NA FALSE 4.31 93 NA NA NA FALSE NA NA 89.77 9 78414747 HCC1395_HCC1395T 30 0.521 59 5,10 17,14 22,24 NA 0/1 NA NA NA NA 21,9,22,7 C/T PANCANCER NA FALSE PGS1 chr17:78414747:78414748:C:T SNV 4:0 chr17:73170562:80208843:4:0:1 NA NA 0.96 +chr17 78484883 78484884 A T 58 235 0.246808510638298 MODERATE DNAH17 ENSG00000187775 T missense_variant Transcript ENST00000389840 protein_coding 48/81 ENST00000389840.7:c.7634T>A ENSP00000374490.6:p.M2545K ENSP00000374490.6 p.M2545K 7761 7634 2545 M/K aTg/aAg -1 SNV HGNC HGNC:2946 YES NM_173628.4 5 P1 CCDS11757.2 ENSP00000374490 Q9UFH2.142 UPI0001B25601 Q9UFH2-1 1 deleterious_low_confidence(0) benign(0.377) PANTHER:PTHR45703&Pfam:PF12775&Gene3D:3.40.50.300&Superfamily:SSF52540 9 NA NA PASS SITE 188,124|36,22 NA NA 1 93 20,20 152,165 60,60 33 1.96 NA 26.74 NA FALSE 6.00 93 NA NA NA FALSE NA NA 131.86 9 78484883 HCC1395_HCC1395T 177 0.247 235 53,14 55,22 115,37 NA 0/1 NA NA NA NA 102,75,36,22 A/T PANCANCER NA FALSE DNAH17_p.M2545K chr17:78484883:78484884:A:T SNV 4:0 chr17:73170562:80208843:4:0:1 NA NA 0.96 +chr17 81117849 81117850 A G 45 214 0.210280373831776 MODIFIER BAIAP2 ENSG00000175866 G downstream_gene_variant Transcript ENST00000321300 protein_coding NA 417 1 SNV HGNC HGNC:947 1 CCDS11775.1 ENSP00000316338 Q9UQB8.197 UPI000000D762 Q9UQB8-1 9 NA NA PASS SITE 165,149|21,24 NA NA 1 93 20,20 162,168 60,60 29 1.98 NA 28.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 111.52 9 81117849 HCC1395_HCC1395T 169 0.222 214 48,13 59,17 111,31 NA 0/1 NA NA NA NA 87,82,21,24 A/G PANCANCER NA FALSE BAIAP2 chr17:81117849:81117850:A:G SNV 5:0 chr17:80208956:82485433:5:0:1 NA NA 0.96 +chr17 81902393 81902394 G T 25 72 0.347222222222222 MODIFIER PCYT2 ENSG00000185813 T downstream_gene_variant Transcript ENST00000331285 protein_coding NA 1933 -1 SNV HGNC HGNC:8756 2 CCDS58610.1 ENSP00000331719 Q99447.190 UPI0001915266 Q99447-2 1 9 NA NA PASS SITE 60,36|15,10 NA NA 1 93 20,20 159,153 60,60 37 1.55 NA 10.23 NA FALSE 6.00 58 NA NA NA FALSE NA NA 56.05 9 81902393 HCC1395_HCC1395T 47 0.341 72 19,10 11,6 32,16 NA 0/1 NA NA NA NA 27,20,15,10 G/T PANCANCER NA FALSE PCYT2 chr17:81902393:81902394:G:T SNV 5:0 chr17:80208956:82485433:5:0:1 NA NA 0.96 +chr17 82239123 82239124 G C 160 364 0.43956043956044 MODIFIER CSNK1D ENSG00000141551 C downstream_gene_variant Transcript ENST00000314028 protein_coding NA 3544 -1 SNV HGNC HGNC:2452 YES NM_001893.6 1 A1 CCDS11805.1 ENSP00000324464 P48730.219 UPI000012DC64 P48730-1 1 9 NA NA PASS SITE 192,194|82,78 NA NA 1 93 20,20 155,160 60,60 33 2.08 NA 35.21 NA FALSE 6.00 93 NA NA NA FALSE NA NA 411.44 9 82239123 HCC1395_HCC1395T 204 0.438 364 52,47 72,51 134,104 NA 0/1 NA NA NA NA 106,98,82,78 G/C PANCANCER NA FALSE CSNK1D chr17:82239123:82239124:G:C SNV 5:0 chr17:80208956:82485433:5:0:1 NA NA 0.96 +chr17 82316017 82316018 C T 81 432 0.1875 MODIFIER CD7 ENSG00000173762 T intron_variant Transcript ENST00000312648 protein_coding 3/3 ENST00000312648.8:c.612+178G>A NA -1 SNV HGNC HGNC:1695 YES NM_006137.7 1 P2 CCDS11807.1 ENSP00000312027 P09564.196 Q29VG3.131 UPI00000359A4 9 NA NA PASS SITE 266,327|36,45 NA NA 1 93 20,20 158,175 60,60 28 2.22 NA 48.02 NA FALSE 6.00 93 NA NA NA FALSE NA NA 171.90 9 82316017 HCC1395_HCC1395T 351 0.185 432 95,23 123,24 235,53 NA 0/1 NA NA NA NA 159,192,36,45 C/T PANCANCER NA FALSE CD7 chr17:82316017:82316018:C:T SNV 5:0 chr17:80208956:82485433:5:0:1 NA NA 0.96 +chr18 5133230 5133231 G A 27 42 0.642857142857143 MODIFIER BOD1P2 ENSG00000215368 A upstream_gene_variant Transcript ENST00000578494 processed_pseudogene NA 1 -1 SNV HGNC HGNC:51436 YES 10 NA NA PASS SITE 19,38|8,19 NA NA 1 92 20,34 169,171 60,60 27 1.50 NA 9.03 NA FALSE 6.00 84 NA NA NA FALSE NA NA 76.92 10 5133230 HCC1395_HCC1395T 15 0.646 42 5,7 5,12 11,21 NA 0/1 NA NA NA NA 4,11,8,19 G/A PANCANCER NA FALSE BOD1P2 chr18:5133230:5133231:G:A SNV 2:0 chr18:196829:12985601:2:0:1 TRUE NA 0.96 +chr18 6824791 6824792 A C 92 216 0.425925925925926 MODIFIER ARHGAP28 ENSG00000088756 C 5_prime_UTR_variant Transcript ENST00000262227 protein_coding 2/17 ENST00000262227.7:c.-5A>C NA 3207 1 SNV HGNC HGNC:25509 1 A2 CCDS92430.1 ENSP00000262227 Q9P2N2.152 UPI0000201994 Q9P2N2-2 10 NA NA PASS SITE 180,120|54,38 NA NA 1 93 20,20 164,151 60,60 39 2.07 NA 35.17 NA FALSE 6.00 93 NA NA NA FALSE NA NA 217.38 10 6824791 HCC1395_HCC1395T 124 0.411 216 29,20 51,35 81,56 NA 0/1 NA NA NA NA 74,50,54,38 A/C PANCANCER NA FALSE ARHGAP28 chr18:6824791:6824792:A:C SNV 2:0 chr18:196829:12985601:2:0:1 TRUE NA 0.96 +chr18 8777675 8777676 C G 8 8 1 MODIFIER MTCL1 ENSG00000168502 G intron_variant Transcript ENST00000306329 protein_coding 3/14 ENST00000306329.16:c.1438-158C>G NA 1 SNV HGNC HGNC:29121 5 A2 CCDS92432.1 ENSP00000305027 Q9Y4B5.152 UPI0001AE65C5 Q9Y4B5-1 10 NA NA PASS SITE 13,0|8,0 NA NA 1 62 39,40 239,196 60,60 31 1.16 NA 3.91 NA FALSE 6.00 67 NA NA NA FALSE NA NA 31.19 10 8777675 HCC1395_HCC1395T 0 0.903 8 0,1 0,6 0,8 NA 0/1 NA NA NA NA 0,0,8,0 C/G PANCANCER NA FALSE MTCL1 chr18:8777675:8777676:C:G SNV 2:0 chr18:196829:12985601:2:0:1 TRUE NA 0.96 +chr18 8828752 8828753 G A 47 47 1 MODIFIER MTCL1 ENSG00000168502 A intron_variant Transcript ENST00000306329 protein_coding 13/14 ENST00000306329.16:c.5680-156G>A NA 1 SNV HGNC HGNC:29121 5 A2 CCDS92432.1 ENSP00000305027 Q9Y4B5.152 UPI0001AE65C5 Q9Y4B5-1 10 NA NA PASS SITE 34,10|37,10 NA NA 1 93 39,34 191,186 60,60 25 1.57 NA 10.54 NA FALSE 6.00 93 NA NA NA FALSE NA NA 154.52 10 8828752 HCC1395_HCC1395T 0 0.976 47 0,16 0,22 0,38 NA 0/1 NA NA NA NA 0,0,37,10 G/A PANCANCER NA FALSE MTCL1 chr18:8828752:8828753:G:A SNV 2:0 chr18:196829:12985601:2:0:1 TRUE NA 0.96 +chr18 8832586 8832587 G A 110 110 1 MODIFIER MTCL1 ENSG00000168502 A 3_prime_UTR_variant Transcript ENST00000306329 protein_coding 15/15 ENST00000306329.16:c.*998G>A NA 6821 rs1334701423 1 SNV HGNC HGNC:29121 5 A2 CCDS92432.1 ENSP00000305027 Q9Y4B5.152 UPI0001AE65C5 Q9Y4B5-1 1.972e-05 2.414e-05 0 0.0001309 0 0 0 0 0 0 0 0.0001309 gnomADg_AMR 10 NA NA PASS SITE 93,64|72,38 NA NA 1 93 20,34 164,188 60,60 32 2.03 NA 32.20 NA FALSE 6.00 93 NA NA NA FALSE NA NA 366.18 10 8832586 HCC1395_HCC1395T 0 0.989 110 0,33 0,49 0,85 NA 0/1 NA NA NA NA 0,0,72,38 G/A PANCANCER NA FALSE MTCL1 chr18:8832586:8832587:G:A SNV 2:0 chr18:196829:12985601:2:0:1 TRUE NA 0.96 +chr18 10670330 10670331 C G 83 172 0.482558139534884 MODIFIER PIEZO2 ENSG00000154864 G 3_prime_UTR_variant Transcript ENST00000302079 protein_coding 51/51 ENST00000302079.10:c.*1197G>C NA 9267 -1 SNV HGNC HGNC:26270 5 ENSP00000303316 Q9H5I5.147 UPI0001EC9662 Q9H5I5-2 1 10 NA NA PASS SITE 102,166|28,55 NA NA 1 93 20,20 151,164 60,60 24 2.05 NA 33.32 NA FALSE 6.00 93 NA NA NA FALSE NA NA 220.88 10 10670330 HCC1395_HCC1395T 89 0.492 172 23,14 28,35 58,56 NA 0/1 NA NA NA NA 32,57,28,55 C/G PANCANCER NA FALSE PIEZO2 chr18:10670330:10670331:C:G SNV 2:0 chr18:196829:12985601:2:0:1 TRUE NA 0.96 +chr18 14106119 14106120 G C 10 25 0.4 MODIFIER ZNF519 ENSG00000175322 C intron_variant&NMD_transcript_variant Transcript ENST00000587419 nonsense_mediated_decay 2/4 ENST00000587419.5:c.130+18231C>G NA -1 SNV HGNC HGNC:30574 2 ENSP00000468250 K7ERG6.56 UPI0000201A45 10 NA NA PASS SITE 31,10|7,3 NA NA 1 63 33,37 175,132 60,60 25 1.35 NA 6.32 NA FALSE 6.00 27 NA NA NA FALSE NA NA 30.21 10 14106119 HCC1395_HCC1395T 15 0.399 25 2,0 9,7 11,7 NA 0/1 NA NA NA NA 11,4,7,3 G/C PANCANCER NA FALSE ZNF519 chr18:14106119:14106120:G:C SNV 3:0 chr18:12986001:14187347:3:0:1 NA NA 0.96 +chr18 23586526 23586527 C T 91 187 0.486631016042781 MODIFIER NPC1 ENSG00000141458 T upstream_gene_variant Transcript ENST00000269228 protein_coding NA 20 -1 SNV HGNC HGNC:7897 YES NM_000271.5 1 P1 CCDS11878.1 ENSP00000269228 O15118.208 UPI000013D80F O15118-1 1 10 NA NA PASS SITE 118,118|42,51 NA NA 1 93 20,20 170,168 60,60 26 -8.242e-01 NA 27.26 NA FALSE 6.00 93 NA NA NA FALSE NA NA 246.36 10 23586526 HCC1395_HCC1395T 96 0.496 187 27,26 36,38 69,68 NA 0/1 NA NA NA NA 46,50,41,50 C/T PANCANCER NA FALSE NPC1 chr18:23586526:23586527:C:T SNV 2:2 chr18:21403805:53535029:2:2:1 FALSE NA 0.96 +chr18 23907904 23907905 C T 63 140 0.45 LOW LAMA3 ENSG00000053747 T synonymous_variant Transcript ENST00000269217 protein_coding 17/38 ENST00000269217.11:c.2157C>T ENSP00000269217.5:p.F719= ENSP00000269217.5 p.F719= 2182 2157 719 F ttC/ttT 1 SNV HGNC HGNC:6483 NM_000227.6 1 CCDS11880.1 ENSP00000269217 Q16787.210 A0A0A6YYF2.59 UPI00000349C1 Q16787-1 1 Coiled-coils_(Ncoils):Coil&Pfam:PF06009 10 NA NA PASS SITE 54,92|21,42 NA NA 1 93 20,20 162,175 60,60 30 1.67 NA 13.55 NA FALSE 6.00 93 NA NA NA FALSE NA NA 168.72 10 23907904 HCC1395_HCC1395T 77 0.461 140 20,25 31,20 55,47 NA 0/1 NA NA NA NA 27,50,21,42 C/T PANCANCER NA FALSE LAMA3_p.F719= chr18:23907904:23907905:C:T SNV 2:2 chr18:21403805:53535029:2:2:1 FALSE NA 0.96 +chr18 26057772 26057773 G C 112 234 0.478632478632479 MODIFIER SS18 ENSG00000141380 C intron_variant Transcript ENST00000269137 protein_coding 3/9 ENST00000269137.11:c.232-30C>G NA -1 SNV HGNC HGNC:11340 1 P4 CCDS54183.1 ENSP00000269137 Q15532.176 Q4VAX0.134 UPI000002B43F Q15532-2 1 10 NA NA PASS SITE 90,146|39,73 NA NA 1 93 20,20 167,170 60,60 39 1.88 NA 21.97 NA FALSE 6.00 93 NA NA NA FALSE NA NA 299.08 10 26057772 HCC1395_HCC1395T 122 0.475 234 28,17 48,49 83,75 NA 0/1 NA NA NA NA 47,75,39,73 G/C PANCANCER NA FALSE SS18 chr18:26057772:26057773:G:C SNV 2:2 chr18:21403805:53535029:2:2:1 FALSE NA 0.96 +chr18 31874325 31874326 G C 157 339 0.463126843657817 MODIFIER TRAPPC8 ENSG00000153339 C intron_variant Transcript ENST00000283351 protein_coding 13/28 ENST00000283351.10:c.1953+155C>G NA -1 SNV HGNC HGNC:29169 YES NM_014939.5 1 P1 CCDS11901.1 ENSP00000283351 Q9Y2L5.171 UPI0000052E22 Q9Y2L5-1 10 NA NA PASS SITE 137,203|60,97 NA NA 1 93 20,20 163,166 60,60 40 2.03 NA 31.30 NA FALSE 6.00 93 NA NA NA FALSE NA NA 406.07 10 31874325 HCC1395_HCC1395T 182 0.466 339 43,36 65,61 118,103 NA 0/1 NA NA NA NA 75,107,60,97 G/C PANCANCER NA FALSE TRAPPC8 chr18:31874325:31874326:G:C SNV 2:2 chr18:21403805:53535029:2:2:1 FALSE NA 0.96 +chr18 36067342 36067343 C G 287 593 0.48397976391231 MODERATE RPRD1A ENSG00000141425 G missense_variant Transcript ENST00000357384 protein_coding 1/8 ENST00000357384.8:c.63G>C ENSP00000349955.4:p.Q21H ENSP00000349955.4 p.Q21H 215 63 21 Q/H caG/caC COSV59823686 -1 SNV HGNC HGNC:25560 5 P1 CCDS11917.1 ENSP00000349955 Q96P16.144 A0A024RC37.57 UPI0000036029 Q96P16-1 deleterious(0.02) probably_damaging(0.981) Gene3D:1.25.40.90&PDB-ENSP_mappings:4jxt.A&PDB-ENSP_mappings:4nac.A&PDB-ENSP_mappings:4nac.B&AlphaFold_DB_import:AF-Q96P16-F1&Pfam:PF04818&PROSITE_profiles:PS51391&PANTHER:PTHR12460&SMART:SM00582&Superfamily:SSF48464&CDD:cd17011 1 1 10 NA NA PASS SITE 376,320|153,134 NA NA 1 93 20,20 168,161 60,60 29 2.44 NA 80.32 NA FALSE 6.00 93 NA NA NA FALSE NA NA 782.26 10 36067342 HCC1395_HCC1395T 306 0.500 593 88,88 103,97 197,197 NA 0/1 NA NA NA NA 165,141,153,134 C/G PANCANCER NA FALSE RPRD1A_p.Q21H chr18:36067342:36067343:C:G SNV 2:2 chr18:21403805:53535029:2:2:1 FALSE NA 0.96 +chr18 45065001 45065002 A T 44 301 0.146179401993355 MODIFIER SETBP1 ENSG00000152217 T 3_prime_UTR_variant Transcript ENST00000649279 protein_coding 6/6 ENST00000649279.2:c.*1303A>T NA 6400 1 SNV HGNC HGNC:15573 YES NM_015559.3 P2 CCDS11923.2 ENSP00000497406 Q9Y6X0.172 UPI0000201C54 Q9Y6X0-1 1 10 NA NA PASS SITE 202,208|22,22 NA NA 1 93 20,20 164,177 60,60 26 1.99 NA 28.85 NA FALSE 6.00 63 NA NA NA FALSE NA NA 97.10 10 45065001 HCC1395_HCC1395T 257 0.156 301 54,7 99,19 162,29 NA 0/1 NA NA NA NA 124,133,22,22 A/T PANCANCER NA FALSE SETBP1 chr18:45065001:45065002:A:T SNV 2:2 chr18:21403805:53535029:2:2:1 FALSE NA 0.96 +chr18 46721543 46721544 C G 63 115 0.547826086956522 MODIFIER ST8SIA5 ENSG00000101638 G intron_variant Transcript ENST00000315087 protein_coding 1/6 ENST00000315087.12:c.132-16879G>C NA -1 SNV HGNC HGNC:17827 YES NM_013305.6 1 P4 CCDS11930.1 ENSP00000321343 O15466.169 UPI000013C72F O15466-1 10 NA NA PASS SITE 52,74|28,35 NA NA 1 93 20,20 161,166 60,60 41 1.69 NA 14.45 NA FALSE 6.00 93 NA NA NA FALSE NA NA 163.28 10 46721543 HCC1395_HCC1395T 52 0.539 115 9,16 23,20 34,40 NA 0/1 NA NA NA NA 22,30,28,35 C/G PANCANCER NA FALSE ST8SIA5 chr18:46721543:46721544:C:G SNV 2:2 chr18:21403805:53535029:2:2:1 FALSE NA 0.96 +chr18 49586912 49586913 G A 21 43 0.488372093023256 MODIFIER LIPG ENSG00000101670 A intron_variant Transcript ENST00000261292 protein_coding 9/9 ENST00000261292.9:c.1481+62G>A NA 1 SNV HGNC HGNC:6623 YES NM_006033.4 1 P1 CCDS11938.1 ENSP00000261292 Q9Y5X9.191 A0A024R2B5.58 UPI000012E706 Q9Y5X9-1 10 NA NA PASS SITE 2,41|2,19 NA NA 1 60 39,36 213,214 60,60 29 1.35 NA 6.32 NA FALSE 6.00 56 NA NA NA FALSE NA NA 66.26 10 49586912 HCC1395_HCC1395T 22 0.476 43 11,5 10,14 21,19 NA 0/1 NA NA NA NA 1,21,2,19 G/A PANCANCER NA FALSE LIPG chr18:49586912:49586913:G:A SNV 2:2 chr18:21403805:53535029:2:2:1 FALSE NA 0.96 +chr18 54357870 54357871 G A 39 344 0.113372093023256 MODIFIER C18orf54 ENSG00000166845 A upstream_gene_variant Transcript ENST00000300091 protein_coding NA rs1183221993 715 1 SNV HGNC HGNC:13796 1 CCDS11956.1 ENSP00000300091 Q8IYD9.134 I7GY12.51 UPI0000074279 Q8IYD9-1 10 NA NA PASS SITE 287,226|25,14 NA NA 1 93 20,20 158,163 60,60 28 2.15 NA 41.54 NA FALSE 6.00 84 NA NA NA FALSE NA NA 75.87 10 54357870 HCC1395_HCC1395T 305 0.117 344 86,12 111,13 207,27 NA 0/1 NA NA NA NA 168,137,25,14 G/A PANCANCER NA FALSE C18orf54 chr18:54357870:54357871:G:A SNV 4:2 chr18:54153851:57701515:4:2:1 NA NA 0.96 +chr18 54907757 54907758 G C 62 433 0.143187066974596 MODIFIER CCDC68 ENSG00000166510 C intron_variant Transcript ENST00000337363 protein_coding 11/11 ENST00000337363.8:c.950+29C>G NA -1 SNV HGNC HGNC:24350 2 P1 CCDS11959.1 ENSP00000337209 Q9H2F9.136 A0A024R2B9.58 UPI00000435F1 10 NA NA PASS SITE 285,220|34,28 NA NA 1 93 20,20 160,165 60,60 39 1.96 NA 26.79 NA FALSE 6.00 59 NA NA NA FALSE NA NA 132.51 10 54907757 HCC1395_HCC1395T 371 0.148 433 69,8 155,32 240,41 NA 0/1 NA NA NA NA 208,163,34,28 G/C PANCANCER NA FALSE CCDC68 chr18:54907757:54907758:G:C SNV 4:2 chr18:54153851:57701515:4:2:1 NA NA 0.96 +chr18 57031501 57031502 C T 66 222 0.297297297297297 MODIFIER WDR7 ENSG00000091157 T downstream_gene_variant Transcript ENST00000254442 protein_coding NA 1709 1 SNV HGNC HGNC:13490 YES NM_015285.3 1 A1 CCDS11962.1 ENSP00000254442 Q9Y4E6.162 UPI000013CE33 Q9Y4E6-1 10 NA NA PASS SITE 29,183|6,60 NA NA 1 93 40,35 200,199 60,60 26 1.71 NA 15.05 NA FALSE 6.00 93 NA NA NA FALSE NA NA 186.42 10 57031501 HCC1395_HCC1395T 156 0.312 222 42,22 80,32 134,60 NA 0/1 NA NA NA NA 23,133,6,60 C/T PANCANCER NA FALSE WDR7 chr18:57031501:57031502:C:T SNV 4:2 chr18:54153851:57701515:4:2:1 NA NA 0.96 +chr18 60371740 60371741 T G 49 51 0.96078431372549 MODERATE MC4R ENSG00000166603 G missense_variant Transcript ENST00000299766 protein_coding 1/1 ENST00000299766.5:c.610A>C ENSP00000299766.3:p.M204L ENSP00000299766.3 p.M204L 1036 610 204 M/L Atg/Ctg COSV55352265 -1 SNV HGNC HGNC:6932 YES NM_005912.3 P1 CCDS11976.1 ENSP00000299766 P32245.211 UPI000013E5E3 1 deleterious(0.03) benign(0.03) PDB-ENSP_mappings:6w25.A&PDB-ENSP_mappings:7aue.R&PDB-ENSP_mappings:7f53.R&PDB-ENSP_mappings:7f54.R&PDB-ENSP_mappings:7f55.R&PDB-ENSP_mappings:7f58.R&PDB-ENSP_mappings:7piu.R&PDB-ENSP_mappings:7piv.R&CDD:cd15353&Gene3D:1.20.1070.10&Pfam:PF00001&SMART:SM01381&Superfamily:SSF81321&PROSITE_profiles:PS50262&PANTHER:PTHR22750&Prints:PR00237&Prints:PR00535&Transmembrane_helices:TMhelix&AlphaFold_DB_import:AF-P32245-F1 1 1 10 NA NA PASS SITE 66,72|22,27 NA NA 1 93 20,35 183,159 60,60 30 2.01 NA 29.80 NA FALSE 6.00 93 NA NA NA FALSE NA NA 163.08 10 60371740 HCC1395_HCC1395T 2 0.927 51 0,14 2,23 2,37 NA 0/1 NA NA NA NA 1,1,22,27 T/G PANCANCER NA FALSE MC4R_p.M204L chr18:60371740:60371741:T:G SNV 1:0 chr18:58628906:80169725:1:0:1 NA NA 0.96 +chr18 72865174 72865175 C G 47 47 1 MODIFIER NETO1 ENSG00000166342 G intron_variant Transcript ENST00000327305 protein_coding 2/10 ENST00000327305.11:c.82+14G>C NA COSV55006500 -1 SNV HGNC HGNC:13823 YES NM_138966.5 1 P1 CCDS12000.1 ENSP00000313088 Q8TDF5.169 A0A024R375.68 UPI000013E59E Q8TDF5-3 1 1 10 NA NA PASS SITE 41,35|27,20 NA NA 1 93 20,20 164,159 60,60 40 1.64 NA 12.90 NA FALSE 6.00 93 NA NA NA FALSE NA NA 129.91 10 72865174 HCC1395_HCC1395T 0 0.967 47 0,13 0,14 0,28 NA 0/1 NA NA NA NA 0,0,27,20 C/G PANCANCER NA FALSE NETO1 chr18:72865174:72865175:C:G SNV 1:0 chr18:58628906:80169725:1:0:1 NA NA 0.96 +chr18 79714627 79714628 C T 18 65 0.276923076923077 LOW CTDP1 ENSG00000060069 T synonymous_variant Transcript ENST00000075430 protein_coding 8/12 ENST00000075430.11:c.1167C>T ENSP00000075430.7:p.A389= ENSP00000075430.7 p.A389= 1269 1167 389 A gcC/gcT rs759434586 1 SNV HGNC HGNC:2498 1 CCDS12018.1 ENSP00000075430 Q9Y5B0.203 UPI0000456BAC Q9Y5B0-4 1 AlphaFold_DB_import:AF-Q9Y5B0-F1&PANTHER:PTHR23081&MobiDB_lite:mobidb-lite 9.49e-05 6.922e-05 5.829e-05 0 0 0.0001867 1.851e-05 0.0001684 0.0004258 3.942e-05 0 0 0 0 0.000193 0.0001883 0 1.47e-05 0 0.0004141 0.0004258 gnomADe_SAS likely_benign 1 10 NA NA PASS SITE 91,101|10,9 NA NA 1 93 20,38 175,223 60,60 26 2.03 NA 30.84 NA FALSE 4.61 63 NA NA NA FALSE NA NA 54.79 10 79714627 HCC1395_HCC1395T 47 0.315 65 15,9 18,6 36,16 NA 0/1 NA NA NA NA 22,25,9,9 C/T PANCANCER NA FALSE CTDP1_p.A389= chr18:79714627:79714628:C:T SNV 1:0 chr18:58628906:80169725:1:0:1 NA NA 0.96 +chr18 80136552 80136553 C T 128 229 0.558951965065502 MODERATE ADNP2 ENSG00000101544 T missense_variant Transcript ENST00000262198 protein_coding 4/4 ENST00000262198.9:c.1139C>T ENSP00000262198.3:p.P380L ENSP00000262198.3 p.P380L 1363 1139 380 P/L cCt/cTt COSV51538036 1 SNV HGNC HGNC:23803 YES NM_014913.4 1 P1 CCDS32853.1 ENSP00000262198 Q6IQ32.167 A0A024R377.48 UPI0000071DEA tolerated(0.07) benign(0.364) AlphaFold_DB_import:AF-Q6IQ32-F1&PANTHER:PTHR15740 1 1 10 NA NA PASS SITE 240,204|73,55 NA NA 1 93 20,20 160,161 60,60 32 2.38 NA 70.43 NA FALSE 6.00 93 NA NA NA FALSE NA NA 341.36 10 80136552 HCC1395_HCC1395T 101 0.568 229 25,34 38,47 66,87 NA 0/1 NA NA NA NA 54,47,73,55 C/T PANCANCER NA FALSE ADNP2_p.P380L chr18:80136552:80136553:C:T SNV 1:0 chr18:58628906:80169725:1:0:1 NA NA 0.96 +chr18 80138229 80138230 G T 35 57 0.614035087719298 MODERATE ADNP2 ENSG00000101544 T missense_variant Transcript ENST00000262198 protein_coding 4/4 ENST00000262198.9:c.2816G>T ENSP00000262198.3:p.R939I ENSP00000262198.3 p.R939I 3040 2816 939 R/I aGa/aTa COSV51538056&COSV51540612 1 SNV HGNC HGNC:23803 YES NM_014913.4 1 P1 CCDS32853.1 ENSP00000262198 Q6IQ32.167 A0A024R377.48 UPI0000071DEA deleterious(0) probably_damaging(0.934) AlphaFold_DB_import:AF-Q6IQ32-F1&Pfam:PF19627&PANTHER:PTHR15740 1&1 1&1 10 NA NA PASS SITE 78,52|21,14 NA NA 1 93 20,20 157,163 60,60 32 1.89 NA 22.48 NA FALSE 6.00 88 NA NA NA FALSE NA NA 90.31 10 80138229 HCC1395_HCC1395T 22 0.581 57 3,7 11,16 17,24 NA 0/1 NA NA NA NA 12,10,21,14 G/T PANCANCER NA FALSE ADNP2_p.R939I chr18:80138229:80138230:G:T SNV 1:0 chr18:58628906:80169725:1:0:1 NA NA 0.96 +chr19 1605357 1605358 C T 371 371 1 MODIFIER TCF3 ENSG00000071564 T downstream_gene_variant Transcript ENST00000262965 protein_coding NA COSV53654301 3935 -1 SNV HGNC HGNC:11633 YES NM_003200.5 1 A1 CCDS12074.1 ENSP00000262965 P15923.242 UPI0000136C80 P15923-1 1 1 1 11 NA NA PASS SITE 286,279|183,188 NA NA 1 93 20,20 150,149 60,60 31 2.55 NA 105.55 NA FALSE 6.00 93 NA NA NA FALSE NA NA 1022.30 11 1605357 HCC1395_HCC1395T 0 0.996 371 0,97 0,115 0,223 NA 0/1 NA NA NA NA 0,0,183,188 C/T PANCANCER NA FALSE TCF3 chr19:1605357:1605358:C:T SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 1905080 1905081 C G 42 42 1 MODIFIER SCAMP4 ENSG00000227500 G upstream_gene_variant Transcript ENST00000316097 protein_coding NA 319 1 SNV HGNC HGNC:30385 YES NM_079834.4 1 P1 CCDS45903.1 ENSP00000316007 Q969E2.137 UPI000006F786 Q969E2-1 11 NA NA PASS SITE 58,29|29,14 NA NA 1 93 20,20 158,173 60,60 24 -8.501e-02 NA 14.69 NA FALSE 6.00 93 NA NA NA FALSE NA NA 129.19 11 1905080 HCC1395_HCC1395T 0 0.971 42 0,17 0,12 0,31 NA 0/1 NA NA NA NA 0,0,28,14 C/G PANCANCER NA FALSE SCAMP4 chr19:1905080:1905081:C:G SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 2235521 2235522 G A 5 5 1 MODIFIER SF3A2 ENSG00000104897 A upstream_gene_variant Transcript ENST00000221494 protein_coding NA 1303 1 SNV HGNC HGNC:10766 YES NM_007165.5 1 P1 CCDS12084.1 ENSP00000221494 Q15428.194 UPI0000135468 11 NA NA PASS SITE 8,0|4,1 NA NA 1 39 40,31 214,167 60,60 39 0.954 NA 2.41 NA FALSE 6.00 51 NA NA NA FALSE NA NA 16.00 11 2235521 HCC1395_HCC1395T 0 0.833 5 0,1 0,3 0,4 NA 0/1 NA NA NA NA 0,0,4,1 G/A PANCANCER NA FALSE SF3A2 chr19:2235521:2235522:G:A SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 2341278 2341279 C T 133 258 0.515503875968992 MODIFIER SPPL2B ENSG00000005206 T downstream_gene_variant Transcript ENST00000585725 protein_coding_CDS_not_defined NA rs1325659861 2752 1 SNV HGNC HGNC:30627 3 7.429e-06 0 0 0 0 0 1.891e-05 0 0 1.891e-05 gnomADe_NFE 11 NA NA PASS SITE 232,267|71,62 NA NA 1 93 20,20 161,170 60,60 26 2.39 NA 72.45 NA FALSE 6.00 93 NA NA NA FALSE NA NA 359.19 11 2341278 HCC1395_HCC1395T 125 0.528 258 32,30 42,55 83,93 NA 0/1 NA NA NA NA 61,64,71,62 C/T PANCANCER NA FALSE SPPL2B chr19:2341278:2341279:C:T SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 2524582 2524583 G A 25 119 0.210084033613445 MODIFIER GNG7 ENSG00000176533 A intron_variant Transcript ENST00000382159 protein_coding 3/4 ENST00000382159.8:c.-37-3857C>T NA -1 SNV HGNC HGNC:4410 YES NM_052847.3 1 P1 CCDS12091.1 ENSP00000371594 O60262.183 UPI000012B22E 11 NA NA PASS SITE 111,98|13,12 NA NA 1 93 20,20 164,186 60,60 20 1.91 NA 23.73 NA FALSE 6.00 42 NA NA NA FALSE NA NA 55.32 11 2524582 HCC1395_HCC1395T 94 0.217 119 31,5 32,11 64,17 NA 0/1 NA NA NA NA 54,40,13,12 G/A PANCANCER NA FALSE GNG7 chr19:2524582:2524583:G:A SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 2576233 2576234 G C 36 36 1 MODIFIER GNG7 ENSG00000176533 C intron_variant Transcript ENST00000382159 protein_coding 2/4 ENST00000382159.8:c.-77-21045C>G NA -1 SNV HGNC HGNC:4410 YES NM_052847.3 1 P1 CCDS12091.1 ENSP00000371594 O60262.183 UPI000012B22E 11 NA NA PASS SITE 23,55|11,25 NA NA 1 93 20,20 168,162 60,60 25 1.77 NA 17.16 NA FALSE 6.00 93 NA NA NA FALSE NA NA 103.40 11 2576233 HCC1395_HCC1395T 0 0.964 36 0,13 0,11 0,25 NA 0/1 NA NA NA NA 0,0,11,25 G/C PANCANCER NA FALSE GNG7 chr19:2576233:2576234:G:C SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 3123263 3123264 A T 147 147 1 MODIFIER GNA11 ENSG00000088256 T 3_prime_UTR_variant Transcript ENST00000078429 protein_coding 7/7 ENST00000078429.9:c.*2084A>T NA 3454 1 SNV HGNC HGNC:4379 YES NM_002067.5 1 P1 CCDS12103.1 ENSP00000078429 P29992.206 UPI000004D209 1 11 NA NA PASS SITE 88,70|81,66 NA NA 1 93 20,20 165,162 60,60 24 1.77 NA 32.76 NA FALSE 6.00 93 NA NA NA FALSE NA NA 462.05 11 3123263 HCC1395_HCC1395T 0 0.991 147 0,35 0,48 0,103 NA 0/1 NA NA NA NA 0,0,81,66 A/T PANCANCER TRUE FALSE GNA11 chr19:3123263:3123264:A:T SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 3493938 3493939 G C 41 41 1 MODIFIER DOHH ENSG00000129932 C intron_variant Transcript ENST00000427575 protein_coding 3/4 ENST00000427575.6:c.351+90C>G NA -1 SNV HGNC HGNC:28662 YES NM_001145165.2 1 P1 CCDS12108.1 ENSP00000398882 Q9BU89.168 UPI0000071C59 1 11 NA NA PASS SITE 33,5|34,7 NA NA 1 93 40,37 203,199 60,60 31 1.55 NA 10.19 NA FALSE 6.00 93 NA NA NA FALSE NA NA 148.88 11 3493938 HCC1395_HCC1395T 0 0.973 41 0,12 0,22 0,35 NA 0/1 NA NA NA NA 0,0,34,7 G/C PANCANCER NA FALSE DOHH chr19:3493938:3493939:G:C SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 4219497 4219498 C G 14 47 0.297872340425532 MODIFIER ANKRD24 ENSG00000089847 G intron_variant Transcript ENST00000262970 protein_coding 16/19 ENST00000262970.9:c.3274-94C>G NA 1 SNV HGNC HGNC:29424 5 P4 ENSP00000262970 Q8TF21.138 UPI000170BA2E Q8TF21-2 11 NA NA PASS SITE 66,22|11,3 NA NA 1 93 35,39 175,185 60,60 29 1.66 NA 12.94 NA FALSE 6.00 67 NA NA NA FALSE NA NA 40.77 11 4219497 HCC1395_HCC1395T 33 0.326 47 13,4 12,8 26,12 NA 0/1 NA NA NA NA 25,8,11,3 C/G PANCANCER NA FALSE ANKRD24 chr19:4219497:4219498:C:G SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 4639528 4639529 G C 125 125 1 MODIFIER TNFAIP8L1 ENSG00000185361 C 5_prime_UTR_variant Transcript ENST00000327473 protein_coding 1/2 ENST00000327473.9:c.-105G>C NA 13 1 SNV HGNC HGNC:28279 YES NM_152362.3 1 P1 CCDS12132.1 ENSP00000331827 Q8WVP5.129 UPI000013EB11 11 NA NA PASS SITE 126,75|82,44 NA NA 1 93 20,20 163,170 60,60 26 1.78 NA 38.22 NA FALSE 6.00 93 NA NA NA FALSE NA NA 389.41 11 4639528 HCC1395_HCC1395T 0 0.989 125 0,39 0,45 0,86 NA 0/1 NA NA NA NA 0,0,81,44 G/C PANCANCER NA FALSE TNFAIP8L1 chr19:4639528:4639529:G:C SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 4772181 4772182 C A 58 58 1 MODIFIER MIR7-3HG ENSG00000176840 A non_coding_transcript_exon_variant Transcript ENST00000317292 lncRNA 3/3 ENST00000317292.9:n.366C>A NA 366 1 SNV HGNC HGNC:30049 1 11 NA NA PASS SITE 42,19|40,18 NA NA 1 93 20,20 164,151 60,60 35 1.67 NA 13.20 NA FALSE 6.00 93 NA NA NA FALSE NA NA 177.54 11 4772181 HCC1395_HCC1395T 0 0.977 58 0,24 0,16 0,41 NA 0/1 NA NA NA NA 0,0,40,18 C/A PANCANCER NA FALSE MIR7-3HG chr19:4772181:4772182:C:A SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 5206760 5206761 G C 114 114 1 MODIFIER PTPRS ENSG00000105426 C 3_prime_UTR_variant Transcript ENST00000262963 protein_coding 38/38 ENST00000262963.11:c.*14C>G NA 6104 -1 SNV HGNC HGNC:9681 YES NM_002850.4 5 A1 CCDS45930.1 ENSP00000262963 Q13332.211 G8JL96.77 UPI000059D63E Q13332-1 11 NA NA PASS SITE 74,69|55,59 NA NA 1 93 20,20 163,168 60,60 23 2.03 NA 30.01 NA FALSE 6.00 93 NA NA NA FALSE NA NA 348.72 11 5206760 HCC1395_HCC1395T 0 0.989 114 0,27 0,46 0,85 NA 0/1 NA NA NA NA 0,0,55,59 G/C PANCANCER NA FALSE PTPRS chr19:5206760:5206761:G:C SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 5928081 5928082 C G 165 166 0.993975903614458 MODERATE RANBP3 ENSG00000031823 G missense_variant Transcript ENST00000034275 protein_coding 8/16 ENST00000034275.12:c.496G>C ENSP00000034275.7:p.E166Q ENSP00000034275.7 p.E166Q 500 496 166 E/Q Gag/Cag rs1391594591&COSV50381068 -1 SNV HGNC HGNC:9850 1 A1 CCDS42477.1 ENSP00000034275 Q9H6Z4.175 UPI00002031A7 Q9H6Z4-3 deleterious_low_confidence(0.04) PANTHER:PTHR23138&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-Q9H6Z4-F1 6.571e-06 0 0 0 0 0 0 0 1.47e-05 0 0 1.47e-05 gnomADg_NFE 0&1 0&1 11 NA NA PASS SITE 60,95|69,96 NA NA 1 93 20,20 166,160 60,60 38 2.02 NA 31.26 NA FALSE 4.61 93 NA NA NA FALSE NA NA 500.19 11 5928081 HCC1395_HCC1395T 1 0.982 166 0,45 1,54 1,110 NA 0/1 NA NA NA NA 0,1,69,96 C/G PANCANCER NA FALSE RANBP3_p.E166Q chr19:5928081:5928082:C:G SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 6044263 6044264 G C 116 116 1 MODERATE RFX2 ENSG00000087903 C missense_variant Transcript ENST00000303657 protein_coding 3/18 ENST00000303657.10:c.110C>G ENSP00000306335.4:p.A37G ENSP00000306335.4 p.A37G 226 110 37 A/G gCc/gGc COSV57942124&COSV57946040 -1 SNV HGNC HGNC:9983 YES NM_000635.4 1 P3 CCDS12157.1 ENSP00000306335 P48378.175 UPI000013D4B1 P48378-1 deleterious_low_confidence(0) benign(0.092) Pfam:PF04589&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&AlphaFold_DB_import:AF-P48378-F1 1&1 1&1 11 NA NA PASS SITE 69,35|70,46 NA NA 1 93 20,20 165,156 60,60 28 1.89 NA 22.48 NA FALSE 6.00 93 NA NA NA FALSE NA NA 352.11 11 6044263 HCC1395_HCC1395T 0 0.988 116 0,20 0,54 0,77 NA 0/1 NA NA NA NA 0,0,70,46 G/C PANCANCER NA FALSE RFX2_p.A37G chr19:6044263:6044264:G:C SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 6755018 6755019 T C 149 149 1 MODERATE SH2D3A ENSG00000125731 C missense_variant Transcript ENST00000245908 protein_coding 5/10 ENST00000245908.11:c.794A>G ENSP00000245908.5:p.E265G ENSP00000245908.5 p.E265G 911 794 265 E/G gAg/gGg COSV55589109 -1 SNV HGNC HGNC:16885 YES NM_005490.3 1 P1 CCDS12173.1 ENSP00000245908 Q9BRG2.155 UPI000006FD60 Q9BRG2-1 tolerated(0.08) benign(0.084) Low_complexity_(Seg):seg&AlphaFold_DB_import:AF-Q9BRG2-F1 1 1 11 NA NA PASS SITE 127,90|91,58 NA NA 1 93 20,34 172,175 60,60 28 2.20 NA 46.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 502.89 11 6755018 HCC1395_HCC1395T 0 0.992 149 0,47 0,52 0,114 NA 0/1 NA NA NA NA 0,0,91,58 T/C PANCANCER NA FALSE SH2D3A_p.E265G chr19:6755018:6755019:T:C SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 8955984 8955985 G A 119 244 0.487704918032787 MODERATE MUC16 ENSG00000181143 A missense_variant Transcript ENST00000397910 protein_coding 3/84 ENST00000397910.8:c.20786C>T ENSP00000381008.2:p.S6929F ENSP00000381008.2 p.S6929F 20990 20786 6929 S/F tCc/tTc COSV67483044 -1 SNV HGNC HGNC:15582 YES 5 P2 CCDS54212.1 ENSP00000381008 Q8WXI7.147 UPI000065CA24 1 MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg 1 1 11 NA NA PASS SITE 190,168|65,54 NA NA 1 93 20,20 157,159 60,60 33 2.18 NA 45.15 NA FALSE 6.00 93 NA NA NA FALSE NA NA 295.76 11 8955984 HCC1395_HCC1395T 125 0.473 244 27,22 56,52 88,79 NA 0/1 NA NA NA NA 61,64,65,54 G/A PANCANCER NA FALSE MUC16_p.S6929F chr19:8955984:8955985:G:A SNV 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 8969814 8969815 ACGTGGAATTTCCTTGTG A 158 159 0.993710691823899 HIGH MUC16 ENSG00000181143 - frameshift_variant Transcript ENST00000397910 protein_coding 2/84 ENST00000397910.8:c.9524_9540del ENSP00000381008.2:p.A3175Vfs*111 ENSP00000381008.2 p.A3175Vfs*111 9728-9744 9524-9540 3175-3180 AQGNST/X gCACAAGGAAATTCCACG/g -1 deletion HGNC HGNC:15582 YES 5 P2 CCDS54212.1 ENSP00000381008 Q8WXI7.147 UPI000065CA24 1 MobiDB_lite:mobidb-lite 11 NA NA PASS SITE 88,77|86,72 NA NA 1 93 20,20 155,176 60,60 34 2.01 NA 30.25 NA FALSE 6.00 93 NA NA NA FALSE NA NA 702.82 11 8969814 HCC1395_HCC1395T 1 0.982 159 0,28 0,61 1,108 NA 0/1 NA NA NA NA 0,1,86,72 ACGTGGAATTTCCTTGTG/A PANCANCER NA FALSE MUC16_p.A3175Vfs*111 chr19:8969814:8969815:ACGTGGAATTTCCTTGTG:A indel 2:0 chr19:282753:11947721:2:0:1 TRUE NA 0.96 +chr19 12580948 12580949 G A 52 272 0.191176470588235 MODERATE ZNF490 ENSG00000188033 A missense_variant Transcript ENST00000311437 protein_coding 5/5 ENST00000311437.11:c.1127C>T ENSP00000311521.6:p.S376F ENSP00000311521.6 p.S376F 1260 1127 376 S/F tCc/tTc COSV61007760&COSV61008254 -1 SNV HGNC HGNC:23705 YES NM_020714.3 1 P1 CCDS12272.1 ENSP00000311521 Q9ULM2.179 UPI0000001C6F tolerated(0.06) benign(0.194) PROSITE_profiles:PS50157&PANTHER:PTHR24390&PROSITE_patterns:PS00028&Pfam:PF00096&Gene3D:3.30.160.60&SMART:SM00355&Superfamily:SSF57667&AlphaFold_DB_import:AF-Q9ULM2-F1 1&1 1&1 11 NA NA PASS SITE 195,159|29,23 NA NA 1 93 20,20 157,158 60,60 32 1.95 NA 26.43 NA FALSE 6.00 93 NA NA NA FALSE NA NA 112.76 11 12580948 HCC1395_HCC1395T 220 0.202 272 51,15 83,18 142,35 NA 0/1 NA NA NA NA 122,98,29,23 G/A PANCANCER NA FALSE ZNF490_p.S376F chr19:12580948:12580949:G:A SNV 2:2 chr19:12380965:16951834:2:2:1 FALSE NA 0.96 +chr19 12702635 12702636 G A 15 30 0.5 MODIFIER TNPO2 ENSG00000105576 A intron_variant Transcript ENST00000356861 protein_coding 20/24 ENST00000356861.9:c.2305+188C>T NA -1 SNV HGNC HGNC:19998 1 P1 CCDS45992.1 ENSP00000349321 O14787.174 A0A024R7F7.49 UPI000013C7F0 O14787-2 1 11 NA NA PASS SITE 31,14|12,3 NA NA 1 57 20,36 165,195 60,60 36 1.33 NA 6.02 NA FALSE 6.00 74 NA NA NA FALSE NA NA 45.71 11 12702635 HCC1395_HCC1395T 15 0.520 30 4,7 7,5 11,12 NA 0/1 NA NA NA NA 11,4,12,3 G/A PANCANCER NA FALSE TNPO2 chr19:12702635:12702636:G:A SNV 2:2 chr19:12380965:16951834:2:2:1 FALSE NA 0.96 +chr19 13262933 13262934 G T 75 155 0.483870967741935 MODIFIER CACNA1A ENSG00000141837 T intron_variant Transcript ENST00000360228 protein_coding 24/46 ENST00000360228.11:c.3990-100C>A NA -1 SNV HGNC HGNC:1388 YES NM_001127222.2 1 CCDS45998.1 ENSP00000353362 O00555.217 UPI0000141565 O00555-8 1 11 NA NA PASS SITE 38,132|19,56 NA NA 1 93 37,33 181,176 60,60 30 1.86 NA 20.68 NA FALSE 6.00 93 NA NA NA FALSE NA NA 208.94 11 13262933 HCC1395_HCC1395T 80 0.465 155 28,23 32,29 67,58 NA 0/1 NA NA NA NA 15,65,19,56 G/T PANCANCER NA FALSE CACNA1A chr19:13262933:13262934:G:T SNV 2:2 chr19:12380965:16951834:2:2:1 FALSE NA 0.96 +chr19 13836644 13836645 G A 63 150 0.42 MODIFIER ZSWIM4 ENSG00000132003 A downstream_gene_variant Transcript ENST00000254323 protein_coding NA 4414 1 SNV HGNC HGNC:25704 2 CCDS32924.1 ENSP00000254323 Q9H7M6.129 UPI00001C2005 11 NA NA PASS SITE 75,111|29,34 NA NA 2 93 20,20 160,141 60,60 34 1.85 NA 20.46 NA FALSE 6.00 93 NA NA NA FALSE NA NA 145.14 11 13836644 HCC1395_HCC1395T 87 0.376 150 25,17 31,17 62,37 NA 0/1 NA NA NA NA 37,50,29,34 G/A PANCANCER NA FALSE ZSWIM4 chr19:13836644:13836645:G:A SNV 2:2 chr19:12380965:16951834:2:2:1 FALSE NA 0.96 +chr19 13912635 13912636 C G 73 131 0.557251908396947 MODIFIER CC2D1A ENSG00000132024 G intron_variant Transcript ENST00000318003 protein_coding 4/28 ENST00000318003.11:c.378+42C>G NA 1 SNV HGNC HGNC:30237 YES NM_017721.5 1 P3 CCDS42512.1 ENSP00000313601 Q6P1N0.156 UPI0000203524 Q6P1N0-1 1 11 NA NA PASS SITE 36,107|20,53 NA NA 1 93 30,20 172,173 60,60 24 1.86 NA 20.46 NA FALSE 6.00 93 NA NA NA FALSE NA NA 207.82 11 13912635 HCC1395_HCC1395T 58 0.539 131 11,20 30,25 46,54 NA 0/1 NA NA NA NA 19,39,20,53 C/G PANCANCER NA FALSE CC2D1A chr19:13912635:13912636:C:G SNV 2:2 chr19:12380965:16951834:2:2:1 FALSE NA 0.96 +chr19 15361609 15361610 C T 10 20 0.5 MODIFIER AKAP8 ENSG00000105127 T intron_variant Transcript ENST00000269701 protein_coding 11/13 ENST00000269701.7:c.1396+120G>A NA -1 SNV HGNC HGNC:378 YES NM_005858.4 1 P2 CCDS12329.1 ENSP00000269701 O43823.189 UPI000012575C 11 NA NA PASS SITE 20,5|9,1 NA NA 1 37 37,37 186,217 60,60 26 1.15 NA 3.91 NA FALSE 6.00 27 NA NA NA FALSE NA NA 28.11 11 15361609 HCC1395_HCC1395T 10 0.522 20 2,1 5,7 8,9 NA 0/1 NA NA NA NA 8,2,9,1 C/T PANCANCER NA FALSE AKAP8 chr19:15361609:15361610:C:T SNV 2:2 chr19:12380965:16951834:2:2:1 FALSE NA 0.96 +chr19 15508442 15508443 G A 43 89 0.48314606741573 MODIFIER CYP4F22 ENSG00000171954 A upstream_gene_variant Transcript ENST00000269703 protein_coding NA 83 1 SNV HGNC HGNC:26820 YES NM_173483.4 2 P1 CCDS12331.1 ENSP00000269703 Q6NT55.157 UPI000013D84B 1 11 NA NA PASS SITE 98,27|33,10 NA NA 1 93 37,33 178,175 60,60 19 1.80 NA 18.36 NA FALSE 6.00 93 NA NA NA FALSE NA NA 118.19 11 15508442 HCC1395_HCC1395T 46 0.462 89 16,16 23,18 40,34 NA 0/1 NA NA NA NA 39,7,33,10 G/A PANCANCER NA FALSE CYP4F22 chr19:15508442:15508443:G:A SNV 2:2 chr19:12380965:16951834:2:2:1 FALSE NA 0.96 +chr19 16093699 16093700 G C 83 155 0.535483870967742 MODIFIER TPM4 ENSG00000167460 C 3_prime_UTR_variant&NMD_transcript_variant Transcript ENST00000300933 nonsense_mediated_decay 8/9 ENST00000300933.9:c.*336G>C NA 587 COSV56290486 1 cds_start_NF SNV HGNC HGNC:12013 1 ENSP00000300933 A0A5F9UKJ4.10 UPI00114858A0 1 1 1 11 NA NA PASS SITE 53,109|27,56 NA NA 1 93 20,20 155,166 60,60 20 1.81 NA 18.66 NA FALSE 6.00 93 NA NA NA FALSE NA NA 230.94 11 16093699 HCC1395_HCC1395T 72 0.527 155 20,21 24,29 52,58 NA 0/1 NA NA NA NA 24,48,27,56 G/C PANCANCER NA FALSE TPM4 chr19:16093699:16093700:G:C SNV 2:2 chr19:12380965:16951834:2:2:1 FALSE NA 0.96 +chr19 16572289 16572290 C G 137 320 0.428125 MODIFIER MED26 ENSG00000105085 G downstream_gene_variant Transcript ENST00000263390 protein_coding NA rs989936448&COSV54659673 2630 -1 SNV HGNC HGNC:2376 YES NM_004831.5 1 P1 CCDS12347.1 ENSP00000263390 O95402.178 UPI000013D3FC O95402-1 0&1 0&1 11 NA NA PASS SITE 169,284|49,88 NA NA 1 93 20,20 152,151 60,60 28 2.24 NA 51.17 NA FALSE 6.00 93 NA NA NA FALSE NA NA 351.76 11 16572289 HCC1395_HCC1395T 183 0.428 320 55,35 54,38 122,91 NA 0/1 NA NA NA NA 66,117,49,88 C/G PANCANCER NA FALSE MED26 chr19:16572289:16572290:C:G SNV 2:2 chr19:12380965:16951834:2:2:1 FALSE NA 0.96 +chr19 16896605 16896606 C G 14 23 0.608695652173913 MODIFIER F2RL3 ENSG00000127533 G downstream_gene_variant Transcript ENST00000248076 protein_coding NA COSV50185381 3999 1 SNV HGNC HGNC:3540 YES NM_003950.4 1 P1 CCDS12350.1 ENSP00000248076 Q96RI0.181 UPI000013CC36 1 1 11 NA NA PASS SITE 8,24|5,9 NA NA 1 52 29,20 184,168 60,60 24 1.28 NA 5.37 NA FALSE 6.00 93 NA NA NA FALSE NA NA 36.57 11 16896605 HCC1395_HCC1395T 9 0.527 23 4,5 4,4 8,9 NA 0/1 NA NA NA NA 2,7,5,9 C/G PANCANCER NA FALSE F2RL3 chr19:16896605:16896606:C:G SNV 2:2 chr19:12380965:16951834:2:2:1 FALSE NA 0.96 +chr19 17555816 17555817 G T 21 46 0.456521739130435 MODERATE COLGALT1 ENSG00000130309 T missense_variant Transcript ENST00000252599 protein_coding 1/12 ENST00000252599.9:c.103G>T ENSP00000252599.3:p.D35Y ENSP00000252599.3 p.D35Y 168 103 35 D/Y Gac/Tac COSV53110205 1 SNV HGNC HGNC:26182 YES NM_024656.4 1 P1 CCDS12363.1 ENSP00000252599 Q8NBJ5.155 UPI000003B0F7 1 deleterious(0.05) benign(0.442) Cleavage_site_(Signalp):SignalP-noTM&AlphaFold_DB_import:AF-Q8NBJ5-F1 1 1 11 NA NA PASS SITE 14,62|3,18 NA NA 1 93 38,35 181,201 60,60 32 1.67 NA 13.24 NA FALSE 6.00 93 NA NA NA FALSE NA NA 69.53 11 17555816 HCC1395_HCC1395T 25 0.500 46 11,10 8,10 21,21 NA 0/1 NA NA NA NA 4,21,3,18 G/T PANCANCER NA FALSE COLGALT1_p.D35Y chr19:17555816:17555817:G:T SNV 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 18177598 18177599 CGGGAGGCGGGGGCCAGACTT C 19 37 0.513513513513513 MODIFIER IFI30 ENSG00000216490 - intron_variant Transcript ENST00000407280 protein_coding 5/6 ENST00000407280.4:c.637-108_637-89del NA 1 deletion HGNC HGNC:5398 YES NM_006332.5 1 P1 CCDS46015.1 ENSP00000384886 P13284.166 A0A024R7N7.49 UPI0000072A2B 4 11 NA NA PASS SITE 41,11|18,1 NA NA 1 62 37,39 189,234 60,60 22 1.48 NA 8.29 NA FALSE 6.00 93 NA NA NA FALSE NA NA 74.12 11 18177598 HCC1395_HCC1395T 18 0.543 37 3,5 5,13 15,18 NA 0/1 NA NA NA NA 14,4,18,1 CGGGAGGCGGGGGCCAGACTT/C PANCANCER NA FALSE IFI30 chr19:18177598:18177599:CGGGAGGCGGGGGCCAGACTT:C indel 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 19336158 19336159 A C 30 236 0.127118644067797 MODERATE MAU2 ENSG00000129933 C missense_variant Transcript ENST00000262815 protein_coding 3/19 ENST00000262815.13:c.331A>C ENSP00000262815.9:p.S111R ENSP00000262815.9 p.S111R 362 331 111 S/R Agt/Cgt 1 SNV HGNC HGNC:29140 YES NM_015329.4 1 P1 CCDS32969.2 ENSP00000262815 Q9Y6X3.157 UPI00001C200D Q9Y6X3-1 1 deleterious_low_confidence(0) probably_damaging(0.986) PANTHER:PTHR21394&Gene3D:1.25.40.10&Pfam:PF10345&SMART:SM00028&Superfamily:SSF48452&AlphaFold_DB_import:AF-Q9Y6X3-F1 11 NA NA PASS SITE 199,158|16,14 NA NA 1 93 20,20 154,157 60,60 39 2.00 NA 29.15 NA FALSE 6.00 74 NA NA NA FALSE NA NA 60.89 11 19336158 HCC1395_HCC1395T 206 0.128 236 50,11 62,5 135,19 NA 0/1 NA NA NA NA 112,94,16,14 A/C PANCANCER NA FALSE MAU2_p.S111R chr19:19336158:19336159:A:C SNV 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 21536794 21536795 TAAGAG T 83 366 0.226775956284153 HIGH ZNF429 ENSG00000197013 - frameshift_variant Transcript ENST00000358491 protein_coding 4/4 ENST00000358491.9:c.744_748del ENSP00000351280.3:p.K248Nfs*11 ENSP00000351280.3 p.K248Nfs*11 912-916 742-746 248-249 KR/X AAGAGa/a 1 deletion HGNC HGNC:20817 YES NM_001001415.4 3 P1 CCDS42537.1 ENSP00000351280 Q86V71.166 UPI000022ABC2 1 Gene3D:3.30.160.60&AlphaFold_DB_import:AF-Q86V71-F1&Pfam:PF00096&PROSITE_patterns:PS00028&PROSITE_profiles:PS50157&PANTHER:PTHR24381&SMART:SM00355&Superfamily:SSF57667 2 11 NA NA PASS SITE 277,212|50,33 NA NA 1 93 20,33 167,188 60,60 34 2.16 NA 43.03 NA FALSE 6.00 93 NA NA NA FALSE NA NA 311.03 11 21536794 HCC1395_HCC1395T 283 0.253 366 47,17 111,36 188,63 NA 0/1 NA NA NA NA 158,125,50,33 TAAGAG/T PANCANCER NA FALSE ZNF429_p.K248Nfs*11 chr19:21536794:21536795:TAAGAG:T indel 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 23492164 23492165 A T 59 252 0.234126984126984 MODIFIER ZNF725P ENSG00000268100 T downstream_gene_variant Transcript ENST00000596753 unprocessed_pseudogene NA 264 -1 SNV HGNC HGNC:32461 YES 11 NA NA PASS SITE 197,121|38,21 NA NA 1 93 20,20 174,181 60,60 34 1.95 NA 26.49 NA FALSE 6.00 93 NA NA NA FALSE NA NA 149.00 11 23492164 HCC1395_HCC1395T 193 0.249 252 82,18 49,22 135,44 NA 0/1 NA NA NA NA 121,72,38,21 A/T PANCANCER NA FALSE ZNF725P chr19:23492164:23492165:A:T SNV 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 23740039 23740040 T C 2 8 0.25 MODIFIER ZNF681 ENSG00000196172 C 3_prime_UTR_variant Transcript ENST00000402377 protein_coding 4/4 ENST00000402377.3:c.*3573A>G NA 5653 -1 SNV HGNC HGNC:26457 YES NM_138286.3 1 P1 CCDS12414.2 ENSP00000384000 Q96N22.166 UPI000022ABC8 Q96N22-1 11 NA NA PASS SITE 3,14|2,0 NA NA 2 32 35,41 215,129 60,60 44 1.06 NA 3.01 NA FALSE 6.00 9 NA NA NA FALSE NA NA 6.60 11 23740039 HCC1395_HCC1395T 6 0.300 8 3,0 3,2 6,2 NA 0|1 0|1 23740039_T_C NA 23740039 1,5,2,0 T|C PANCANCER NA FALSE ZNF681 chr19:23740039:23740040:T:C SNV 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 23740042 23740043 A T 2 8 0.25 MODIFIER ZNF681 ENSG00000196172 T 3_prime_UTR_variant Transcript ENST00000402377 protein_coding 4/4 ENST00000402377.3:c.*3570T>A NA 5650 -1 SNV HGNC HGNC:26457 YES NM_138286.3 1 P1 CCDS12414.2 ENSP00000384000 Q96N22.166 UPI000022ABC8 Q96N22-1 11 NA NA PASS SITE 3,14|2,0 NA NA 2 32 39,37 215,129 60,60 47 1.04 NA 3.01 NA FALSE 6.00 20 NA NA NA FALSE NA NA 6.60 11 23740042 HCC1395_HCC1395T 6 0.300 8 3,0 3,2 6,2 NA 0|1 0|1 23740039_T_C NA 23740039 1,5,2,0 A|T PANCANCER NA FALSE ZNF681 chr19:23740042:23740043:A:T SNV 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 31128450 31128451 C A 42 253 0.16600790513834 MODIFIER ENSG00000284430 A non_coding_transcript_exon_variant Transcript ENST00000638312 lncRNA 3/6 ENST00000638312.1:n.3067C>A NA 3067 1 SNV YES 5 11 NA NA PASS SITE 173,156|21,21 NA NA 1 93 20,20 167,167 60,60 30 1.93 NA 24.98 NA FALSE 6.00 60 NA NA NA FALSE NA NA 92.36 11 31128450 HCC1395_HCC1395T 211 0.168 253 53,10 89,19 153,30 NA 0/1 NA NA NA NA 111,100,21,21 C/A PANCANCER NA FALSE chr19:31128450:31128451:C:A SNV 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 33211055 33211056 C G 44 114 0.385964912280702 MODIFIER SLC7A10 ENSG00000130876 G intron_variant Transcript ENST00000253188 protein_coding 7/10 ENST00000253188.8:c.1017-157G>C NA -1 SNV HGNC HGNC:11058 YES NM_019849.3 1 P1 CCDS12431.1 ENSP00000253188 Q9NS82.161 UPI0000001C3E 11 NA NA PASS SITE 72,82|21,23 NA NA 1 93 20,20 156,155 60,60 18 1.76 NA 16.81 NA FALSE 6.00 93 NA NA NA FALSE NA NA 119.48 11 33211055 HCC1395_HCC1395T 70 0.412 114 21,11 25,20 47,33 NA 0/1 NA NA NA NA 34,36,21,23 C/G PANCANCER NA FALSE SLC7A10 chr19:33211055:33211056:C:G SNV 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 33772343 33772344 C T 121 521 0.232245681381958 LOW CHST8 ENSG00000124302 T synonymous_variant Transcript ENST00000262622 protein_coding 4/4 ENST00000262622.4:c.555C>T ENSP00000262622.3:p.F185= ENSP00000262622.3 p.F185= 1313 555 185 F ttC/ttT rs1431563735&COSV52857904 1 SNV HGNC HGNC:15993 1 P1 CCDS12433.1 ENSP00000262622 Q9H2A9.143 UPI000006F966 1 AlphaFold_DB_import:AF-Q9H2A9-F1&Pfam:PF03567&PANTHER:PTHR12137 4.177e-06 0 0 0 0 0 9.302e-06 0 0 9.302e-06 gnomADe_NFE 0&1 0&1 11 NA NA PASS SITE 443,316|64,57 NA NA 1 93 20,20 162,158 60,60 29 2.41 NA 76.41 NA FALSE 6.00 93 NA NA NA FALSE NA NA 272.08 11 33772343 HCC1395_HCC1395T 400 0.223 521 131,32 143,47 288,82 NA 0/1 NA NA NA NA 225,175,64,57 C/T PANCANCER NA FALSE CHST8_p.F185= chr19:33772343:33772344:C:T SNV 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 35488723 35488724 GTTAGGA G 172 323 0.532507739938081 MODIFIER KRTDAP ENSG00000188508 - intron_variant Transcript ENST00000338897 protein_coding 2/5 ENST00000338897.4:c.127-26_127-21del NA -1 deletion HGNC HGNC:16313 YES NM_207392.3 1 P1 CCDS12462.1 ENSP00000339251 P60985.116 UPI0000035979 P60985-1 11 NA NA PASS SITE 211,175|93,79 NA NA 2 93 20,20 151,175 60,60 34 2.17 NA 43.92 NA FALSE 6.00 93 NA NA NA FALSE NA NA 707.08 11 35488723 HCC1395_HCC1395T 151 0.549 323 32,29 52,67 96,117 NA 0|1 0|1 35488723_GTTAGGA_G NA 35488723 86,65,93,79 GTTAGGA|G PANCANCER NA FALSE KRTDAP chr19:35488723:35488724:GTTAGGA:G indel 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 35488730 35488731 A C 172 321 0.53582554517134 MODIFIER KRTDAP ENSG00000188508 C intron_variant Transcript ENST00000338897 protein_coding 2/5 ENST00000338897.4:c.127-27T>G NA -1 SNV HGNC HGNC:16313 YES NM_207392.3 1 P1 CCDS12462.1 ENSP00000339251 P60985.116 UPI0000035979 P60985-1 11 NA NA PASS SITE 207,173|93,79 NA NA 2 93 20,27 151,175 60,60 34 2.17 NA 43.60 NA FALSE 6.00 93 NA NA NA FALSE NA NA 707.41 11 35488730 HCC1395_HCC1395T 149 0.552 321 30,29 55,65 95,117 NA 0|1 0|1 35488723_GTTAGGA_G NA 35488723 85,64,93,79 A|C PANCANCER NA FALSE KRTDAP chr19:35488730:35488731:A:C SNV 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 35726507 35726508 C T 29 145 0.2 MODIFIER KMT2B ENSG00000272333 T intron_variant Transcript ENST00000420124 protein_coding 14/36 ENST00000420124.4:c.4003+154C>T NA rs911318377 1 SNV HGNC HGNC:15840 YES NM_014727.3 1 P2 CCDS46055.1 ENSP00000398837 Q9UMN6.222 UPI00001376B5 1 1.315e-05 0 0 6.55e-05 0 0 0 0 1.47e-05 0 0 6.55e-05 gnomADg_AMR 11 NA NA PASS SITE 56,129|11,18 NA NA 1 93 20,20 164,151 60,60 26 1.74 NA 15.91 NA FALSE 4.31 45 NA NA NA FALSE NA NA 65.08 11 35726507 HCC1395_HCC1395T 116 0.191 145 31,5 43,13 84,19 NA 0/1 NA NA NA NA 39,77,11,18 C/T PANCANCER NA FALSE KMT2B chr19:35726507:35726508:C:T SNV 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 35843401 35843402 C T 92 335 0.274626865671642 MODIFIER NPHS1 ENSG00000161270 T intron_variant Transcript ENST00000353632 protein_coding 17/27 ENST00000353632.6:c.2334+71G>A NA -1 SNV HGNC HGNC:7908 5 A2 ENSP00000343634 O60500.194 UPI000002AF84 O60500-2 1 11 NA NA PASS SITE 280,193|56,36 NA NA 1 93 20,20 160,165 60,60 30 2.18 NA 44.16 NA FALSE 6.00 93 NA NA NA FALSE NA NA 210.30 11 35843401 HCC1395_HCC1395T 243 0.271 335 56,26 94,32 158,58 NA 0/1 NA NA NA NA 142,101,56,36 C/T PANCANCER NA FALSE NPHS1 chr19:35843401:35843402:C:T SNV 2:2 chr19:17271696:36991166:2:2:1 FALSE NA 0.96 +chr19 38477823 38477824 G A 123 232 0.530172413793103 LOW RYR1 ENSG00000196218 A synonymous_variant Transcript ENST00000355481 protein_coding 30/105 ENST00000355481.8:c.4407G>A ENSP00000347667.3:p.R1469= ENSP00000347667.3 p.R1469= 4538 4407 1469 R cgG/cgA COSV62094744 1 SNV HGNC HGNC:10483 1 P4 CCDS42563.1 ENSP00000347667 P21817.239 UPI0000418CBC P21817-2 1 Gene3D:2.60.120.920&Pfam:PF00622&PROSITE_profiles:PS50188&PANTHER:PTHR46399&SMART:SM00449&CDD:cd12879 1 1 11 NA NA PASS SITE 85,154|44,79 NA NA 1 93 20,20 162,165 60,60 30 1.95 NA 26.49 NA FALSE 6.00 93 NA NA NA FALSE NA NA 321.93 11 38477823 HCC1395_HCC1395T 109 0.515 232 27,39 41,33 77,82 NA 0/1 NA NA NA NA 38,71,44,79 G/A PANCANCER NA FALSE RYR1_p.R1469= chr19:38477823:38477824:G:A SNV 2:1 chr19:37693361:38616284:2:1:1 TRUE NA 0.96 +chr19 38802099 38802100 G A 65 65 1 MODERATE LGALS4 ENSG00000171747 A missense_variant Transcript ENST00000307751 protein_coding 9/10 ENST00000307751.9:c.718C>T ENSP00000302100.3:p.R240C ENSP00000302100.3 p.R240C 777 718 240 R/C Cgc/Tgc rs144418886 -1 SNV HGNC HGNC:6565 YES NM_006149.4 1 P1 CCDS12521.1 ENSP00000302100 P56470.186 Q6FHZ4.140 UPI0000001651 deleterious(0.01) PDB-ENSP_mappings:1x50.A&PDB-ENSP_mappings:4ylz.A&PDB-ENSP_mappings:4ylz.B&PDB-ENSP_mappings:4ylz.C&PDB-ENSP_mappings:4ylz.D&PDB-ENSP_mappings:4ym0.A&PDB-ENSP_mappings:4ym0.B&PDB-ENSP_mappings:4ym0.C&PDB-ENSP_mappings:4ym0.D&PDB-ENSP_mappings:4ym1.A&PDB-ENSP_mappings:4ym1.B&PDB-ENSP_mappings:4ym1.C&PDB-ENSP_mappings:4ym1.D&PDB-ENSP_mappings:4ym2.A&PDB-ENSP_mappings:4ym2.B&PDB-ENSP_mappings:4ym2.C&PDB-ENSP_mappings:4ym2.D&PDB-ENSP_mappings:4ym3.A&PDB-ENSP_mappings:4ym3.B&PDB-ENSP_mappings:4ym3.C&PDB-ENSP_mappings:4ym3.D&PDB-ENSP_mappings:5cbl.A&PDB-ENSP_mappings:5cbl.B&PDB-ENSP_mappings:5cbl.C&PDB-ENSP_mappings:5cbl.D&PDB-ENSP_mappings:6wab.A&PDB-ENSP_mappings:6wab.B&PDB-ENSP_mappings:6wab.C&PDB-ENSP_mappings:6wab.D&PROSITE_profiles:PS51304&CDD:cd00070&PANTHER:PTHR11346&Pfam:PF00337&Gene3D:2.60.120.200&SMART:SM00908&SMART:SM00276&Superfamily:SSF49899&AlphaFold_DB_import:AF-P56470-F1 0.0004 0.0008 0 0.001 0 0 4.378e-05 0.0003695 2.893e-05 0 0.0001088 0 1.761e-05 0 0 0.0001051 0.0003138 0 0 0 0.0001925 0 0 2.939e-05 0 0 0.001 EAS 11 NA NA PASS SITE 19,41|19,46 NA NA 1 93 34,36 184,174 60,60 24 1.71 NA 14.75 NA FALSE 4.61 93 NA NA NA FALSE NA NA 216.07 11 38802099 HCC1395_HCC1395T 0 0.981 65 0,16 0,25 0,49 NA 0/1 NA NA NA NA 0,0,19,46 G/A PANCANCER NA FALSE LGALS4_p.R240C chr19:38802099:38802100:G:A SNV 2:0 chr19:38706105:49429505:2:0:1 TRUE NA 0.96 +chr19 40006247 40006248 G C 21 21 1 MODIFIER ZNF546 ENSG00000187187 C intron_variant Transcript ENST00000347077 protein_coding 4/6 ENST00000347077.9:c.171+65G>C NA 1 SNV HGNC HGNC:28671 YES NM_178544.5 1 P2 CCDS12548.1 ENSP00000339823 Q86UE3.160 UPI00001984E3 11 NA NA PASS SITE 3,23|4,17 NA NA 1 93 37,41 194,182 60,60 28 1.40 NA 7.22 NA FALSE 6.00 93 NA NA NA FALSE NA NA 75.69 11 40006247 HCC1395_HCC1395T 0 0.947 21 0,5 0,10 0,17 NA 0/1 NA NA NA NA 0,0,4,17 G/C PANCANCER NA FALSE ZNF546 chr19:40006247:40006248:G:C SNV 2:0 chr19:38706105:49429505:2:0:1 TRUE NA 0.96 +chr19 40702770 40702771 C T 7 10 0.7 MODIFIER COQ8B ENSG00000123815 T intron_variant Transcript ENST00000243583 protein_coding 8/13 ENST00000243583.10:c.677-77G>A NA -1 SNV HGNC HGNC:19041 1 CCDS46081.1 ENSP00000243583 Q96D53.157 A0A024R0Q9.63 UPI000007089F Q96D53-2 1 11 NA NA PASS SITE 4,19|1,6 NA NA 1 52 37,39 194,221 60,60 29 1.25 NA 5.02 NA FALSE 6.00 16 NA NA NA FALSE NA NA 29.96 11 40702770 HCC1395_HCC1395T 3 0.668 10 3,0 0,7 3,7 NA 0/1 NA NA NA NA 0,3,1,6 C/T PANCANCER NA FALSE COQ8B chr19:40702770:40702771:C:T SNV 2:0 chr19:38706105:49429505:2:0:1 TRUE NA 0.96 +chr19 40741994 40741995 C T 87 87 1 MODIFIER ITPKC ENSG00000086544 T downstream_gene_variant Transcript ENST00000263370 protein_coding NA 1134 1 SNV HGNC HGNC:14897 YES NM_025194.3 1 P1 CCDS12563.1 ENSP00000263370 Q96DU7.153 A0A024R0N8.64 UPI000006E1AC 11 NA NA PASS SITE 73,56|45,42 NA NA 1 93 20,20 154,162 60,60 32 1.93 NA 24.94 NA FALSE 6.00 93 NA NA NA FALSE NA NA 272.40 11 40741994 HCC1395_HCC1395T 0 0.985 87 0,23 0,35 0,62 NA 0/1 NA NA NA NA 0,0,45,42 C/T PANCANCER NA FALSE ITPKC chr19:40741994:40741995:C:T SNV 2:0 chr19:38706105:49429505:2:0:1 TRUE NA 0.96 +chr19 41619241 41619242 C T 12 12 1 MODIFIER CEACAM4 ENSG00000105352 T 3_prime_UTR_variant Transcript ENST00000221954 protein_coding 7/7 ENST00000221954.7:c.*89G>A NA 935 -1 SNV HGNC HGNC:1816 YES NM_001817.4 1 P2 CCDS33033.1 ENSP00000221954 O75871.148 UPI0000070B54 11 NA NA PASS SITE 7,4|9,3 NA NA 1 55 20,39 210,236 60,60 42 0.992 NA 2.41 NA FALSE 6.00 92 NA NA NA FALSE NA NA 48.51 11 41619241 HCC1395_HCC1395T 0 0.929 12 0,3 0,8 0,12 NA 0/1 NA NA NA NA 0,0,9,3 C/T PANCANCER NA FALSE CEACAM4 chr19:41619241:41619242:C:T SNV 2:0 chr19:38706105:49429505:2:0:1 TRUE NA 0.96 +chr19 42274467 42274468 C T 54 130 0.415384615384615 MODERATE CIC ENSG00000079432 T missense_variant Transcript ENST00000572681 protein_coding 2/21 ENST00000572681.6:c.2684C>T ENSP00000459719.1:p.P895L ENSP00000459719.1 p.P895L 2752 2684 895 P/L cCt/cTt 1 SNV HGNC HGNC:14214 5 ENSP00000459719 I3L2J0.75 UPI00025A2C1A 1 deleterious_low_confidence(0) possibly_damaging(0.856) PANTHER:PTHR13059 11 NA NA PASS SITE 149,133|30,24 NA NA 1 93 20,20 144,167 60,60 36 2.12 NA 39.13 NA FALSE 6.00 90 NA NA NA FALSE NA NA 142.39 11 42274467 HCC1395_HCC1395T 76 0.443 130 14,12 32,25 48,38 NA 0/1 NA NA NA NA 37,39,30,24 C/T PANCANCER TRUE TRUE CIC_p.P895L chr19:42274467:42274468:C:T SNV 2:0 chr19:38706105:49429505:2:0:1 TRUE NA 0.96 +chr19 43204756 43204757 C A 176 177 0.994350282485876 MODIFIER PSG4 ENSG00000243137 A intron_variant Transcript ENST00000244295 protein_coding 1/4 ENST00000244295.13:c.65-505G>T NA rs1351547494&COSV104546157 -1 SNV HGNC HGNC:9521 1 CCDS33039.1 ENSP00000244295 Q00888.200 UPI000037541D Q00888-2 1.104e-05 0 0 0 0 0 2.705e-05 0 0 2.705e-05 gnomADe_NFE 0&1 0&1 11 NA NA PASS SITE 108,55|120,56 NA NA 1 93 20,20 155,152 60,60 25 2.05 NA 32.51 NA FALSE 6.00 93 NA NA NA FALSE NA NA 531.81 11 43204756 HCC1395_HCC1395T 1 0.984 177 1,48 0,68 1,120 NA 0/1 NA NA NA NA 1,0,120,56 C/A PANCANCER NA FALSE PSG4 chr19:43204756:43204757:C:A SNV 2:0 chr19:38706105:49429505:2:0:1 TRUE NA 0.96 +chr19 44113365 44113366 C G 8 31 0.258064516129032 MODIFIER ZNF225 ENSG00000256294 G upstream_gene_variant Transcript ENST00000262894 protein_coding NA 34 1 SNV HGNC HGNC:13018 YES NM_013362.4 1 P1 CCDS46100.1 ENSP00000262894 Q9UK10.183 UPI000016960F 11 NA NA PASS SITE 38,24|5,3 NA NA 2 82 20,28 152,170 60,60 36 1.42 NA 7.48 NA FALSE 6.00 35 NA NA NA FALSE NA NA 20.85 11 44113365 HCC1395_HCC1395T 23 0.292 31 7,1 9,4 16,6 NA 0/1 NA NA NA NA 16,7,5,3 C/G PANCANCER NA FALSE ZNF225 chr19:44113365:44113366:C:G SNV 2:0 chr19:38706105:49429505:2:0:1 TRUE NA 0.96 +chr19 44213096 44213097 G C 4 11 0.363636363636364 MODIFIER ZNF227 ENSG00000131115 C 5_prime_UTR_variant Transcript ENST00000313040 protein_coding 2/6 ENST00000313040.12:c.-151G>C NA 61 1 SNV HGNC HGNC:13020 YES NM_182490.3 1 P1 CCDS12636.1 ENSP00000321049 Q86WZ6.164 UPI000000DC17 Q86WZ6-1 11 NA NA PASS SITE 21,10|3,1 NA NA 1 51 20,29 156,164 60,60 13 1.25 NA 5.07 NA FALSE 6.00 45 NA NA NA FALSE NA NA 10.75 11 44213096 HCC1395_HCC1395T 7 0.361 11 2,2 4,1 6,3 NA 0/1 NA NA NA NA 6,1,3,1 G/C PANCANCER NA FALSE ZNF227 chr19:44213096:44213097:G:C SNV 2:0 chr19:38706105:49429505:2:0:1 TRUE NA 0.96 +chr19 44919295 44919296 A G 80 80 1 MODIFIER APOC1 ENSG00000130208 G 3_prime_UTR_variant Transcript ENST00000586638 protein_coding 3/3 ENST00000586638.5:c.*72A>G NA 374 1 SNV HGNC HGNC:607 3 ENSP00000466146 K7ELM9.53 UPI0002840C14 11 NA NA PASS SITE 84,74|40,40 NA NA 1 93 20,20 164,171 60,60 36 1.98 NA 28.55 NA FALSE 6.00 93 NA NA NA FALSE NA NA 225.02 11 44919295 HCC1395_HCC1395T 0 0.980 80 0,18 0,27 0,49 NA 0/1 NA NA NA NA 0,0,40,40 A/G PANCANCER NA FALSE APOC1 chr19:44919295:44919296:A:G SNV 2:0 chr19:38706105:49429505:2:0:1 TRUE NA 0.96 +chr19 47843282 47843283 C G 47 47 1 MODIFIER CRX ENSG00000105392 G 3_prime_UTR_variant Transcript ENST00000221996 protein_coding 4/4 ENST00000221996.12:c.*3315C>G NA 4324 1 SNV HGNC HGNC:2383 YES NM_000554.6 2 P1 CCDS12706.1 ENSP00000221996 O43186.206 UPI00001284E0 1 11 NA NA PASS SITE 24,31|23,24 NA NA 1 93 20,20 145,155 60,60 35 1.54 NA 10.23 NA FALSE 6.00 93 NA NA NA FALSE NA NA 143.49 11 47843282 HCC1395_HCC1395T 0 0.970 47 0,11 0,16 0,31 NA 0/1 NA NA NA NA 0,0,23,24 C/G PANCANCER NA FALSE CRX chr19:47843282:47843283:C:G SNV 2:0 chr19:38706105:49429505:2:0:1 TRUE NA 0.96 +chr19 49182562 49182563 C T 97 176 0.551136363636364 LOW TRPM4 ENSG00000130529 T splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000252826 protein_coding 10/24 ENST00000252826.10:c.1264-16C>T NA 1 SNV HGNC HGNC:17993 YES NM_017636.4 1 P1 CCDS33073.1 ENSP00000252826 Q8TD43.157 UPI0000070598 Q8TD43-1 1 11 NA NA PASS SITE 238,170|58,39 NA NA 1 93 20,20 154,162 60,60 38 2.34 NA 65.26 NA FALSE 6.00 93 NA NA NA FALSE NA NA 246.11 11 49182562 HCC1395_HCC1395T 79 0.542 176 20,21 23,40 54,64 NA 0/1 NA NA NA NA 43,36,58,39 C/T PANCANCER NA FALSE TRPM4 chr19:49182562:49182563:C:T SNV 2:0 chr19:38706105:49429505:2:0:1 TRUE NA 0.96 +chr19 49342311 49342312 G C 32 32 1 MODIFIER TEAD2 ENSG00000074219 C intron_variant Transcript ENST00000311227 protein_coding 11/11 ENST00000311227.6:c.1230+127C>G NA -1 SNV HGNC HGNC:11715 1 A1 CCDS12761.1 ENSP00000310701 Q15562.193 UPI0000136B7D Q15562-1 11 NA NA PASS SITE 30,15|22,10 NA NA 1 93 35,20 187,148 60,60 34 1.54 NA 10.23 NA FALSE 6.00 93 NA NA NA FALSE NA NA 104.22 11 49342311 HCC1395_HCC1395T 0 0.962 32 0,8 0,13 0,24 NA 0/1 NA NA NA NA 0,0,22,10 G/C PANCANCER NA FALSE TEAD2 chr19:49342311:49342312:G:C SNV 2:0 chr19:38706105:49429505:2:0:1 TRUE NA 0.96 +chr19 50625546 50625547 G A 21 94 0.223404255319149 MODERATE SYT3 ENSG00000213023 A missense_variant Transcript ENST00000338916 protein_coding 6/9 ENST00000338916.8:c.1421C>T ENSP00000340914.3:p.S474F ENSP00000340914.3 p.S474F 2055 1421 474 S/F tCc/tTc COSV58899619 -1 SNV HGNC HGNC:11511 1 P1 CCDS12798.1 ENSP00000340914 Q9BQG1.179 A0A024R4I9.66 UPI0000047AEB deleterious(0) Gene3D:2.60.40.150&AlphaFold_DB_import:AF-Q9BQG1-F1&Pfam:PF00168&PROSITE_profiles:PS50004&PANTHER:PTHR10024&SMART:SM00239&Superfamily:SSF49562&CDD:cd08403 1 1 11 NA NA PASS SITE 64,86|10,11 NA NA 1 93 20,29 154,177 60,60 36 1.74 NA 15.95 NA FALSE 6.00 68 NA NA NA FALSE NA NA 51.48 11 50625546 HCC1395_HCC1395T 73 0.274 94 23,6 17,9 44,16 NA 0/1 NA NA NA NA 31,42,10,11 G/A PANCANCER NA FALSE SYT3_p.S474F chr19:50625546:50625547:G:A SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 50798096 50798097 C G 70 129 0.542635658914729 MODIFIER ACP4 ENSG00000142513 G downstream_gene_variant Transcript ENST00000270593 protein_coding NA 2877 1 SNV HGNC HGNC:14376 YES NM_033068.3 1 P1 CCDS12802.1 ENSP00000270593 Q9BZG2.138 UPI0000048D54 Q9BZG2-1 1 11 NA NA PASS SITE 86,66|39,31 NA NA 1 93 35,37 176,203 60,60 31 1.86 NA 21.07 NA FALSE 6.00 93 NA NA NA FALSE NA NA 219.06 11 50798096 HCC1395_HCC1395T 59 0.538 129 23,23 23,31 48,56 NA 0/1 NA NA NA NA 35,24,39,31 C/G PANCANCER NA FALSE ACP4 chr19:50798096:50798097:C:G SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 51079713 51079714 C T 22 123 0.178861788617886 LOW KLK14 ENSG00000129437 T splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000156499 protein_coding 4/7 ENST00000156499.7:c.213-11G>A NA rs908205782 -1 SNV HGNC HGNC:6362 1 P1 CCDS12823.3 ENSP00000156499 A0A1R3UHJ7.25 UPI000004CA08 6.663e-06 0 0 0 0 0 1.701e-05 0 0 1.701e-05 gnomADe_NFE 11 NA NA PASS SITE 39,156|2,20 NA NA 1 93 36,35 180,177 60,60 13 1.88 NA 22.23 NA FALSE 6.00 68 NA NA NA FALSE NA NA 57.25 11 51079713 HCC1395_HCC1395T 101 0.198 123 28,7 44,13 84,20 NA 0/1 NA NA NA NA 19,82,2,20 C/T PANCANCER NA FALSE KLK14 chr19:51079713:51079714:C:T SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 51601700 51601701 C T 146 588 0.248299319727891 MODIFIER ENSG00000269388 T non_coding_transcript_exon_variant Transcript ENST00000596210 transcribed_processed_pseudogene 2/2 ENST00000596210.1:n.922C>T NA 922 rs1025938376 1 SNV YES 11 NA NA PASS SITE 493,458|76,70 NA NA 1 93 20,20 147,163 60,60 35 2.50 NA 93.92 NA FALSE 6.00 93 NA NA NA FALSE NA NA 325.75 11 51601700 HCC1395_HCC1395T 442 0.255 588 124,41 146,50 280,95 NA 0/1 NA NA NA NA 225,217,76,70 C/T PANCANCER NA FALSE chr19:51601700:51601701:C:T SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 51717343 51717344 A T 32 154 0.207792207792208 MODIFIER HAS1 ENSG00000105509 T intron_variant Transcript ENST00000222115 protein_coding 2/4 ENST00000222115.5:c.703-150T>A NA -1 SNV HGNC HGNC:4818 1 A1 CCDS12838.1 ENSP00000222115 Q92839.179 UPI000006D531 11 NA NA PASS SITE 111,109|15,17 NA NA 1 93 20,20 161,157 60,60 35 1.79 NA 18.36 NA FALSE 6.00 93 NA NA NA FALSE NA NA 70.13 11 51717343 HCC1395_HCC1395T 122 0.219 154 34,9 39,9 76,21 NA 0/1 NA NA NA NA 62,60,15,17 A/T PANCANCER NA FALSE HAS1 chr19:51717343:51717344:A:T SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 52915359 52915360 G C 59 104 0.567307692307692 MODIFIER ZNF888 ENSG00000213793 C intron_variant&non_coding_transcript_variant Transcript ENST00000596623 protein_coding_CDS_not_defined 3/4 ENST00000596623.2:n.425-37C>G NA -1 SNV HGNC HGNC:38695 5 11 NA NA PASS SITE 70,91|22,37 NA NA 1 93 20,20 182,203 49,55 37 1.95 NA 25.28 NA FALSE 6.00 93 NA NA NA FALSE NA NA 171.14 11 52915359 HCC1395_HCC1395T 45 0.570 104 14,11 11,16 33,44 NA 0/1 NA NA NA NA 21,24,22,37 G/C PANCANCER NA FALSE ZNF888 chr19:52915359:52915360:G:C SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 54821683 54821684 G A 145 420 0.345238095238095 LOW KIR3DL1 ENSG00000167633 A synonymous_variant Transcript ENST00000326542 protein_coding 5/8 ENST00000326542.11:c.774G>A ENSP00000326868.7:p.E258= ENSP00000326868.7 p.E258= 788 774 258 E gaG/gaA rs112686751 1 SNV HGNC HGNC:6338 1 A2 ENSP00000326868 W5QJC1.53 UPI000013E084 1 Pfam:PF00047&Gene3D:2.60.40.10&SMART:SM00409&Superfamily:SSF48726&AlphaFold_DB_import:AF-W5QJC1-F1 5.566e-06 7.602e-05 0 0 0 0 0 0 0 6.61e-06 0 0 0 0 0 0 0 1.472e-05 0 0 7.602e-05 gnomADe_AFR 11 NA NA PASS SITE 290,232|78,67 NA NA 1 93 20,20 159,165 60,60 37 2.20 NA 46.67 NA FALSE 6.00 93 NA NA NA FALSE NA NA 340.34 11 54821683 HCC1395_HCC1395T 275 0.338 420 78,38 97,51 181,92 NA 0/1 NA NA NA NA 152,123,78,67 G/A PANCANCER NA FALSE KIR3DL1_p.E258= chr19:54821683:54821684:G:A SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 55226999 55227000 G C 58 108 0.537037037037037 MODIFIER TMEM86B ENSG00000180089 C 3_prime_UTR_variant Transcript ENST00000327042 protein_coding 3/3 ENST00000327042.5:c.*182C>G NA 885 -1 SNV HGNC HGNC:28448 YES NM_173804.5 1 P1 CCDS12920.1 ENSP00000321038 Q8N661.131 UPI0000141ABB 11 NA NA PASS SITE 77,81|28,30 NA NA 1 93 20,20 148,150 60,60 44 1.82 NA 19.57 NA FALSE 6.00 93 NA NA NA FALSE NA NA 147.81 11 55226999 HCC1395_HCC1395T 50 0.493 108 17,15 20,21 38,37 NA 0/1 NA NA NA NA 26,24,28,30 G/C PANCANCER NA FALSE TMEM86B chr19:55226999:55227000:G:C SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 55440641 55440642 G T 104 700 0.148571428571429 MODERATE SHISA7 ENSG00000187902 T missense_variant Transcript ENST00000376325 protein_coding 2/4 ENST00000376325.10:c.796C>A ENSP00000365503.3:p.L266I ENSP00000365503.3 p.L266I 1233 796 266 L/I Ctc/Atc COSV100890883 -1 SNV HGNC HGNC:35409 YES NM_001145176.2 2 P2 CCDS46193.1 ENSP00000365503 A6NL88.100 UPI000193055E deleterious(0.03) benign(0.34) PANTHER:PTHR31774&AlphaFold_DB_import:AF-A6NL88-F1 1 1 11 NA NA PASS SITE 529,554|50,54 NA NA 1 93 20,20 158,162 60,60 33 2.51 NA 95.36 NA FALSE 6.00 93 NA NA NA FALSE NA NA 225.94 11 55440641 HCC1395_HCC1395T 596 0.155 700 176,30 186,34 391,72 NA 0/1 NA NA NA NA 293,303,50,54 G/T PANCANCER NA FALSE SHISA7_p.L266I chr19:55440641:55440642:G:T SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 55486070 55486071 C A 78 158 0.493670886075949 MODIFIER NAT14 ENSG00000090971 A intron_variant Transcript ENST00000205194 protein_coding 2/2 ENST00000205194.5:c.72+290C>A NA 1 SNV HGNC HGNC:28918 YES NM_020378.4 1 P1 CCDS12926.1 ENSP00000205194 Q8WUY8.144 UPI000006EC7E 11 NA NA PASS SITE 109,101|38,40 NA NA 1 93 20,20 157,163 60,60 31 1.94 NA 25.88 NA FALSE 6.00 49 NA NA NA FALSE NA NA 192.16 11 55486070 HCC1395_HCC1395T 80 0.481 158 18,10 36,37 56,52 NA 0/1 NA NA NA NA 42,38,38,40 C/A PANCANCER NA FALSE NAT14 chr19:55486070:55486071:C:A SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 55732557 55732558 C T 52 285 0.182456140350877 MODERATE NLRP9 ENSG00000185792 T missense_variant Transcript ENST00000332836 protein_coding 2/9 ENST00000332836.7:c.1274G>A ENSP00000331857.2:p.G425D ENSP00000331857.2 p.G425D 1302 1274 425 G/D gGc/gAc COSV60468733 -1 SNV HGNC HGNC:22941 YES NM_176820.4 1 P1 CCDS12934.1 ENSP00000331857 Q7RTR0.156 UPI00001B6B39 Q7RTR0-1 tolerated(0.39) benign(0.006) AlphaFold_DB_import:AF-Q7RTR0-F1&Pfam:PF17779&PANTHER:PTHR45690 1 1 11 NA NA PASS SITE 159,230|18,34 NA NA 1 93 20,20 158,180 60,60 30 2.02 NA 30.31 NA FALSE 6.00 85 NA NA NA FALSE NA NA 113.19 11 55732557 HCC1395_HCC1395T 233 0.198 285 57,13 75,17 149,36 NA 0/1 NA NA NA NA 99,134,18,34 C/T PANCANCER NA FALSE NLRP9_p.G425D chr19:55732557:55732558:C:T SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 55924760 55924761 G C 12 77 0.155844155844156 MODIFIER NLRP13 ENSG00000173572 C intron_variant Transcript ENST00000342929 protein_coding 2/10 ENST00000342929.4:c.389-102C>G NA -1 SNV HGNC HGNC:22937 YES NM_176810.2 1 P2 CCDS33119.1 ENSP00000343891 Q86W25.155 UPI00001AEEC8 11 NA NA PASS SITE 33,67|5,7 NA NA 1 93 20,20 181,137 60,60 31 1.41 NA 7.22 NA FALSE 6.00 69 NA NA NA FALSE NA NA 23.91 11 55924760 HCC1395_HCC1395T 65 0.150 77 18,3 29,5 50,8 NA 0/1 NA NA NA NA 17,48,5,7 G/C PANCANCER NA FALSE NLRP13 chr19:55924760:55924761:G:C SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 57130037 57130038 C G 131 242 0.541322314049587 LOW USP29 ENSG00000131864 G synonymous_variant Transcript ENST00000254181 protein_coding 4/4 ENST00000254181.9:c.1362C>G ENSP00000254181.3:p.L454= ENSP00000254181.3 p.L454= 1874 1362 454 L ctC/ctG COSV54141827 1 SNV HGNC HGNC:18563 YES NM_020903.3 1 P1 CCDS33124.1 ENSP00000254181 Q9HBJ7.155 UPI0000137A01 PROSITE_profiles:PS50235&CDD:cd02257&PANTHER:PTHR24006&Gene3D:3.90.70.10&Pfam:PF00443&Superfamily:SSF54001&AlphaFold_DB_import:AF-Q9HBJ7-F1 1 1 11 NA NA PASS SITE 114,129|71,60 NA NA 1 93 20,20 173,177 60,60 30 1.98 NA 27.69 NA FALSE 6.00 93 NA NA NA FALSE NA NA 373.90 11 57130037 HCC1395_HCC1395T 111 0.543 242 32,30 39,57 78,93 NA 0/1 NA NA NA NA 53,58,71,60 C/G PANCANCER NA FALSE USP29_p.L454= chr19:57130037:57130038:C:G SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 57213066 57213067 G C 47 47 1 MODIFIER ZNF264 ENSG00000083844 C 3_prime_UTR_variant Transcript ENST00000263095 protein_coding 4/4 ENST00000263095.10:c.*85G>C NA 2383 rs1398684423 1 SNV HGNC HGNC:13057 YES NM_003417.5 2 P1 CCDS33127.1 ENSP00000263095 O43296.187 UPI000013C33B 11 NA NA PASS SITE 17,21|20,27 NA NA 1 93 20,20 167,174 60,60 29 1.46 NA 8.43 NA FALSE 6.00 93 NA NA NA FALSE NA NA 154.61 11 57213066 HCC1395_HCC1395T 0 0.973 47 0,15 0,17 0,34 NA 0/1 NA NA NA NA 0,0,20,27 G/C PANCANCER NA FALSE ZNF264 chr19:57213066:57213067:G:C SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 57397066 57397067 G T 154 349 0.441260744985673 MODERATE ZNF548 ENSG00000188785 T missense_variant Transcript ENST00000336128 protein_coding 3/4 ENST00000336128.12:c.70G>T ENSP00000337555.6:p.D24Y ENSP00000337555.6 p.D24Y 316 70 24 D/Y Gac/Tac COSV60240767 1 SNV HGNC HGNC:26561 YES NM_001172773.2 2 A2 CCDS54324.1 ENSP00000337555 Q8NEK5.159 UPI000059D7C2 Q8NEK5-2 deleterious(0) probably_damaging(0.98) PROSITE_profiles:PS50805&CDD:cd07765&PANTHER:PTHR24381&Pfam:PF01352&Gene3D:6.10.140.140&SMART:SM00349&Superfamily:SSF109640&AlphaFold_DB_import:AF-Q8NEK5-F1 1 1 11 NA NA PASS SITE 213,181|84,71 NA NA 1 93 20,20 161,158 60,60 31 2.13 NA 39.54 NA FALSE 6.00 93 NA NA NA FALSE NA NA 390.59 11 57397066 HCC1395_HCC1395T 195 0.466 349 45,42 69,59 123,107 NA 0/1 NA NA NA NA 105,90,84,70 G/T PANCANCER NA FALSE ZNF548_p.D24Y chr19:57397066:57397067:G:T SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 58279880 58279881 T A 12 57 0.210526315789474 MODIFIER ZNF544 ENSG00000198131 A downstream_gene_variant Transcript ENST00000595981 protein_coding NA 2385 1 SNV HGNC HGNC:16759 3 CCDS92700.1 ENSP00000470843 M0QZY0.58 UPI0002A470E5 11 NA NA PASS SITE 38,58|3,9 NA NA 1 93 20,25 177,145 60,60 29 1.58 NA 10.84 NA FALSE 6.00 15 NA NA NA FALSE NA NA 21.23 11 58279880 HCC1395_HCC1395T 45 0.205 57 8,0 12,3 36,9 NA 0/1 NA NA NA NA 18,27,3,9 T/A PANCANCER NA FALSE ZNF544 chr19:58279880:58279881:T:A SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 58387450 58387451 G C 76 76 1 MODIFIER RPS5 ENSG00000083845 C intron_variant Transcript ENST00000196551 protein_coding 1/5 ENST00000196551.8:c.-2+111G>C NA 1 SNV HGNC HGNC:10426 YES NM_001009.4 1 P1 CCDS12978.1 ENSP00000196551 P46782.213 A0A024R4Q8.48 UPI0000135052 11 NA NA PASS SITE 21,21|32,44 NA NA 1 93 37,35 197,174 60,60 22 1.57 NA 10.53 NA FALSE 6.00 93 NA NA NA FALSE NA NA 261.92 11 58387450 HCC1395_HCC1395T 0 0.984 76 0,18 0,38 0,60 NA 0/1 NA NA NA NA 0,0,32,44 G/C PANCANCER NA FALSE RPS5 chr19:58387450:58387451:G:C SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr19 58408619 58408620 C T 130 130 1 MODIFIER ZNF584 ENSG00000171574 T upstream_gene_variant Transcript ENST00000306910 protein_coding NA 30 1 SNV HGNC HGNC:27318 YES NM_173548.3 1 P1 CCDS12979.1 ENSP00000306756 Q8IVC4.148 UPI000007465A 11 NA NA PASS SITE 78,63|77,53 NA NA 1 93 20,20 155,162 60,60 35 1.97 NA 27.95 NA FALSE 6.00 93 NA NA NA FALSE NA NA 367.40 11 58408619 HCC1395_HCC1395T 0 0.989 130 0,29 0,51 0,85 NA 0/1 NA NA NA NA 0,0,77,53 C/T PANCANCER NA FALSE ZNF584 chr19:58408619:58408620:C:T SNV 3:0 chr19:49451759:58478128:3:0:1 NA NA 0.96 +chr20 646781 646782 G T 9 498 0.0180722891566265 MODIFIER SRXN1 ENSG00000271303 T 3_prime_UTR_variant Transcript ENST00000381962 protein_coding 2/2 ENST00000381962.4:c.*1933C>A NA 2362 -1 SNV HGNC HGNC:16132 YES NM_080725.3 1 P1 CCDS13005.1 ENSP00000371388 Q9BYN0.167 UPI000000DC3B 13 NA NA PASS SITE 455,347|5,4 NA NA 1 93 20,37 169,179 60,60 27 2.37 NA 67.62 NA FALSE 6.00 36 NA NA NA FALSE NA NA 14.16 13 646781 HCC1395_HCC1395T 489 0.022 498 130,3 201,4 362,7 NA 0/1 NA NA NA NA 285,204,5,4 G/T PANCANCER NA FALSE SRXN1 chr20:646781:646782:G:T SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 2312958 2312959 C T 122 208 0.586538461538462 MODERATE TGM3 ENSG00000125780 T missense_variant Transcript ENST00000381458 protein_coding 5/13 ENST00000381458.6:c.601C>T ENSP00000370867.5:p.R201C ENSP00000370867.5 p.R201C 664 601 201 R/C Cgt/Tgt rs143880505&COSV67350329 1 SNV HGNC HGNC:11779 YES NM_003245.4 1 P1 CCDS33435.1 ENSP00000370867 Q08188.207 UPI0000136CCC 1 deleterious(0) probably_damaging(0.998) PDB-ENSP_mappings:1l9m.A&PDB-ENSP_mappings:1l9m.B&PDB-ENSP_mappings:1l9n.A&PDB-ENSP_mappings:1l9n.B&PDB-ENSP_mappings:1nud.A&PDB-ENSP_mappings:1nud.B&PDB-ENSP_mappings:1nuf.A&PDB-ENSP_mappings:1nug.A&PDB-ENSP_mappings:1nug.B&PANTHER:PTHR11590&Gene3D:3.90.260.10&PIRSF:PIRSF000459&Superfamily:SSF54001&AlphaFold_DB_import:AF-Q08188-F1 3.185e-05 6.152e-05 0 0 5.438e-05 0 2.643e-05 0 9.799e-05 1.314e-05 0 0 0 0.0002882 0 0 0 1.47e-05 0 0 0.0002882 gnomADg_ASJ 0&1 0&1 13 NA NA PASS SITE 101,148|42,80 NA NA 1 93 20,20 161,165 60,60 38 2.04 NA 32.50 NA FALSE 4.61 93 NA NA NA FALSE NA NA 338.39 13 2312958 HCC1395_HCC1395T 86 0.614 208 16,23 32,51 53,85 NA 0/1 NA NA NA NA 34,52,42,80 C/T PANCANCER NA FALSE TGM3_p.R201C chr20:2312958:2312959:C:T SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 4182497 4182498 C A 86 140 0.614285714285714 MODERATE SMOX ENSG00000088826 A missense_variant Transcript ENST00000278795 protein_coding 6/9 ENST00000278795.7:c.859C>A ENSP00000278795.3:p.Q287K ENSP00000278795.3 p.Q287K 1084 859 287 Q/K Cag/Aag COSV53869357 1 SNV HGNC HGNC:15862 1 CCDS13078.1 ENSP00000278795 Q9NWM0.170 UPI0000160842 Q9NWM0-4 deleterious(0.03) benign(0.02) PANTHER:PTHR10742&Gene3D:3.50.50.60&Gene3D:3.90.660.10&Pfam:PF01593&Superfamily:SSF51905&AlphaFold_DB_import:AF-Q9NWM0-F1 1 1 13 NA NA PASS SITE 96,147|30,56 NA NA 1 93 20,20 162,168 60,60 28 2.10 NA 37.88 NA FALSE 6.00 93 NA NA NA FALSE NA NA 248.72 13 4182497 HCC1395_HCC1395T 54 0.609 140 16,33 22,27 41,64 NA 0/1 NA NA NA NA 21,33,30,56 C/A PANCANCER NA FALSE SMOX_p.Q287K chr20:4182497:4182498:C:A SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 4780598 4780599 C A 15 34 0.441176470588235 MODIFIER RASSF2 ENSG00000101265 A 3_prime_UTR_variant Transcript ENST00000379376 protein_coding 11/11 ENST00000379376.2:c.*3675G>T NA 4710 -1 SNV HGNC HGNC:9883 1 P1 CCDS13083.1 ENSP00000368684 P50749.174 UPI0000001C0A P50749-1 13 NA NA PASS SITE 21,36|8,7 NA NA 1 79 20,20 164,177 60,60 41 1.41 NA 7.53 NA FALSE 6.00 41 NA NA NA FALSE NA NA 39.80 13 4780598 HCC1395_HCC1395T 19 0.480 34 5,3 4,7 12,11 NA 0/1 NA NA NA NA 8,11,8,7 C/A PANCANCER NA FALSE RASSF2 chr20:4780598:4780599:C:A SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 5168677 5168678 C T 41 72 0.569444444444444 MODIFIER CDS2 ENSG00000101290 T intron_variant Transcript ENST00000450570 protein_coding 1/8 ENST00000450570.1:c.30-6506C>T NA 1 cds_end_NF SNV HGNC HGNC:1801 3 ENSP00000403205 O95674.180 UPI0000470AAD O95674-2 13 NA NA PASS SITE 24,57|10,31 NA NA 1 93 20,32 166,186 60,60 26 1.59 NA 11.09 NA FALSE 6.00 93 NA NA NA FALSE NA NA 112.90 13 5168677 HCC1395_HCC1395T 31 0.593 72 7,11 14,16 21,31 NA 0/1 NA NA NA NA 10,21,10,31 C/T PANCANCER NA FALSE CDS2 chr20:5168677:5168678:C:T SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 5186614 5186615 A T 92 133 0.691729323308271 MODIFIER CDS2 ENSG00000101290 T intron_variant&non_coding_transcript_variant Transcript ENST00000379070 protein_coding_CDS_not_defined 6/9 ENST00000379070.3:n.1084-73A>T NA rs76319104 1 SNV HGNC HGNC:1801 2 0.0144 0.0492 0.0072 0 0.002 0 0.01031 0.03437 0 0.005634 0.00346 0 0 0.01274 0.0003677 0.009091 0 0.0492 AFR 13 NA NA PASS SITE 128,34|67,25 NA NA 1 93 36,33 182,173 60,60 30 1.99 NA 28.59 NA FALSE 2.05 93 NA NA NA FALSE NA NA 275.65 13 5186614 HCC1395_HCC1395T 41 0.670 133 7,33 26,36 34,70 NA 0/1 NA NA NA NA 34,7,67,25 A/T PANCANCER NA FALSE CDS2 chr20:5186614:5186615:A:T SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 5943958 5943959 C A 38 70 0.542857142857143 HIGH TRMT6 ENSG00000089195 A stop_gained Transcript ENST00000203001 protein_coding 5/11 ENST00000203001.7:c.532G>T ENSP00000203001.2:p.G178* ENSP00000203001.2 p.G178* 660 532 178 G/* Gga/Tga COSV52546233 -1 SNV HGNC HGNC:20900 YES NM_015939.5 1 P1 CCDS13093.1 ENSP00000203001 Q9UJA5.160 UPI000006D9E4 Q9UJA5-1 PDB-ENSP_mappings:5ccb.B&PDB-ENSP_mappings:5ccx.B&PDB-ENSP_mappings:5cd1.B&PDB-ENSP_mappings:5cd1.E&AlphaFold_DB_import:AF-Q9UJA5-F1&Pfam:PF04189&PIRSF:PIRSF038170&PANTHER:PTHR12945 1 1 13 NA NA PASS SITE 35,32|20,18 NA NA 1 76 20,20 173,153 60,60 25 1.39 NA 6.92 NA FALSE 6.00 76 NA NA NA FALSE NA NA 87.45 13 5943958 HCC1395_HCC1395T 32 0.537 70 6,8 10,13 18,21 NA 0/1 NA NA NA NA 16,16,20,18 C/A PANCANCER NA FALSE TRMT6_p.G178* chr20:5943958:5943959:C:A SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 6006318 6006319 G C 29 47 0.617021276595745 LOW CRLS1 ENSG00000088766 C synonymous_variant Transcript ENST00000378863 protein_coding 1/7 ENST00000378863.9:c.72G>C ENSP00000368140.4:p.R24= ENSP00000368140.4 p.R24= 196 72 24 R cgG/cgC 1 SNV HGNC HGNC:16148 YES NM_019095.6 1 P2 CCDS13096.1 ENSP00000368140 Q9UJA2.155 UPI000003B001 Q9UJA2-1 AlphaFold_DB_import:AF-Q9UJA2-F1 13 NA NA PASS SITE 59,40|14,15 NA NA 1 93 20,37 167,171 60,60 27 1.75 NA 16.51 NA FALSE 6.00 93 NA NA NA FALSE NA NA 88.96 13 6006318 HCC1395_HCC1395T 18 0.622 47 5,12 7,9 13,22 NA 0/1 NA NA NA NA 12,6,14,15 G/C PANCANCER NA FALSE CRLS1_p.R24= chr20:6006318:6006319:G:C SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 10054509 10054510 G C 60 85 0.705882352941177 MODERATE ANKEF1 ENSG00000132623 C missense_variant Transcript ENST00000378380 protein_coding 9/10 ENST00000378380.4:c.2082G>C ENSP00000367631.3:p.K694N ENSP00000367631.3 p.K694N 2411 2082 694 K/N aaG/aaC COSV65693250&COSV65694056 1 SNV HGNC HGNC:15803 2 P1 CCDS13108.1 ENSP00000367631 Q9NU02.165 UPI0000125B51 deleterious(0.05) benign(0.001) Gene3D:1.25.40.20&AlphaFold_DB_import:AF-Q9NU02-F1&PANTHER:PTHR24127 1&1 1&1 13 NA NA PASS SITE 71,46|36,24 NA NA 1 93 20,20 161,166 60,60 29 1.81 NA 18.96 NA FALSE 6.00 83 NA NA NA FALSE NA NA 178.94 13 10054509 HCC1395_HCC1395T 25 0.733 85 4,8 11,33 15,43 NA 0/1 NA NA NA NA 15,10,36,24 G/C PANCANCER NA FALSE ANKEF1_p.K694N chr20:10054509:10054510:G:C SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 17693696 17693697 GAGGAACAAAGGTAAGGCAGATTGGTCTGACTTCCTTGCTCA G 23 99 0.232323232323232 HIGH BANF2 ENSG00000125888 - splice_donor_variant&splice_donor_5th_base_variant&coding_sequence_variant&intron_variant Transcript ENST00000545418 protein_coding 1/3 1/2 ENST00000545418.2:c.9_18+31del NA 26-? 9-? 3-? 1 deletion HGNC HGNC:16172 3 CCDS54449.1 ENSP00000439128 Q9H503.150 UPI00019D3EDD Q9H503-2 13 NA NA PASS SITE 68,122|1,22 NA NA 2 93 20,40 169,170 60,60 29 1.89 NA 23.18 NA FALSE 6.00 93 NA NA NA FALSE NA NA 82.54 13 17693696 HCC1395_HCC1395T 76 0.316 99 6,3 28,2 49,22 NA 0|1 0|1 17693692_CTG_C NA 17693692 30,46,1,22 GAGGAACAAAGGTAAGGCAGATTGGTCTGACTTCCTTGCTCA|G PANCANCER NA FALSE BANF2 chr20:17693696:17693697:GAGGAACAAAGGTAAGGCAGATTGGTCTGACTTCCTTGCTCA:G indel 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 23354059 23354060 C G 95 225 0.422222222222222 MODERATE NXT1 ENSG00000132661 G missense_variant Transcript ENST00000254998 protein_coding 2/2 ENST00000254998.3:c.18C>G ENSP00000254998.2:p.F6L ENSP00000254998.2 p.F6L 350 18 6 F/L ttC/ttG 1 SNV HGNC HGNC:15913 YES NM_013248.3 1 P1 CCDS13150.1 ENSP00000254998 Q9UKK6.173 UPI0000111F8B tolerated(0.43) benign(0.197) PDB-ENSP_mappings:1jkg.A&PDB-ENSP_mappings:1jn5.A&PDB-ENSP_mappings:4wyk.B&PDB-ENSP_mappings:4wyk.D&PDB-ENSP_mappings:6e5u.B&PDB-ENSP_mappings:6e5u.D&PDB-ENSP_mappings:6e5u.F&PDB-ENSP_mappings:6e5u.H&Gene3D:3.10.450.50&Superfamily:SSF54427&AlphaFold_DB_import:AF-Q9UKK6-F1 13 NA NA PASS SITE 139,132|44,51 NA NA 1 93 20,20 154,154 60,60 34 1.97 NA 27.69 NA FALSE 6.00 93 NA NA NA FALSE NA NA 223.17 13 23354059 HCC1395_HCC1395T 130 0.403 225 44,25 38,28 85,57 NA 0/1 NA NA NA NA 64,66,44,51 C/G PANCANCER NA FALSE NXT1_p.F6L chr20:23354059:23354060:C:G SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 25297805 25297806 C T 14 74 0.189189189189189 MODIFIER PYGB ENSG00000100994 T 3_prime_UTR_variant Transcript ENST00000216962 protein_coding 20/20 ENST00000216962.9:c.*1283C>T NA 3909 rs201924587 1 SNV HGNC HGNC:9723 YES NM_002862.4 1 P1 CCDS13171.1 ENSP00000216962 P11216.233 UPI0000131A0A 3.995e-05 0 0 0 0 0 0 0 8.885e-05 0 0 8.885e-05 gnomADg_NFE 13 NA NA PASS SITE 59,73|7,7 NA NA 1 93 20,20 155,148 60,60 27 1.68 NA 14.15 NA FALSE 4.61 53 NA NA NA FALSE NA NA 31.65 13 25297805 HCC1395_HCC1395T 60 0.208 74 18,4 20,4 41,10 NA 0/1 NA NA NA NA 27,33,7,7 C/T PANCANCER NA FALSE PYGB chr20:25297805:25297806:C:T SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 31412779 31412780 A T 61 247 0.246963562753036 MODIFIER DEFB121 ENSG00000204548 T non_coding_transcript_exon_variant Transcript ENST00000376312 protein_coding_CDS_not_defined 1/2 ENST00000376312.3:n.60T>A NA 60 -1 SNV HGNC HGNC:18101 1 13 NA NA PASS SITE 108,238|18,43 NA NA 1 93 20,20 165,176 60,60 28 2.07 NA 34.61 NA FALSE 6.00 93 NA NA NA FALSE NA NA 150.03 13 31412779 HCC1395_HCC1395T 186 0.263 247 46,15 70,22 128,45 NA 0/1 NA NA NA NA 60,126,18,43 A/T PANCANCER NA FALSE DEFB121 chr20:31412779:31412780:A:T SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 31514436 31514437 C G 21 71 0.295774647887324 MODIFIER HM13 ENSG00000101294 G 5_prime_UTR_variant Transcript ENST00000340852 protein_coding 1/12 ENST00000340852.9:c.-116C>G NA 9 rs544785957 1 SNV HGNC HGNC:16435 1 P2 CCDS13182.1 ENSP00000343032 Q8TCT9.186 A0A0S2Z5V7.32 UPI000000D7D8 Q8TCT9-1 0.0002 0.0008 0 0 0 0 6.575e-06 2.415e-05 0 0 0 0 0 0 0 0 0 0.0008 AFR 13 NA NA PASS SITE 79,52|14,7 NA NA 1 93 20,20 160,175 60,60 29 1.72 NA 15.35 NA FALSE 6.00 78 NA NA NA FALSE NA NA 50.78 13 31514436 HCC1395_HCC1395T 50 0.304 71 14,5 21,8 35,15 NA 0/1 NA NA NA NA 32,18,14,7 C/G PANCANCER NA FALSE HM13 chr20:31514436:31514437:C:G SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 31666142 31666143 G A 48 184 0.260869565217391 MODIFIER BCL2L1 ENSG00000171552 A intron_variant Transcript ENST00000307677 protein_coding 2/2 ENST00000307677.5:c.565-56C>T NA -1 SNV HGNC HGNC:992 YES NM_138578.3 1 P1 CCDS13189.1 ENSP00000302564 Q07817.248 A0A0S2Z3C5.44 UPI0000000CEC Q07817-1 13 NA NA PASS SITE 126,184|25,24 NA NA 1 93 20,20 159,182 60,60 34 2.04 NA 32.44 NA FALSE 6.00 90 NA NA NA FALSE NA NA 98.43 13 31666142 HCC1395_HCC1395T 136 0.248 184 34,11 48,15 89,29 NA 0/1 NA NA NA NA 53,83,25,23 G/A PANCANCER NA FALSE BCL2L1 chr20:31666142:31666143:G:A SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 32216942 32216943 C T 48 85 0.564705882352941 MODIFIER POFUT1 ENSG00000101346 T intron_variant Transcript ENST00000375730 protein_coding 4/4 ENST00000375730.3:c.543-66C>T NA rs62207420 1 SNV HGNC HGNC:14988 1 CCDS13199.1 ENSP00000364882 Q9H488.181 UPI000002B016 Q9H488-2 1 13 NA NA PASS SITE 88,41|33,15 NA NA 1 93 20,20 174,197 60,60 28 1.84 NA 20.17 NA FALSE 6.00 93 NA NA NA FALSE NA NA 136.43 13 32216942 HCC1395_HCC1395T 37 0.602 85 9,11 15,22 24,37 NA 0/1 NA NA NA NA 23,14,33,15 C/T PANCANCER NA FALSE POFUT1 chr20:32216942:32216943:C:T SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 32358684 32358685 C G 22 58 0.379310344827586 MODIFIER ASXL1 ENSG00000171456 G upstream_gene_variant Transcript ENST00000306058 protein_coding NA rs886056592 1063 1 SNV HGNC HGNC:18318 1 ENSP00000305119 Q76L82.115 UPI00001DFBE9 1 1 13 NA NA PASS SITE 61,21|17,5 NA NA 1 93 36,26 176,161 60,60 17 1.61 NA 11.44 NA FALSE 6.00 81 NA NA NA FALSE NA NA 51.72 13 32358684 HCC1395_HCC1395T 36 0.375 58 11,12 18,5 29,17 NA 0/1 NA NA NA NA 25,11,17,5 C/G PANCANCER NA FALSE ASXL1 chr20:32358684:32358685:C:G SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 33217479 33217480 C G 37 54 0.685185185185185 MODIFIER BPIFA3 ENSG00000131059 G 5_prime_UTR_variant Transcript ENST00000375452 protein_coding 1/6 ENST00000375452.3:c.-58C>G NA 128 1 SNV HGNC HGNC:16204 1 CCDS42865.1 ENSP00000364601 Q9BQP9.146 UPI000023C877 Q9BQP9-2 13 NA NA PASS SITE 40,47|13,24 NA NA 1 93 20,36 178,167 60,60 19 1.70 NA 14.75 NA FALSE 6.00 93 NA NA NA FALSE NA NA 118.09 13 33217479 HCC1395_HCC1395T 17 0.698 54 3,9 7,16 12,29 NA 0/1 NA NA NA NA 7,10,13,24 C/G PANCANCER NA FALSE BPIFA3 chr20:33217479:33217480:C:G SNV 2:1 chr20:145888:33678033:2:1:1 TRUE NA 0.96 +chr20 34882686 34882687 C T 14 71 0.197183098591549 MODIFIER ACSS2 ENSG00000131069 T intron_variant Transcript ENST00000253382 protein_coding 1/18 ENST00000253382.5:c.179-108C>T NA 1 SNV HGNC HGNC:15814 2 A1 CCDS42868.2 ENSP00000253382 Q9NR19.174 UPI00004709E0 Q9NR19-2 13 NA NA PASS SITE 81,34|9,5 NA NA 1 93 35,28 172,161 60,60 37 1.63 NA 12.29 NA FALSE 6.00 39 NA NA NA FALSE NA NA 33.92 13 34882686 HCC1395_HCC1395T 57 0.196 71 21,3 25,8 48,11 NA 0/1 NA NA NA NA 44,13,9,5 C/T PANCANCER NA FALSE ACSS2 chr20:34882686:34882687:C:T SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 35092906 35092907 G A 47 396 0.118686868686869 MODIFIER TRPC4AP ENSG00000100991 A upstream_gene_variant Transcript ENST00000252015 protein_coding NA rs888922171 99 -1 SNV HGNC HGNC:16181 YES NM_015638.3 1 P4 CCDS13246.1 ENSP00000252015 Q8TEL6.161 UPI000004FADD Q8TEL6-1 13 NA NA PASS SITE 307,322|23,24 NA NA 1 93 20,20 163,170 60,60 29 2.26 NA 52.58 NA FALSE 6.00 91 NA NA NA FALSE NA NA 95.91 13 35092906 HCC1395_HCC1395T 349 0.129 396 86,12 119,16 215,31 NA 0/1 NA NA NA NA 167,182,23,24 G/A PANCANCER NA FALSE TRPC4AP chr20:35092906:35092907:G:A SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 35384132 35384133 C G 99 217 0.456221198156682 MODERATE UQCC1 ENSG00000101019 G missense_variant&splice_region_variant Transcript ENST00000349714 protein_coding 3/9 ENST00000349714.9:c.131G>C ENSP00000335364.6:p.W44S ENSP00000335364.6 p.W44S 131 131 44 W/S tGg/tCg COSV62903951 -1 SNV HGNC HGNC:15891 5 ENSP00000335364 Q9NVA1.164 UPI00002371A9 Q9NVA1-4 tolerated_low_confidence(0.44) benign(0.003) PANTHER:PTHR12184&AlphaFold_DB_import:AF-Q9NVA1-F1 1 1 13 NA NA PASS SITE 119,149|44,55 NA NA 1 93 20,20 159,164 60,60 37 2.00 NA 29.15 NA FALSE 6.00 93 NA NA NA FALSE NA NA 261.92 13 35384132 HCC1395_HCC1395T 118 0.479 217 27,20 35,37 73,67 NA 0/1 NA NA NA NA 53,65,44,55 C/G PANCANCER NA FALSE UQCC1_p.W44S chr20:35384132:35384133:C:G SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 35411782 35411783 C G 19 40 0.475 MODIFIER UQCC1 ENSG00000101019 G intron_variant Transcript ENST00000349714 protein_coding 1/8 ENST00000349714.9:c.24+158G>C NA -1 SNV HGNC HGNC:15891 5 ENSP00000335364 Q9NVA1.164 UPI00002371A9 Q9NVA1-4 13 NA NA PASS SITE 38,6|18,1 NA NA 1 60 39,42 182,198 60,60 26 1.36 NA 6.32 NA FALSE 6.00 75 NA NA NA FALSE NA NA 66.92 13 35411782 HCC1395_HCC1395T 21 0.500 40 5,5 13,13 18,18 NA 0/1 NA NA NA NA 18,3,18,1 C/G PANCANCER NA FALSE UQCC1 chr20:35411782:35411783:C:G SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 35650480 35650481 C G 151 335 0.450746268656716 MODIFIER CPNE1 ENSG00000214078 G intron_variant Transcript ENST00000317677 protein_coding 1/15 ENST00000317677.9:c.15+3048G>C NA -1 SNV HGNC HGNC:2314 1 CCDS46595.1 ENSP00000317257 B0QZ18.112 UPI0000D4B36B 13 NA NA PASS SITE 248,158|98,53 NA NA 1 93 20,20 173,175 60,60 40 2.18 NA 45.15 NA FALSE 6.00 93 NA NA NA FALSE NA NA 404.91 13 35650480 HCC1395_HCC1395T 184 0.454 335 51,40 71,59 125,104 NA 0/1 NA NA NA NA 115,69,98,53 C/G PANCANCER NA FALSE CPNE1 chr20:35650480:35650481:C:G SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 35734879 35734880 C T 102 238 0.428571428571429 MODIFIER RBM39 ENSG00000131051 T intron_variant Transcript ENST00000253363 protein_coding 3/16 ENST00000253363.11:c.102-2744G>A NA -1 SNV HGNC HGNC:15923 YES NM_184234.3 1 CCDS13266.1 ENSP00000253363 Q14498.225 A0A384NQ03.22 UPI0000134418 Q14498-1 13 NA NA PASS SITE 192,160|61,41 NA NA 1 93 20,20 175,196 60,60 25 2.20 NA 46.66 NA FALSE 6.00 93 NA NA NA FALSE NA NA 276.05 13 35734879 HCC1395_HCC1395T 136 0.421 238 40,25 55,44 105,76 NA 0/1 NA NA NA NA 78,58,61,41 C/T PANCANCER NA FALSE RBM39 chr20:35734879:35734880:C:T SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 37859763 37859764 A T 28 53 0.528301886792453 MODIFIER CTNNBL1 ENSG00000132792 T intron_variant Transcript ENST00000361383 protein_coding 13/15 ENST00000361383.11:c.1393-136A>T NA 1 SNV HGNC HGNC:15879 YES NM_030877.5 1 P1 CCDS13298.1 ENSP00000355050 Q8WYA6.171 UPI0000061E09 Q8WYA6-1 1 13 NA NA PASS SITE 37,10|20,8 NA NA 1 49 36,20 186,167 60,60 19 1.28 NA 5.42 NA FALSE 6.00 91 NA NA NA FALSE NA NA 73.09 13 37859763 HCC1395_HCC1395T 25 0.500 53 4,7 16,12 20,20 NA 0/1 NA NA NA NA 20,5,20,8 A/T PANCANCER NA FALSE CTNNBL1 chr20:37859763:37859764:A:T SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 38000259 38000260 G A 10 42 0.238095238095238 MODIFIER TTI1 ENSG00000101407 A intron_variant Transcript ENST00000373447 protein_coding 4/7 ENST00000373447.8:c.2653-931C>T NA -1 SNV HGNC HGNC:29029 YES NM_001303457.2 1 P1 CCDS13300.1 ENSP00000362546 O43156.173 UPI000012DB27 13 NA NA PASS SITE 54,10|7,3 NA NA 1 93 39,36 194,168 60,60 32 1.45 NA 8.13 NA FALSE 6.00 15 NA NA NA FALSE NA NA 25.18 13 38000259 HCC1395_HCC1395T 32 0.230 42 13,1 16,7 29,8 NA 0/1 NA NA NA NA 29,3,7,3 G/A PANCANCER NA FALSE TTI1 chr20:38000259:38000260:G:A SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 41164014 41164015 G C 173 279 0.620071684587814 LOW PLCG1 ENSG00000124181 C splice_region_variant&intron_variant Transcript ENST00000244007 protein_coding 12/32 ENST00000244007.7:c.1096+8G>C NA 1 SNV HGNC HGNC:9065 5 P3 CCDS13313.1 ENSP00000244007 P19174.256 UPI00001B94DD P19174-2 1 13 NA NA PASS SITE 178,141|89,84 NA NA 1 93 20,20 161,159 60,60 31 2.17 NA 43.60 NA FALSE 6.00 93 NA NA NA FALSE NA NA 457.66 13 41164014 HCC1395_HCC1395T 106 0.601 279 31,47 40,57 76,115 NA 0/1 NA NA NA NA 59,47,89,84 G/C PANCANCER TRUE FALSE PLCG1 chr20:41164014:41164015:G:C SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 41165772 41165773 C G 71 135 0.525925925925926 MODERATE PLCG1 ENSG00000124181 G missense_variant Transcript ENST00000244007 protein_coding 17/33 ENST00000244007.7:c.1745C>G ENSP00000244007.3:p.S582C ENSP00000244007.3 p.S582C 1942 1745 582 S/C tCc/tGc COSV54822565 1 SNV HGNC HGNC:9065 5 P3 CCDS13313.1 ENSP00000244007 P19174.256 UPI00001B94DD P19174-2 1 deleterious_low_confidence(0) probably_damaging(0.912) PDB-ENSP_mappings:4ey0.A&PDB-ENSP_mappings:4ey0.B&PDB-ENSP_mappings:4ey0.C&PDB-ENSP_mappings:4ey0.D&PDB-ENSP_mappings:4fbn.A&PDB-ENSP_mappings:7nxe.A&CDD:cd10341&PIRSF:PIRSF000952&Gene3D:3.30.505.10&Pfam:PF00017&SMART:SM00233&SMART:SM00252&Superfamily:SSF55550&Superfamily:SSF51695&PROSITE_profiles:PS50001&PANTHER:PTHR10336&AlphaFold_DB_import:AF-P19174-F1 1 1 13 NA NA PASS SITE 117,64|40,31 NA NA 1 93 36,20 176,148 60,60 35 1.97 NA 27.39 NA FALSE 6.00 93 NA NA NA FALSE NA NA 200.86 13 41165772 HCC1395_HCC1395T 64 0.500 135 17,18 31,31 50,50 NA 0/1 NA NA NA NA 43,21,40,31 C/G PANCANCER TRUE TRUE PLCG1_p.S582C chr20:41165772:41165773:C:G SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 41267637 41267638 G C 4 10 0.4 MODIFIER ZHX3 ENSG00000174306 C intron_variant Transcript ENST00000309060 protein_coding 2/4 ENST00000309060.7:c.-199+1342C>G NA -1 SNV HGNC HGNC:15935 5 P1 CCDS13315.1 ENSP00000312222 Q9H4I2.187 UPI000000D72C Q9H4I2-1 13 NA NA PASS SITE 4,13|1,3 NA NA 1 24 37,30 185,184 60,60 47 0.954 NA 2.41 NA FALSE 6.00 51 NA NA NA FALSE NA NA 10.99 13 41267637 HCC1395_HCC1395T 6 0.364 10 2,1 2,2 6,3 NA 0/1 NA NA NA NA 0,6,1,3 G/C PANCANCER NA FALSE ZHX3 chr20:41267637:41267638:G:C SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 41440135 41440136 C G 210 415 0.506024096385542 LOW CHD6 ENSG00000124177 G splice_region_variant&splice_polypyrimidine_tract_variant&intron_variant Transcript ENST00000373233 protein_coding 25/36 ENST00000373233.8:c.3878-6G>C NA rs755873030&COSV58553726 -1 SNV HGNC HGNC:19057 YES NM_032221.5 1 P1 CCDS13317.1 ENSP00000362330 Q8TD26.191 UPI0000168656 Q8TD26-1 7.97e-06 6.152e-05 0 0 0 0 8.821e-06 0 0 1.971e-05 7.239e-05 0 0 0 0 0 0 0 0 0 7.239e-05 gnomADg_AFR 0&1 0&1 13 NA NA PASS SITE 210,257|99,111 NA NA 1 93 20,20 155,154 60,60 38 2.21 NA 48.46 NA FALSE 6.00 93 NA NA NA FALSE NA NA 525.76 13 41440135 HCC1395_HCC1395T 205 0.495 415 45,46 76,80 133,130 NA 0/1 NA NA NA NA 91,114,99,111 C/G PANCANCER NA FALSE CHD6 chr20:41440135:41440136:C:G SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 44054176 44054177 G A 57 138 0.41304347826087 MODIFIER TOX2 ENSG00000124191 A intron_variant Transcript ENST00000341197 protein_coding 4/8 ENST00000341197.9:c.652-123G>A NA rs866063716 1 SNV HGNC HGNC:16095 YES NM_001098797.2 2 P4 CCDS46603.1 ENSP00000344724 Q96NM4.177 UPI000040F535 Q96NM4-4 0.0003353 0.0001933 0 0.0002617 0 0 0 0 0.0002352 0.0004789 0.004561 0.004561 gnomADg_SAS 13 NA NA PASS SITE 96,103|29,28 NA NA 1 93 20,20 153,148 60,60 33 1.90 NA 23.43 NA FALSE 4.13 93 NA NA NA FALSE NA NA 135.15 13 44054176 HCC1395_HCC1395T 81 0.407 138 24,17 27,18 54,37 NA 0/1 NA NA NA NA 38,43,29,28 G/A PANCANCER NA FALSE TOX2 chr20:44054176:44054177:G:A SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 44492757 44492758 C T 140 266 0.526315789473684 MODIFIER SERINC3 ENSG00000132824 T downstream_gene_variant Transcript ENST00000255175 protein_coding NA 3467 -1 SNV HGNC HGNC:11699 5 P1 CCDS13333.1 ENSP00000255175 Q13530.177 UPI0000136B4D Q13530-1 13 NA NA PASS SITE 149,121|73,67 NA NA 1 93 20,20 176,178 60,60 28 2.00 NA 29.20 NA FALSE 6.00 93 NA NA NA FALSE NA NA 376.13 13 44492757 HCC1395_HCC1395T 126 0.521 266 34,27 57,67 92,100 NA 0/1 NA NA NA NA 71,55,73,67 C/T PANCANCER NA FALSE SERINC3 chr20:44492757:44492758:C:T SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 44619552 44619553 G A 32 69 0.463768115942029 MODIFIER PKIG ENSG00000168734 A downstream_gene_variant Transcript ENST00000349959 protein_coding NA rs188755077 515 1 SNV HGNC HGNC:9019 1 P1 CCDS13334.1 ENSP00000338067 Q9Y2B9.157 Q549H9.150 UPI000012D7F5 0.0008 0 0.0043 0 0.001 0 0.0005655 0.0001449 0 0.001309 0 0 0 0 0.000853 0.0009569 0 0.0043 AMR likely_benign 1 13 NA NA PASS SITE 50,32|22,10 NA NA 1 55 20,20 159,172 60,60 35 1.48 NA 8.73 NA FALSE 3.18 80 NA NA NA FALSE NA NA 83.19 13 44619552 HCC1395_HCC1395T 37 0.482 69 6,8 17,15 26,24 NA 0/1 NA NA NA NA 23,14,22,10 G/A PANCANCER NA FALSE PKIG chr20:44619552:44619553:G:A SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 44727434 44727435 C G 24 56 0.428571428571429 MODIFIER CCN5 ENSG00000064205 G 3_prime_UTR_variant Transcript ENST00000190983 protein_coding 4/4 ENST00000190983.5:c.*127C>G NA 902 1 SNV HGNC HGNC:12770 YES NM_003881.4 1 P1 CCDS13336.1 ENSP00000190983 O76076.179 UPI0000037219 O76076-1 13 NA NA PASS SITE 34,40|13,11 NA NA 1 92 20,20 175,131 60,60 35 1.51 NA 9.33 NA FALSE 6.00 86 NA NA NA FALSE NA NA 64.25 13 44727434 HCC1395_HCC1395T 32 0.408 56 9,6 11,8 24,16 NA 0/1 NA NA NA NA 14,18,13,11 C/G PANCANCER NA FALSE CCN5 chr20:44727434:44727435:C:G SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 45421558 45421559 C T 10 57 0.175438596491228 LOW PIGT ENSG00000124155 T synonymous_variant Transcript ENST00000279035 protein_coding 7/10 ENST00000279035.14:c.903C>T ENSP00000279035.8:p.T301= ENSP00000279035.8 p.T301= 976 903 301 T acC/acT 1 SNV HGNC HGNC:14938 2 CCDS54466.1 ENSP00000279035 Q969N2.173 UPI000023FF17 Q969N2-4 1 AlphaFold_DB_import:AF-Q969N2-F1&Pfam:PF04113&PANTHER:PTHR12959 13 NA NA PASS SITE 33,53|3,7 NA NA 1 93 20,37 163,177 60,60 34 1.50 NA 9.03 NA FALSE 6.00 17 NA NA NA FALSE NA NA 26.03 13 45421558 HCC1395_HCC1395T 47 0.219 57 10,1 20,7 31,8 NA 0/1 NA NA NA NA 20,27,3,7 C/T PANCANCER NA FALSE PIGT_p.T301= chr20:45421558:45421559:C:T SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 51693765 51693766 G A 7 42 0.166666666666667 MODIFIER ATP9A ENSG00000054793 A intron_variant Transcript ENST00000311637 protein_coding 4/22 ENST00000311637.9:c.392-17557C>T NA rs761419563 -1 SNV HGNC HGNC:13540 1 ENSP00000309086 A0A0A0MR22.53 UPI00004709CC 1 13 NA NA PASS SITE 31,24|3,4 NA NA 1 59 20,20 155,140 60,60 41 1.09 NA 3.31 NA FALSE 6.00 23 NA NA NA FALSE NA NA 13.24 13 51693765 HCC1395_HCC1395T 35 0.167 42 11,1 12,2 24,4 NA 0/1 NA NA NA NA 22,13,3,4 G/A PANCANCER NA FALSE ATP9A chr20:51693765:51693766:G:A SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 57340103 57340104 CTA C 106 216 0.490740740740741 HIGH SPO11 ENSG00000054796 - frameshift_variant&splice_region_variant Transcript ENST00000345868 protein_coding 10/12 ENST00000345868.8:c.772_773del ENSP00000316034.4:p.M258Vfs*3 ENSP00000316034.4 p.M258Vfs*3 826-827 771-772 257-258 SM/SX tcTAtg/tctg 1 deletion HGNC HGNC:11250 1 CCDS13457.1 ENSP00000316034 Q9Y5K1.177 UPI000007217D Q9Y5K1-2 Gene3D:3.40.1360.10&AlphaFold_DB_import:AF-Q9Y5K1-F1&Prints:PR01551&PANTHER:PTHR10848&Superfamily:SSF56726&CDD:cd00223 1 13 NA NA PASS SITE 121,104|57,49 NA NA 1 93 20,20 169,164 60,60 36 1.89 NA 22.57 NA FALSE 6.00 93 NA NA NA FALSE NA NA 284.97 13 57340103 HCC1395_HCC1395T 110 0.486 216 21,19 38,39 70,66 NA 0/1 NA NA NA NA 59,51,57,49 CTA/C PANCANCER NA FALSE SPO11_p.M258Vfs*3 chr20:57340103:57340104:CTA:C indel 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 58771335 58771336 C G 28 122 0.229508196721311 MODIFIER PIEZO1P2 ENSG00000237121 G intron_variant&non_coding_transcript_variant Transcript ENST00000416241 unprocessed_pseudogene 5/13 ENST00000416241.1:n.743+813G>C NA -1 SNV HGNC HGNC:42861 YES 13 NA NA PASS SITE 91,95|13,15 NA NA 1 93 20,20 153,152 60,60 43 1.76 NA 16.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 72.11 13 58771335 HCC1395_HCC1395T 94 0.256 122 17,9 36,11 60,20 NA 0/1 NA NA NA NA 45,49,13,15 C/G PANCANCER NA FALSE PIEZO1P2 chr20:58771335:58771336:C:G SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 59026831 59026832 C T 57 106 0.537735849056604 MODIFIER TUBB1 ENSG00000101162 T downstream_gene_variant Transcript ENST00000217133 protein_coding NA 177 1 SNV HGNC HGNC:16257 YES NM_030773.4 1 P1 CCDS13475.1 ENSP00000217133 Q9H4B7.173 UPI0000071B14 1 13 NA NA PASS SITE 42,81|19,38 NA NA 1 93 38,33 196,191 60,60 32 1.77 NA 17.46 NA FALSE 6.00 93 NA NA NA FALSE NA NA 164.06 13 59026831 HCC1395_HCC1395T 49 0.528 106 18,18 19,28 41,46 NA 0/1 NA NA NA NA 17,32,19,38 C/T PANCANCER NA FALSE TUBB1 chr20:59026831:59026832:C:T SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 59944226 59944227 A G 100 211 0.4739336492891 MODERATE FAM217B ENSG00000196227 G missense_variant Transcript ENST00000358293 protein_coding 5/5 ENST00000358293.7:c.283A>G ENSP00000351040.3:p.S95G ENSP00000351040.3 p.S95G 698 283 95 S/G Agt/Ggt rs1180582304&COSV62565297 1 SNV HGNC HGNC:16170 2 P1 CCDS13484.1 ENSP00000351040 Q9NTX9.135 UPI0000128624 deleterious(0) probably_damaging(0.986) Low_complexity_(Seg):seg&PANTHER:PTHR22145&Pfam:PF15344&AlphaFold_DB_import:AF-Q9NTX9-F1 6.571e-06 0 0 0 0 0.0001925 0 0 0 0 0 0.0001925 gnomADg_EAS 0&1 0&1 13 NA NA PASS SITE 117,89|58,42 NA NA 1 93 20,20 165,152 60,60 26 1.82 NA 19.26 NA FALSE 4.61 93 NA NA NA FALSE NA NA 263.82 13 59944226 HCC1395_HCC1395T 111 0.491 211 32,31 39,33 72,70 NA 0/1 NA NA NA NA 63,48,58,42 A/G PANCANCER NA FALSE FAM217B_p.S95G chr20:59944226:59944227:A:G SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 62965800 62965801 G A 16 33 0.484848484848485 MODIFIER SLC17A9 ENSG00000101194 A intron_variant Transcript ENST00000370349 protein_coding 11/13 ENST00000370349.7:c.1043+75G>A NA 1 SNV HGNC HGNC:16192 1 CCDS77600.1 ENSP00000359374 Q9BYT1.155 UPI0000073A78 Q9BYT1-2 1 13 NA NA PASS SITE 4,33|2,14 NA NA 1 51 39,35 220,223 60,60 34 1.28 NA 5.42 NA FALSE 6.00 62 NA NA NA FALSE NA NA 50.65 13 62965800 HCC1395_HCC1395T 17 0.500 33 7,5 7,10 15,15 NA 0/1 NA NA NA NA 2,15,2,14 G/A PANCANCER NA FALSE SLC17A9 chr20:62965800:62965801:G:A SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 63587963 63587964 G T 84 178 0.471910112359551 MODIFIER GMEB2 ENSG00000101216 T 3_prime_UTR_variant Transcript ENST00000266068 protein_coding 9/9 ENST00000266068.5:c.*2126C>A NA 4198 -1 SNV HGNC HGNC:4371 2 P1 CCDS13528.1 ENSP00000266068 Q9UKD1.174 UPI000012B8AD 13 NA NA PASS SITE 109,107|43,41 NA NA 1 93 20,20 157,171 60,60 35 1.90 NA 23.43 NA FALSE 6.00 93 NA NA NA FALSE NA NA 219.39 13 63587963 HCC1395_HCC1395T 94 0.496 178 28,23 29,33 60,59 NA 0/1 NA NA NA NA 45,49,43,41 G/T PANCANCER NA FALSE GMEB2 chr20:63587963:63587964:G:T SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 63694680 63694681 G A 65 134 0.485074626865672 MODIFIER RTEL1 ENSG00000258366 A intron_variant Transcript ENST00000318100 protein_coding 30/33 ENST00000318100.9:c.2441-61G>A NA 1 SNV HGNC HGNC:15888 2 CCDS74751.1 ENSP00000322287 Q9NZ71.181 UPI00019B221C Q9NZ71-9 1 13 NA NA PASS SITE 86,54|42,23 NA NA 1 93 20,20 169,173 60,60 30 1.73 NA 15.35 NA FALSE 6.00 93 NA NA NA FALSE NA NA 171.47 13 63694680 HCC1395_HCC1395T 69 0.501 134 15,18 27,27 46,46 NA 0/1 NA NA NA NA 43,26,42,23 G/A PANCANCER NA FALSE RTEL1 chr20:63694680:63694681:G:A SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 64027784 64027785 C T 37 76 0.486842105263158 MODIFIER PRPF6 ENSG00000101161 T intron_variant Transcript ENST00000266079 protein_coding 17/20 ENST00000266079.5:c.2339+48C>T NA COSV53881513 1 SNV HGNC HGNC:15860 YES NM_012469.4 1 P1 CCDS13550.1 ENSP00000266079 O94906.211 UPI0000132356 O94906-1 1 1 1 13 NA NA PASS SITE 11,75|5,32 NA NA 1 93 39,34 198,198 60,60 19 1.63 NA 12.29 NA FALSE 6.00 93 NA NA NA FALSE NA NA 108.71 13 64027784 HCC1395_HCC1395T 39 0.478 76 16,15 15,16 35,32 NA 0/1 NA NA NA NA 4,35,5,32 C/T PANCANCER NA FALSE PRPF6 chr20:64027784:64027785:C:T SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr20 64038223 64038224 C A 60 263 0.228136882129278 MODIFIER C20orf204 ENSG00000196421 A non_coding_transcript_exon_variant Transcript ENST00000358393 retained_intron 1/2 ENST00000358393.1:n.84C>A NA 84 rs1487964095 1 SNV HGNC HGNC:27655 2 1.971e-05 4.823e-05 0 0 0 0 0 0 1.47e-05 0 0 4.823e-05 gnomADg_AFR 13 NA NA PASS SITE 144,213|27,33 NA NA 1 93 20,20 164,156 60,60 19 2.03 NA 31.90 NA FALSE 4.61 93 NA NA NA FALSE NA NA 131.65 13 64038223 HCC1395_HCC1395T 203 0.236 263 64,18 60,16 134,41 NA 0/1 NA NA NA NA 78,125,27,33 C/A PANCANCER NA FALSE C20orf204 chr20:64038223:64038224:C:A SNV 2:2 chr20:33707735:64276168:2:2:1 FALSE NA 0.96 +chr21 29601072 29601073 C T 13 25 0.52 MODIFIER GRIK1 ENSG00000171189 T intron_variant Transcript ENST00000327783 protein_coding 7/17 ENST00000327783.9:c.1099-2135G>A NA -1 SNV HGNC HGNC:4579 YES NM_001330994.2 5 A1 CCDS82659.1 ENSP00000327687 E7ENK3.87 UPI0000E5A39C 14 NA NA PASS SITE 32,11|10,3 NA NA 1 76 37,25 173,209 60,60 30 1.44 NA 7.83 NA FALSE 6.00 58 NA NA NA FALSE NA NA 33.95 14 29601072 HCC1395_HCC1395T 12 0.542 25 0,3 8,5 9,11 NA 0/1 NA NA NA NA 6,6,10,3 C/T PANCANCER NA FALSE GRIK1 chr21:29601072:29601073:C:T SNV 1:1 chr21:13384722:45735402:1:1:1 NA NA 0.96 +chr21 30755336 30755337 C T 53 102 0.519607843137255 MODERATE KRTAP21-1 ENSG00000187005 T missense_variant Transcript ENST00000335093 protein_coding 1/1 ENST00000335093.5:c.43G>A ENSP00000335566.3:p.G15S ENSP00000335566.3 p.G15S 93 43 15 G/S Ggc/Agc rs757919425&COSV58645871&COSV58646235 -1 SNV HGNC HGNC:18945 YES NM_181619.2 P1 CCDS13606.1 ENSP00000335566 Q3LI58.98 UPI00001A9E4A deleterious_low_confidence(0.02) unknown(0) Low_complexity_(Seg):seg&AlphaFold_DB_import:AF-Q3LI58-F1 1.599e-05 0 2.894e-05 0 0 0 8.875e-06 0 6.543e-05 1.974e-05 0 0 6.558e-05 0 0 0 0 1.47e-05 0 0.0002081 0.0002081 gnomADg_SAS 0&1&1 0&1&1 14 NA NA PASS SITE 74,67|29,24 NA NA 1 93 20,20 154,167 60,60 32 1.84 NA 20.12 NA FALSE 6.00 93 NA NA NA FALSE NA NA 132.87 14 30755336 HCC1395_HCC1395T 49 0.507 102 19,15 13,18 32,33 NA 0/1 NA NA NA NA 27,22,29,24 C/T PANCANCER NA FALSE KRTAP21-1_p.G15S chr21:30755336:30755337:C:T SNV 1:1 chr21:13384722:45735402:1:1:1 NA NA 0.96 +chr21 33355811 33355812 A T 2 5 0.4 MODIFIER IFNAR1 ENSG00000142166 T 3_prime_UTR_variant Transcript ENST00000270139 protein_coding 11/11 ENST00000270139.8:c.*262A>T NA 2022 1 SNV HGNC HGNC:5432 YES NM_000629.3 1 P2 CCDS13624.1 ENSP00000270139 P17181.205 UPI000006FE3C P17181-1 1 14 NA NA PASS SITE 1,10|1,1 NA NA 2 24 33,20 230,140 60,40 51 0.954 NA 2.41 NA FALSE 6.00 21 NA NA NA FALSE NA NA 7.70 14 33355811 HCC1395_HCC1395T 3 0.333 5 0,0 1,1 3,1 NA 0|1 0|1 33355811_A_T NA 33355811 1,2,1,1 A|T PANCANCER NA FALSE IFNAR1 chr21:33355811:33355812:A:T SNV 1:1 chr21:13384722:45735402:1:1:1 NA NA 0.96 +chr21 33355813 33355814 C T 2 5 0.4 MODIFIER IFNAR1 ENSG00000142166 T 3_prime_UTR_variant Transcript ENST00000270139 protein_coding 11/11 ENST00000270139.8:c.*264C>T NA 2024 rs949990564 1 SNV HGNC HGNC:5432 YES NM_000629.3 1 P2 CCDS13624.1 ENSP00000270139 P17181.205 UPI000006FE3C P17181-1 1 1.316e-05 0 0 0 0 0.000193 0 0 1.47e-05 0 0 0.000193 gnomADg_EAS 14 NA NA PASS SITE 1,10|1,1 NA NA 2 24 30,20 230,140 60,40 51 0.954 NA 2.41 NA FALSE 6.00 18 NA NA NA FALSE NA NA 7.70 14 33355813 HCC1395_HCC1395T 3 0.333 5 0,0 1,1 3,1 NA 0|1 0|1 33355811_A_T NA 33355811 1,2,1,1 C|T PANCANCER NA FALSE IFNAR1 chr21:33355813:33355814:C:T SNV 1:1 chr21:13384722:45735402:1:1:1 NA NA 0.96 +chr21 41445861 41445862 C T 8 21 0.380952380952381 MODIFIER MX1 ENSG00000157601 T intron_variant Transcript ENST00000288383 protein_coding 12/16 ENST00000288383.11:c.1132-139C>T NA 1 SNV HGNC HGNC:7532 2 ENSP00000288383 F8W8T1.83 UPI00194B05A0 14 NA NA PASS SITE 25,9|7,1 NA NA 1 49 28,37 178,198 60,60 38 1.23 NA 4.82 NA FALSE 6.00 58 NA NA NA FALSE NA NA 24.69 14 41445861 HCC1395_HCC1395T 13 0.421 21 2,3 8,4 10,7 NA 0/1 NA NA NA NA 10,3,7,1 C/T PANCANCER NA FALSE MX1 chr21:41445861:41445862:C:T SNV 1:1 chr21:13384722:45735402:1:1:1 NA NA 0.96 +chr21 42482740 42482741 C G 11 24 0.458333333333333 MODIFIER RSPH1 ENSG00000160188 G intron_variant Transcript ENST00000291536 protein_coding 5/8 ENST00000291536.8:c.502-32G>C NA -1 SNV HGNC HGNC:12371 YES NM_080860.4 1 P1 CCDS13688.1 ENSP00000291536 Q8WYR4.149 UPI000004FA34 Q8WYR4-1 1 14 NA NA PASS SITE 11,29|2,9 NA NA 1 58 20,35 180,185 60,60 13 1.33 NA 5.97 NA FALSE 6.00 67 NA NA NA FALSE NA NA 33.86 14 42482740 HCC1395_HCC1395T 13 0.500 24 5,3 3,6 9,9 NA 0/1 NA NA NA NA 4,9,2,9 C/G PANCANCER NA FALSE RSPH1 chr21:42482740:42482741:C:G SNV 1:1 chr21:13384722:45735402:1:1:1 NA NA 0.96 +chr21 44330789 44330790 AGGCAGCCGCGGCCCCTAGCGGCCC A 103 227 0.45374449339207 MODIFIER CFAP410 ENSG00000160226 - intron_variant Transcript ENST00000325223 protein_coding 6/6 ENST00000325223.7:c.639+10_639+33del NA -1 deletion HGNC HGNC:1260 1 A1 CCDS59445.1 ENSP00000317302 O43822.183 UPI0000206F95 O43822-3 1 14 NA NA PASS SITE 274,286|48,55 NA NA 1 93 20,36 163,182 60,60 37 2.46 NA 83.87 NA FALSE 6.00 93 NA NA NA FALSE NA NA 414.58 14 44330789 HCC1395_HCC1395T 124 0.455 227 22,19 29,34 85,70 NA 0/1 NA NA NA NA 64,60,48,55 AGGCAGCCGCGGCCCCTAGCGGCCC/A PANCANCER NA FALSE CFAP410 chr21:44330789:44330790:AGGCAGCCGCGGCCCCTAGCGGCCC:A indel 1:1 chr21:13384722:45735402:1:1:1 NA NA 0.96 +chr21 44575226 44575227 G T 6 9 0.666666666666667 MODIFIER TSPEAR ENSG00000175894 T intron_variant Transcript ENST00000323084 protein_coding 1/11 ENST00000323084.9:c.83-7221C>A NA -1 SNV HGNC HGNC:1268 YES NM_144991.3 1 P1 CCDS13712.1 ENSP00000321987 Q8WU66.157 UPI0000137746 Q8WU66-1 1 14 NA NA PASS SITE 1,15|2,4 NA NA 1 37 40,28 202,174 60,60 22 1.11 NA 3.61 NA FALSE 6.00 18 NA NA NA FALSE NA NA 16.25 14 44575226 HCC1395_HCC1395T 3 0.600 9 0,3 3,1 3,5 NA 0/1 NA NA NA NA 0,3,2,4 G/T PANCANCER NA FALSE TSPEAR chr21:44575226:44575227:G:T SNV 1:1 chr21:13384722:45735402:1:1:1 NA NA 0.96 +chr21 46209725 46209727 GG AA 15 72 0.208333333333333 MODIFIER LSS ENSG00000160285 AA intron_variant Transcript ENST00000356396 protein_coding 12/22 ENST00000356396.8:c.1195-101_1195-100delinsTT NA -1 substitution HGNC HGNC:6708 1 P1 CCDS13733.1 ENSP00000348762 P48449.203 UPI000012A14D P48449-1 1 14 NA NA PASS SITE 44,97|6,9 NA NA 1 93 20,20 177,153 60,60 23 1.80 NA 18.36 NA FALSE 6.00 56 NA NA NA FALSE NA NA 55.03 14 46209725 HCC1395_HCC1395T 57 0.196 72 14,5 23,4 40,9 NA 0/1 NA NA NA NA 18,39,6,9 GG/AA PANCANCER NA FALSE LSS chr21:46209725:46209727:GG:AA indel 2:1 chr21:45900891:46664908:2:1:1 TRUE NA 0.96 +chr21 46315256 46315257 C T 25 91 0.274725274725275 MODIFIER C21orf58 ENSG00000160298 T intron_variant Transcript ENST00000291691 protein_coding 4/7 ENST00000291691.12:c.444+218G>A NA -1 SNV HGNC HGNC:1300 YES NM_058180.5 2 A2 CCDS13735.1 ENSP00000291691 P58505.135 UPI0000231C71 P58505-1 14 NA NA PASS SITE 57,49|16,9 NA NA 1 93 20,20 154,182 60,60 42 1.49 NA 8.43 NA FALSE 6.00 85 NA NA NA FALSE NA NA 59.97 14 46315256 HCC1395_HCC1395T 66 0.273 91 19,9 27,8 47,17 NA 0/1 NA NA NA NA 36,30,16,9 C/T PANCANCER NA FALSE C21orf58 chr21:46315256:46315257:C:T SNV 2:1 chr21:45900891:46664908:2:1:1 TRUE NA 0.96 +chr22 20065629 20065630 C T 46 46 1 MODIFIER TANGO2 ENSG00000183597 T 3_prime_UTR_variant Transcript ENST00000327374 protein_coding 9/9 ENST00000327374.9:c.*967C>T NA 1974 1 SNV HGNC HGNC:25439 YES NM_152906.7 1 P1 CCDS13772.1 ENSP00000332721 Q6ICL3.130 UPI0000050339 Q6ICL3-1 1 15 NA NA PASS SITE 28,15|32,14 NA NA 1 93 20,20 155,156 60,60 29 1.51 NA 9.33 NA FALSE 6.00 93 NA NA NA FALSE NA NA 145.30 15 20065629 HCC1395_HCC1395T 0 0.971 46 0,15 0,17 0,32 NA 0/1 NA NA NA NA 0,0,32,14 C/T PANCANCER NA FALSE TANGO2 chr22:20065629:20065630:C:T SNV 2:0 chr22:16574679:22668473:2:0:1 TRUE NA 0.96 +chr22 23573199 23573201 AG TA 220 702 0.313390313390313 MODIFIER IGLL1 ENSG00000128322 TA 3_prime_UTR_variant Transcript ENST00000249053 protein_coding 2/2 ENST00000249053.3:c.*337_*338delinsTA NA 641-642 -1 substitution HGNC HGNC:5870 1 CCDS13810.1 ENSP00000249053 P15814.197 UPI00001607AD P15814-2 1 15 NA NA PASS SITE 486,343|132,88 NA NA 1 93 20,20 156,163 60,60 35 2.34 NA 65.32 NA FALSE 6.00 93 NA NA NA FALSE NA NA 781.91 15 23573199 HCC1395_HCC1395T 482 0.320 702 114,50 178,87 312,146 NA 0/1 NA NA NA NA 288,194,132,88 AG/TA PANCANCER NA FALSE IGLL1 chr22:23573199:23573201:AG:TA indel 4:1 chr22:22704256:35067186:4:1:1 NA NA 0.96 +chr22 23765262 23765263 G C 39 84 0.464285714285714 MODIFIER C22orf15 ENSG00000169314 C intron_variant Transcript ENST00000305199 protein_coding 5/5 ENST00000305199.9:c.440+360G>C NA 1 SNV HGNC HGNC:15558 3 CCDS82698.1 ENSP00000305096 F8W7S3.61 UPI000059D870 15 NA NA PASS SITE 78,11|36,3 NA NA 1 93 39,38 183,197 60,60 17 1.61 NA 11.65 NA FALSE 6.00 93 NA NA NA FALSE NA NA 126.52 15 23765262 HCC1395_HCC1395T 45 0.475 84 20,16 19,18 40,36 NA 0/1 NA NA NA NA 39,6,36,3 G/C PANCANCER NA FALSE C22orf15 chr22:23765262:23765263:G:C SNV 4:1 chr22:22704256:35067186:4:1:1 NA NA 0.96 +chr22 23958385 23958386 GCCTGGTCCATGGCAGTCCTGTTGCGTTCCACCTTCTC G 13 898 0.0144766146993318 HIGH GSTT2B ENSG00000133433 - frameshift_variant Transcript ENST00000290765 protein_coding 4/5 ENST00000290765.9:c.388_424del ENSP00000290765.4:p.E130Pfs*21 ENSP00000290765.4 p.E130Pfs*21 452-488 388-424 130-142 EKVERNRTAMDQA/X GAGAAGGTGGAACGCAACAGGACTGCCATGGACCAGGcc/cc -1 deletion HGNC HGNC:33437 YES NM_001080843.4 1 P1 CCDS33617.1 ENSP00000290765 P0CG30.87 G9J6Q5.91 UPI000011244D PDB-ENSP_mappings:1ljr.A&PDB-ENSP_mappings:1ljr.B&PDB-ENSP_mappings:2ljr.A&PDB-ENSP_mappings:2ljr.B&PDB-ENSP_mappings:3ljr.A&PDB-ENSP_mappings:3ljr.B&PDB-ENSP_mappings:4mpg.A&PDB-ENSP_mappings:4mpg.B&PROSITE_profiles:PS50405&CDD:cd03183&PANTHER:PTHR43917&Pfam:PF00043&Gene3D:1.20.1050.10&Superfamily:SSF47616&AlphaFold_DB_import:AF-P0CG30-F1&SFLD:SFLDG00358&SFLD:SFLDG01153 15 NA NA PASS SITE 804,582|7,6 NA NA 1 93 20,20 164,205 43,40 42 2.50 NA 93.81 NA FALSE 6.00 93 NA NA NA FALSE NA NA 38.52 15 23958385 HCC1395_HCC1395T 885 0.015 898 215,2 148,5 534,7 NA 0/1 NA NA NA NA 514,371,7,6 GCCTGGTCCATGGCAGTCCTGTTGCGTTCCACCTTCTC/G PANCANCER NA FALSE GSTT2B_p.E130Pfs*21 chr22:23958385:23958386:GCCTGGTCCATGGCAGTCCTGTTGCGTTCCACCTTCTC:G indel 4:1 chr22:22704256:35067186:4:1:1 NA NA 0.96 +chr22 24628226 24628227 C T 20 155 0.129032258064516 MODIFIER GGT1 ENSG00000100031 T intron_variant Transcript ENST00000400380 protein_coding 15/16 ENST00000400380.5:c.1449+33C>T NA 1 SNV HGNC HGNC:4250 1 P1 CCDS42992.1 ENSP00000383231 P19440.229 A0A140VJJ9.29 UPI000007080C P19440-1 1 15 NA NA PASS SITE 114,110|12,8 NA NA 1 93 20,20 165,160 47,44 41 1.77 NA 17.15 NA FALSE 6.00 43 NA NA NA FALSE NA NA 36.06 15 24628226 HCC1395_HCC1395T 135 0.135 155 47,8 29,4 82,12 NA 0/1 NA NA NA NA 66,69,12,8 C/T PANCANCER NA FALSE GGT1 chr22:24628226:24628227:C:T SNV 4:1 chr22:22704256:35067186:4:1:1 NA NA 0.96 +chr22 25894918 25894919 GAGTGAGCACTCAAGAACTTTAGAC G 49 128 0.3828125 MODIFIER MYO18B ENSG00000133454 - intron_variant Transcript ENST00000335473 protein_coding 27/43 ENST00000335473.12:c.4544-234_4544-211del NA 1 deletion HGNC HGNC:18150 YES NM_032608.7 1 P4 CCDS54507.1 ENSP00000334563 Q8IUG5.172 UPI0000207402 Q8IUG5-1 1 3 15 NA NA PASS SITE 84,53|33,16 NA NA 1 93 20,37 159,192 60,60 29 1.62 NA 11.97 NA FALSE 6.00 93 NA NA NA FALSE NA NA 194.96 15 25894918 HCC1395_HCC1395T 79 0.431 128 17,6 21,28 47,35 NA 0/1 NA NA NA NA 45,34,33,16 GAGTGAGCACTCAAGAACTTTAGAC/G PANCANCER NA FALSE MYO18B chr22:25894918:25894919:GAGTGAGCACTCAAGAACTTTAGAC:G indel 4:1 chr22:22704256:35067186:4:1:1 NA NA 0.96 +chr22 29141977 29141978 G A 175 361 0.484764542936288 LOW KREMEN1 ENSG00000183762 A synonymous_variant Transcript ENST00000327813 protein_coding 9/10 ENST00000327813.9:c.1293G>A ENSP00000331242.5:p.R431= ENSP00000331242.5 p.R431= 1306 1293 431 R agG/agA rs16987147 1 SNV HGNC HGNC:17550 2 CCDS13849.1 ENSP00000331242 Q96MU8.181 UPI000002AD01 Q96MU8-2 1 AlphaFold_DB_import:AF-Q96MU8-F1&PIRSF:PIRSF036961 0.0082 0 0.0173 0.0268 0 0.002 0.008704 0.00156 0.03626 0.0001006 0.0408 0.0003254 0.0001334 0.00605 0.00395 0.003523 0.001762 0 0.01419 0 0.03734 0.0006594 0 0.000147 0.004298 0.005399 0.0408 gnomADe_EAS benign 1 15 NA NA PASS SITE 191,154|95,80 NA NA 1 93 20,20 162,155 60,60 32 2.02 NA 31.26 NA FALSE 2.42 93 NA NA NA FALSE NA NA 432.31 15 29141977 HCC1395_HCC1395T 186 0.480 361 38,41 80,67 122,112 NA 0/1 NA NA NA NA 102,84,95,80 G/A PANCANCER NA FALSE KREMEN1_p.R431= chr22:29141977:29141978:G:A SNV 4:1 chr22:22704256:35067186:4:1:1 NA NA 0.96 +chr22 29536548 29536549 A G 18 80 0.225 MODIFIER THOC5 ENSG00000100296 G intron_variant&NMD_transcript_variant Transcript ENST00000358079 nonsense_mediated_decay 6/18 ENST00000358079.8:c.*344+76T>C NA -1 SNV HGNC HGNC:19074 5 ENSP00000444493 F5GZF3.51 UPI000204A807 15 NA NA PASS SITE 77,15|12,6 NA NA 1 91 38,35 192,176 60,60 20 1.45 NA 7.83 NA FALSE 6.00 77 NA NA NA FALSE NA NA 46.40 15 29536548 HCC1395_HCC1395T 62 0.214 80 22,7 31,7 54,14 NA 0/1 NA NA NA NA 51,11,12,6 A/G PANCANCER NA FALSE THOC5 chr22:29536548:29536549:A:G SNV 4:1 chr22:22704256:35067186:4:1:1 NA NA 0.96 +chr22 31275055 31275056 G T 102 224 0.455357142857143 MODIFIER LIMK2 ENSG00000182541 T intron_variant Transcript ENST00000331728 protein_coding 14/15 ENST00000331728.9:c.1615-96G>T NA 1 SNV HGNC HGNC:6614 YES NM_005569.4 1 A1 CCDS13891.1 ENSP00000332687 P53671.214 A0A024R1H6.58 UPI00000534BD P53671-1 15 NA NA PASS SITE 170,61|69,33 NA NA 1 93 26,20 166,166 60,60 27 1.92 NA 24.64 NA FALSE 6.00 93 NA NA NA FALSE NA NA 273.83 15 31275055 HCC1395_HCC1395T 122 0.441 224 32,27 59,43 93,73 NA 0/1 NA NA NA NA 91,31,69,33 G/T PANCANCER NA FALSE LIMK2 chr22:31275055:31275056:G:T SNV 4:1 chr22:22704256:35067186:4:1:1 NA NA 0.96 +chr22 32082082 32082083 C G 44 88 0.5 MODIFIER SLC5A1 ENSG00000100170 G intron_variant Transcript ENST00000266088 protein_coding 6/14 ENST00000266088.9:c.583+111C>G NA 1 SNV HGNC HGNC:11036 YES NM_000343.4 1 P1 CCDS13902.1 ENSP00000266088 P13866.211 UPI00001359EA P13866-1 1 15 NA NA PASS SITE 16,53|10,34 NA NA 1 60 38,36 196,184 60,60 28 1.33 NA 5.72 NA FALSE 6.00 87 NA NA NA FALSE NA NA 128.55 15 32082082 HCC1395_HCC1395T 44 0.486 88 14,9 18,24 36,34 NA 0/1 NA NA NA NA 10,34,10,34 C/G PANCANCER NA FALSE SLC5A1 chr22:32082082:32082083:C:G SNV 4:1 chr22:22704256:35067186:4:1:1 NA NA 0.96 +chr22 32517993 32517994 C G 166 410 0.404878048780488 MODIFIER SYN3 ENSG00000185666 G intron_variant Transcript ENST00000358763 protein_coding 13/13 ENST00000358763.7:c.1610+50G>C NA -1 SNV HGNC HGNC:11496 YES NM_003490.4 5 P1 CCDS13908.1 ENSP00000351614 O14994.191 A0A024R1I8.53 UPI00001365D3 15 NA NA PASS SITE 270,154|107,59 NA NA 1 93 20,20 164,169 60,60 32 2.11 NA 37.79 NA FALSE 6.00 93 NA NA NA FALSE NA NA 443.44 15 32517993 HCC1395_HCC1395T 244 0.417 410 59,50 97,65 165,118 NA 0/1 NA NA NA NA 151,93,107,59 C/G PANCANCER NA FALSE SYN3 chr22:32517993:32517994:C:G SNV 4:1 chr22:22704256:35067186:4:1:1 NA NA 0.96 +chr22 36864105 36864106 G T 7 595 0.0117647058823529 MODERATE NCF4 ENSG00000100365 T missense_variant Transcript ENST00000248899 protein_coding 2/10 ENST00000248899.11:c.93G>T ENSP00000248899.6:p.E31D ENSP00000248899.6 p.E31D 259 93 31 E/D gaG/gaT COSV50621159 1 SNV HGNC HGNC:7662 YES NM_000631.5 1 P1 CCDS13934.1 ENSP00000248899 Q15080.214 UPI0000049C2C Q15080-1 1 deleterious(0) probably_damaging(0.997) PDB-ENSP_mappings:1h6h.A&PDB-ENSP_mappings:2dyb.A&PDB-ENSP_mappings:2dyb.B&PROSITE_profiles:PS50195&CDD:cd06882&PANTHER:PTHR15706&Gene3D:3.30.1520.10&SMART:SM00312&Superfamily:SSF64268&AlphaFold_DB_import:AF-Q15080-F1 1 1 15 NA NA PASS SITE 463,346|3,4 NA NA 1 93 20,20 158,167 60,60 28 2.15 NA 41.49 NA FALSE 6.00 18 NA NA NA FALSE NA NA 8.60 15 36864105 HCC1395_HCC1395T 588 0.015 595 135,1 237,2 395,5 NA 0/1 NA NA NA NA 344,244,3,4 G/T PANCANCER NA FALSE NCF4_p.E31D chr22:36864105:36864106:G:T SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 37024193 37024194 CCCGCAGCCCGAGTGTCGCCGCCATGGCTTCGCCGCAGCTCTGCCGCGCGCTGGTGT C 5 618 0.00809061488673139 MODIFIER TST ENSG00000128311 - upstream_gene_variant Transcript ENST00000249042 protein_coding NA 4747 -1 deletion HGNC HGNC:12388 YES NM_003312.6 1 P1 CCDS13938.1 ENSP00000249042 Q16762.185 A0A384NKQ2.19 UPI0000167B82 15 NA NA PASS SITE 552,415|2,3 NA NA 1 93 20,39 157,202 60,60 30 2.35 NA 66.21 NA FALSE 6.00 93 NA NA NA FALSE NA NA 13.03 15 37024193 HCC1395_HCC1395T 613 0.010 618 104,1 99,1 394,9 NA 0/1 NA NA NA NA 356,257,2,3 CCCGCAGCCCGAGTGTCGCCGCCATGGCTTCGCCGCAGCTCTGCCGCGCGCTGGTGT/C PANCANCER NA FALSE TST chr22:37024193:37024194:CCCGCAGCCCGAGTGTCGCCGCCATGGCTTCGCCGCAGCTCTGCCGCGCGCTGGTGT:C indel 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 37374978 37374979 G A 106 657 0.161339421613394 MODERATE ELFN2 ENSG00000166897 A missense_variant Transcript ENST00000402918 protein_coding 3/3 ENST00000402918.7:c.557C>T ENSP00000385277.1:p.P186L ENSP00000385277.1 p.P186L 1352 557 186 P/L cCc/cTc -1 SNV HGNC HGNC:29396 YES NM_052906.5 4 P1 CCDS33642.1 ENSP00000385277 Q5R3F8.144 UPI000004E87D deleterious(0) probably_damaging(1) Gene3D:3.80.10.10&AlphaFold_DB_import:AF-Q5R3F8-F1&PANTHER:PTHR24369&Superfamily:SSF52058 15 NA NA PASS SITE 419,495|47,59 NA NA 1 93 20,20 161,170 60,60 28 2.39 NA 72.19 NA FALSE 6.00 93 NA NA NA FALSE NA NA 247.40 15 37374978 HCC1395_HCC1395T 551 0.167 657 148,29 208,43 388,77 NA 0/1 NA NA NA NA 256,295,47,59 G/A PANCANCER NA FALSE ELFN2_p.P186L chr22:37374978:37374979:G:A SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 37570268 37570269 C G 233 541 0.430683918669131 MODERATE LGALS2 ENSG00000100079 G missense_variant Transcript ENST00000215886 protein_coding 4/4 ENST00000215886.6:c.394G>C ENSP00000215886.4:p.E132Q ENSP00000215886.4 p.E132Q 576 394 132 E/Q Gaa/Caa rs1434020843&COSV50759560 -1 SNV HGNC HGNC:6562 YES NM_006498.3 1 P1 CCDS13950.1 ENSP00000215886 P05162.199 UPI00000012CF 1 deleterious_low_confidence(0) unknown(0) PDB-ENSP_mappings:1hlc.A&PDB-ENSP_mappings:1hlc.B&Gene3D:2.60.120.200&PDB-ENSP_mappings:5dg1.A&PDB-ENSP_mappings:5dg1.B&PDB-ENSP_mappings:5dg1.C&PDB-ENSP_mappings:5dg1.D&PDB-ENSP_mappings:5dg1.H&PDB-ENSP_mappings:5dg1.I&PDB-ENSP_mappings:5dg2.A&PDB-ENSP_mappings:5dg2.B&AlphaFold_DB_import:AF-P05162-F1 4.017e-06 0 0 0 0 0 8.874e-06 0 0 8.874e-06 gnomADe_NFE 0&1 0&1 15 NA NA PASS SITE 267,248|123,110 NA NA 1 93 20,20 159,162 60,60 32 2.14 NA 40.94 NA FALSE 6.00 93 NA NA NA FALSE NA NA 576.34 15 37570268 HCC1395_HCC1395T 308 0.419 541 64,47 129,93 204,147 NA 0/1 NA NA NA NA 160,148,123,110 C/G PANCANCER NA FALSE LGALS2_p.E132Q chr22:37570268:37570269:C:G SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 37631021 37631022 C G 76 182 0.417582417582418 MODERATE GGA1 ENSG00000100083 G missense_variant Transcript ENST00000325180 protein_coding 12/15 ENST00000325180.12:c.1189C>G ENSP00000321288.8:p.P397A ENSP00000321288.8 p.P397A 1205 1189 397 P/A Ccc/Gcc COSV57332205 1 SNV HGNC HGNC:17842 1 CCDS33643.1 ENSP00000321288 Q9UJY5.223 UPI000000DA9D Q9UJY5-4 tolerated(0.34) benign(0.001) AlphaFold_DB_import:AF-Q9UJY5-F1&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg 1 1 15 NA NA PASS SITE 103,93|35,41 NA NA 1 93 20,20 148,150 60,60 36 1.72 NA 15.56 NA FALSE 6.00 93 NA NA NA FALSE NA NA 175.76 15 37631021 HCC1395_HCC1395T 106 0.412 182 22,21 39,25 66,46 NA 0/1 NA NA NA NA 54,52,35,41 C/G PANCANCER NA FALSE GGA1_p.P397A chr22:37631021:37631022:C:G SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 37723212 37723213 GA G 75 330 0.227272727272727 MODIFIER TRIOBP ENSG00000100106 - 3_prime_UTR_variant&NMD_transcript_variant Transcript ENST00000344404 nonsense_mediated_decay 5/22 ENST00000344404.10:c.*140del NA 591 1 deletion HGNC HGNC:17009 2 ENSP00000340312 H7BXW4.43 UPI0000410329 1 15 NA NA PASS SITE 259,216|41,34 NA NA 1 93 20,20 153,169 60,60 37 2.18 NA 45.13 NA FALSE 6.00 93 NA NA NA FALSE NA NA 135.71 15 37723212 HCC1395_HCC1395T 255 0.213 330 58,20 85,23 173,46 NA 0/1 NA NA NA NA 142,113,41,34 GA/G PANCANCER NA FALSE TRIOBP chr22:37723212:37723213:GA:G indel 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 38862340 38862341 C T 38 87 0.436781609195402 MODIFIER CBX6 ENSG00000183741 T downstream_gene_variant Transcript ENST00000216083 protein_coding NA 1889 -1 SNV HGNC HGNC:1556 2 A2 CCDS77675.1 ENSP00000216083 B0QXZ6.102 UPI0001611156 15 NA NA PASS SITE 47,61|17,21 NA NA 1 93 20,20 155,174 60,60 30 1.58 NA 10.78 NA FALSE 6.00 93 NA NA NA FALSE NA NA 97.81 15 38862340 HCC1395_HCC1395T 49 0.464 87 8,11 18,13 29,25 NA 0/1 NA NA NA NA 22,27,17,21 C/T PANCANCER NA FALSE CBX6 chr22:38862340:38862341:C:T SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 39025819 39025820 T G 14 71 0.197183098591549 MODIFIER APOBEC3D ENSG00000243811 G intron_variant Transcript ENST00000216099 protein_coding 4/6 ENST00000216099.13:c.605+148T>G NA 1 SNV HGNC HGNC:17354 YES NM_152426.4 2 P1 CCDS46709.1 ENSP00000216099 Q96AK3.149 B2CML4.96 UPI000006D7ED 15 NA NA PASS SITE 28,89|5,9 NA NA 1 93 20,20 171,142 60,60 26 1.68 NA 13.84 NA FALSE 6.00 69 NA NA NA FALSE NA NA 27.73 15 39025819 HCC1395_HCC1395T 57 0.176 71 18,3 20,5 44,9 NA 0/1 NA NA NA NA 13,44,5,9 T/G PANCANCER NA FALSE APOBEC3D chr22:39025819:39025820:T:G SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 41301487 41301488 G A 22 79 0.278481012658228 MODIFIER ZC3H7B ENSG00000100403 A upstream_gene_variant Transcript ENST00000352645 protein_coding NA 38 1 SNV HGNC HGNC:30869 YES NM_017590.6 1 P1 CCDS14013.1 ENSP00000345793 Q9UGR2.191 UPI000002B2AD 15 NA NA PASS SITE 67,43|13,9 NA NA 1 93 20,20 153,163 60,60 34 1.53 NA 9.93 NA FALSE 6.00 47 NA NA NA FALSE NA NA 48.16 15 41301487 HCC1395_HCC1395T 57 0.274 79 17,9 19,4 36,13 NA 0/1 NA NA NA NA 35,22,13,9 G/A PANCANCER NA FALSE ZC3H7B chr22:41301487:41301488:G:A SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 41524891 41524892 G C 144 564 0.25531914893617 MODERATE ACO2 ENSG00000100412 C missense_variant Transcript ENST00000216254 protein_coding 13/18 ENST00000216254.9:c.1528G>C ENSP00000216254.4:p.E510Q ENSP00000216254.4 p.E510Q 1558 1528 510 E/Q Gag/Cag COSV53446677 1 SNV HGNC HGNC:118 YES NM_001098.3 1 P2 CCDS14017.1 ENSP00000216254 Q99798.212 UPI000003CA3B 1 tolerated_low_confidence(0.37) benign(0.003) PANTHER:PTHR43160&TIGRFAM:TIGR01340&Gene3D:3.30.499.10&Superfamily:SSF53732&AlphaFold_DB_import:AF-Q99798-F1 1 1 15 NA NA PASS SITE 411,335|86,58 NA NA 1 93 20,20 160,161 60,60 33 2.34 NA 64.41 NA FALSE 6.00 93 NA NA NA FALSE NA NA 346.54 15 41524891 HCC1395_HCC1395T 420 0.259 564 101,34 159,58 273,95 NA 0/1 NA NA NA NA 236,184,86,58 G/C PANCANCER NA FALSE ACO2_p.E510Q chr22:41524891:41524892:G:C SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 42126774 42126775 C T 16 28 0.571428571428571 MODIFIER CYP2D6 ENSG00000100197 T intron_variant Transcript ENST00000359033 protein_coding 7/7 ENST00000359033.4:c.1163-22G>A NA -1 SNV HGNC HGNC:2625 1 CCDS33657.1 ENSP00000351927 P10635.228 UPI0000EE5AC5 P10635-2 1 15 NA NA PASS SITE 20,21|2,14 NA NA 1 70 38,34 205,186 40,40 14 1.42 NA 7.22 NA FALSE 6.00 74 NA NA NA FALSE NA NA 47.23 15 42126774 HCC1395_HCC1395T 12 0.557 28 5,5 4,7 12,15 NA 0/1 NA NA NA NA 6,6,2,14 C/T PANCANCER NA FALSE CYP2D6 chr22:42126774:42126775:C:T SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 42614995 42614997 GG AA 50 175 0.285714285714286 MODIFIER POLDIP3 ENSG00000100227 AA upstream_gene_variant Transcript ENST00000252115 protein_coding NA 112 -1 substitution HGNC HGNC:23782 YES NM_032311.5 1 P1 CCDS14038.1 ENSP00000252115 Q9BY77.173 UPI000006EEA7 Q9BY77-1 15 NA NA PASS SITE 98,138|20,30 NA NA 1 93 20,25 174,182 60,60 33 1.88 NA 22.28 NA FALSE 6.00 93 NA NA NA FALSE NA NA 186.76 15 42614995 HCC1395_HCC1395T 125 0.291 175 31,15 48,19 89,36 NA 0/1 NA NA NA NA 57,68,20,30 GG/AA PANCANCER NA FALSE POLDIP3 chr22:42614995:42614997:GG:AA indel 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 44570681 44570683 TG GT 13 33 0.393939393939394 MODIFIER LINC00207 ENSG00000187012 GT intron_variant&non_coding_transcript_variant Transcript ENST00000334566 lncRNA 2/3 ENST00000334566.9:n.192+93_192+94delinsGT NA 1 substitution HGNC HGNC:37255 5 15 NA NA PASS SITE 1,34|0,13 NA NA 1 46 37,39 215,233 60,60 19 1.20 NA 4.51 NA FALSE 6.00 51 NA NA NA FALSE NA NA 47.62 15 44570681 HCC1395_HCC1395T 20 0.400 33 8,3 11,9 20,13 NA 0/1 NA NA NA NA 0,20,0,13 TG/GT PANCANCER NA FALSE LINC00207 chr22:44570681:44570683:TG:GT indel 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 45330831 45330832 C G 2 8 0.25 MODIFIER FAM118A ENSG00000100376 G intron_variant Transcript ENST00000216214 protein_coding 6/9 ENST00000216214.7:c.651+100C>G NA 1 SNV HGNC HGNC:1313 2 P1 CCDS14065.1 ENSP00000216214 Q9NWS6.140 A0A024R4V3.53 UPI000022B897 Q9NWS6-1 15 NA NA PASS SITE 0,14|0,2 NA NA 1 26 41,40 208,249 60,60 28 0.974 NA 2.41 NA FALSE 6.00 22 NA NA NA FALSE NA NA 6.55 15 45330831 HCC1395_HCC1395T 6 0.300 8 3,0 3,2 6,2 NA 0/1 NA NA NA NA 0,6,0,2 C/G PANCANCER NA FALSE FAM118A chr22:45330831:45330832:C:G SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 46256398 46256400 AG GA 71 162 0.438271604938272 MODIFIER PKDREJ ENSG00000130943 GA 3_prime_UTR_variant Transcript ENST00000253255 protein_coding 1/1 ENST00000253255.7:c.*162_*163delinsTC NA 6945-6946 -1 substitution HGNC HGNC:9015 YES NM_006071.2 P1 CCDS14073.1 ENSP00000253255 Q9NTG1.162 UPI0000031D01 15 NA NA PASS SITE 100,97|38,33 NA NA 1 93 20,20 165,160 60,60 31 1.86 NA 21.07 NA FALSE 6.00 74 NA NA NA FALSE NA NA 243.86 15 46256398 HCC1395_HCC1395T 91 0.437 162 24,13 36,32 62,48 NA 0/1 NA NA NA NA 50,41,38,33 AG/GA PANCANCER NA FALSE PKDREJ chr22:46256398:46256400:AG:GA indel 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 46257699 46257700 G A 52 235 0.221276595744681 MODERATE PKDREJ ENSG00000130943 A missense_variant Transcript ENST00000253255 protein_coding 1/1 ENST00000253255.7:c.5624C>T ENSP00000253255.5:p.T1875I ENSP00000253255.5 p.T1875I 5645 5624 1875 T/I aCc/aTc rs1203491707&COSV53554066 -1 SNV HGNC HGNC:9015 YES NM_006071.2 P1 CCDS14073.1 ENSP00000253255 Q9NTG1.162 UPI0000031D01 deleterious(0) probably_damaging(0.998) AlphaFold_DB_import:AF-Q9NTG1-F1&Pfam:PF20519&PANTHER:PTHR10877&Transmembrane_helices:TMhelix 2.387e-05 0 0.0001156 0 0 0 1.759e-05 0 0 0.0001156 gnomADe_AMR 0&1 0&1 15 NA NA PASS SITE 143,162|25,27 NA NA 1 93 20,20 171,173 60,60 34 1.94 NA 25.49 NA FALSE 6.00 93 NA NA NA FALSE NA NA 119.19 15 46257699 HCC1395_HCC1395T 183 0.220 235 41,15 85,21 134,37 NA 0/1 NA NA NA NA 87,96,25,27 G/A PANCANCER NA FALSE PKDREJ_p.T1875I chr22:46257699:46257700:G:A SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 47461797 47461798 C T 198 325 0.609230769230769 MODIFIER LINC01644 ENSG00000218357 T non_coding_transcript_exon_variant Transcript ENST00000405369 lncRNA 3/3 ENST00000405369.3:n.486G>A NA 486 rs1243044202 -1 SNV HGNC HGNC:52431 1 15 NA NA PASS SITE 152,148|101,97 NA NA 1 93 20,20 153,151 60,60 34 2.01 NA 30.40 NA FALSE 6.00 93 NA NA NA FALSE NA NA 491.93 15 47461797 HCC1395_HCC1395T 127 0.590 325 29,48 47,63 81,117 NA 0/1 NA NA NA NA 63,64,101,97 C/T PANCANCER NA FALSE LINC01644 chr22:47461797:47461798:C:T SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 50177152 50177153 C T 953 957 0.995820271682341 MODERATE PANX2 ENSG00000073150 T missense_variant Transcript ENST00000159647 protein_coding 2/4 ENST00000159647.9:c.440C>T ENSP00000159647.5:p.S147F ENSP00000159647.5 p.S147F 440 440 147 S/F tCc/tTc rs941735789&COSV50320705 1 SNV HGNC HGNC:8600 1 A2 CCDS54544.1 ENSP00000159647 Q96RD6.155 UPI000173A361 Q96RD6-1 deleterious(0) probably_damaging(0.989) AlphaFold_DB_import:AF-Q96RD6-F1&Pfam:PF00876&PROSITE_profiles:PS51013&PANTHER:PTHR15759 6.568e-06 0 0 0 0 0 0 0 1.47e-05 0 0 1.47e-05 gnomADg_NFE 0&1 0&1 15 NA NA PASS SITE 305,276|502,451 NA NA 1 93 20,20 159,164 60,60 33 2.58 NA 112.23 NA FALSE 6.00 93 NA NA NA FALSE NA NA 2896.05 15 50177152 HCC1395_HCC1395T 4 0.997 957 0,244 1,379 2,655 NA 0/1 NA NA NA NA 2,2,502,451 C/T PANCANCER NA FALSE PANX2_p.S147F chr22:50177152:50177153:C:T SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 50185829 50185830 GCGTGGGACTACACTTCCCGGCATGCCACGCGGCCGCCGGCGCCCTCGGCC G 10 10 1 MODIFIER TRABD ENSG00000170638 - upstream_gene_variant Transcript ENST00000303434 protein_coding NA 38 1 deletion HGNC HGNC:28805 1 P1 CCDS14086.1 ENSP00000305664 Q9H4I3.144 UPI0000049DAE Q9H4I3-1 15 NA NA PASS SITE 13,8|9,1 NA NA 1 48 37,32 163,159 60,60 40 1.18 NA 4.21 NA FALSE 6.00 93 NA NA NA FALSE NA NA 43.67 15 50185829 HCC1395_HCC1395T 0 0.909 10 0,1 0,8 0,9 NA 0/1 NA NA NA NA 0,0,9,1 GCGTGGGACTACACTTCCCGGCATGCCACGCGGCCGCCGGCGCCCTCGGCC/G PANCANCER NA FALSE TRABD chr22:50185829:50185830:GCGTGGGACTACACTTCCCGGCATGCCACGCGGCCGCCGGCGCCCTCGGCC:G indel 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 50243801 50243802 T C 244 310 0.787096774193548 MODIFIER HDAC10 ENSG00000100429 C downstream_gene_variant Transcript ENST00000216271 protein_coding NA 1382 -1 SNV HGNC HGNC:18128 YES NM_032019.6 1 P1 CCDS14088.1 ENSP00000216271 Q969S8.175 UPI000012C3A6 Q969S8-1 15 NA NA PASS SITE 109,111|123,121 NA NA 1 93 20,20 167,163 60,60 30 2.05 NA 33.06 NA FALSE 6.00 93 NA NA NA FALSE NA NA 687.43 15 50243801 HCC1395_HCC1395T 66 0.788 310 17,59 24,95 44,166 NA 0/1 NA NA NA NA 30,36,123,121 T/C PANCANCER NA FALSE HDAC10 chr22:50243801:50243802:T:C SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 50281816 50281817 G T 154 568 0.27112676056338 MODIFIER PLXNB2 ENSG00000196576 T intron_variant Transcript ENST00000359337 protein_coding 20/36 ENST00000359337.9:c.3345+38C>A NA -1 SNV HGNC HGNC:9104 YES NM_012401.4 5 P1 CCDS43035.1 ENSP00000352288 O15031.183 UPI000003812D 15 NA NA PASS SITE 361,419|73,81 NA NA 1 93 20,20 164,166 60,60 33 2.39 NA 72.49 NA FALSE 6.00 93 NA NA NA FALSE NA NA 358.58 15 50281816 HCC1395_HCC1395T 414 0.264 568 120,44 140,52 283,101 NA 0/1 NA NA NA NA 193,221,73,81 G/T PANCANCER NA FALSE PLXNB2 chr22:50281816:50281817:G:T SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chr22 50460629 50460630 C G 82 461 0.177874186550976 LOW SBF1 ENSG00000100241 G synonymous_variant Transcript ENST00000348911 protein_coding 24/40 ENST00000348911.11:c.3051G>C ENSP00000252027.8:p.P1017= ENSP00000252027.8 p.P1017= 3236 3051 1017 P ccG/ccC -1 SNV HGNC HGNC:10542 5 A1 CCDS93185.1 ENSP00000252027 A0A8J8YTQ8.3 UPI000002B347 1 Pfam:PF02893&PANTHER:PTHR10807&Superfamily:SSF50729 15 NA NA PASS SITE 243,345|32,50 NA NA 1 93 20,20 157,155 60,60 36 2.12 NA 38.22 NA FALSE 6.00 84 NA NA NA FALSE NA NA 169.90 15 50460629 HCC1395_HCC1395T 379 0.172 461 95,13 123,34 248,51 NA 0/1 NA NA NA NA 156,223,32,50 C/G PANCANCER NA FALSE SBF1_p.P1017= chr22:50460629:50460630:C:G SNV 3:1 chr22:35718000:50740572:3:1:1 NA NA 0.96 +chrX 649980 649981 C G 78 211 0.369668246445498 MODIFIER SHOX ENSG00000185960 G intron_variant Transcript ENST00000334060 protein_coding 5/5 ENST00000334060.8:c.634-8805C>G NA rs28664665 1 SNV HGNC HGNC:10853 5 CCDS14106.1 ENSP00000335505 O15266.205 UPI000002B3A4 O15266-2 1 0.4443 0.4956 0.5012 0.4652 0.5391 0.3668 0.3677 0.4167 0.5024 0.4248 0.4908 0.3183 0.4667 0.4547 0.5428 0.3909 0.5 0.3654 0.4321 0.5035 0.5428 gnomADg_EAS 23 NA NA PASS SITE 87,99|37,41 NA NA 1 82 20,20 159,152 60,60 31 1.59 NA 11.14 NA FALSE 0.397 93 NA NA NA FALSE NA NA 194.22 23 649980 HCC1395_HCC1395T 133 0.376 211 26,15 55,31 87,52 NA 0/1 NA NA NA NA 61,72,37,41 C/G PANCANCER NA FALSE SHOX chrX:649980:649981:C:G SNV 8:0 chrX:346920:3323243:8:0:1 NA NA 0.96 +chrX 1419026 1419027 G A 113 236 0.478813559322034 MODERATE ASMTL ENSG00000169093 A missense_variant Transcript ENST00000381317 protein_coding 10/13 ENST00000381317.9:c.1334C>T ENSP00000370718.3:p.T445M ENSP00000370718.3 p.T445M 1403 1334 445 T/M aCg/aTg rs745929353 -1 SNV HGNC HGNC:751 YES NM_004192.4 1 P1 CCDS43917.1 ENSP00000370718 O95671.188 UPI0000141AF9 O95671-1 deleterious(0.02) possibly_damaging(0.898) Gene3D:3.40.50.150&AlphaFold_DB_import:AF-O95671-F1&Pfam:PF00891&PROSITE_profiles:PS51683&Superfamily:SSF53335 9.305e-05 0.0001308 0 0 0 9.395e-05 0.0001699 0 0 0.0001182 4.824e-05 0 6.541e-05 0 0 0 0 0.0002205 0 0 0.0002205 gnomADg_NFE 23 NA NA PASS SITE 112,88|62,51 NA NA 1 93 20,20 161,153 60,60 31 1.71 NA 15.05 NA FALSE 4.31 93 NA NA NA FALSE NA NA 296.03 23 1419026 HCC1395_HCC1395T 123 0.496 236 35,35 42,38 79,78 NA 0/1 NA NA NA NA 66,57,62,51 G/A PANCANCER NA FALSE ASMTL_p.T445M chrX:1419026:1419027:G:A SNV 8:0 chrX:346920:3323243:8:0:1 NA NA 0.96 +chrX 2488848 2488849 G A 241 541 0.44547134935305 MODIFIER DHRSX ENSG00000169084 A intron_variant Transcript ENST00000334651 protein_coding 1/6 ENST00000334651.11:c.109+11969C>T NA rs138416455 -1 SNV HGNC HGNC:18399 YES NM_145177.3 1 P1 CCDS35195.1 ENSP00000334113 Q8N5I4.163 UPI0000D61D1C 0.0005111 0.0003696 0 0 0.0004899 0.0003245 0.0008674 0.000491 0.0001635 0.0005059 0.0002172 0 6.545e-05 0 0.0007704 0.0003767 0 0.0008672 0 0 0.0008674 gnomADe_NFE 23 NA NA PASS SITE 247,241|128,113 NA NA 1 93 20,20 156,157 60,60 32 2.10 NA 37.02 NA FALSE 3.38 93 NA NA NA FALSE NA NA 625.30 23 2488848 HCC1395_HCC1395T 300 0.445 541 83,63 113,90 205,164 NA 0/1 NA NA NA NA 153,147,128,113 G/A PANCANCER NA FALSE DHRSX chrX:2488848:2488849:G:A SNV 8:0 chrX:346920:3323243:8:0:1 NA NA 0.96 +chrX 3027436 3027437 C T 169 340 0.497058823529412 MODERATE ARSH ENSG00000205667 T missense_variant Transcript ENST00000381130 protein_coding 7/9 ENST00000381130.3:c.1160C>T ENSP00000370522.3:p.T387M ENSP00000370522.3 p.T387M 1227 1160 387 T/M aCg/aTg rs61751925&COSV66962970 1 SNV HGNC HGNC:32488 YES NM_001011719.2 1 P1 CCDS35198.1 ENSP00000370522 Q5FYA8.124 UPI00001D7C2E deleterious(0) probably_damaging(0.979) Gene3D:3.40.720.10&AlphaFold_DB_import:AF-Q5FYA8-F1&Pfam:PF00884&PANTHER:PTHR42693&Superfamily:SSF53649 0.0379 0.001 0.0477 0.0118 0.0927 0.0515 0.06845 0.01064 0.02623 0.1007 0.01032 0.0887 0.09957 0.07663 0.04626 0.06445 0.01268 0.08321 0.04325 0.1002 0.01246 0.08715 0.05462 0.09848 0.06574 0.04389 0.1007 gnomADe_ASJ benign 0&1 1&1 23 NA NA PASS SITE 149,142|89,80 NA NA 1 93 20,20 162,161 60,60 34 1.89 NA 22.83 NA FALSE 1.12 93 NA NA NA FALSE NA NA 422.86 23 3027436 HCC1395_HCC1395T 171 0.491 340 42,37 62,63 112,108 NA 0/1 NA NA NA NA 85,86,89,80 C/T PANCANCER NA FALSE ARSH_p.T387M chrX:3027436:3027437:C:T SNV 8:0 chrX:346920:3323243:8:0:1 NA NA 0.96 +chrX 3713482 3713483 G A 31 31 1 MODIFIER PRKX ENSG00000183943 A 5_prime_UTR_variant Transcript ENST00000262848 protein_coding 1/9 ENST00000262848.6:c.-229C>T NA 168 rs59479399 -1 SNV HGNC HGNC:9441 YES NM_005044.5 1 P1 CCDS14125.1 ENSP00000262848 P51817.188 A0A024RBU5.65 UPI000000D998 0.2964 0.0738 0.4218 0.4228 0.2389 0.4429 0.2035 0.07435 0.09783 0.3851 0.1949 0.3899 0.1949 0.2208 0.2207 0.2481 0.4304 0.4429 SAS 23 NA NA PASS SITE 14,17|18,13 NA NA 1 13 20,20 143,151 60,60 48 1.29 NA 5.42 NA FALSE 0.708 93 NA NA NA FALSE NA NA 86.19 23 3713482 HCC1395_HCC1395T 0 0.952 31 0,10 0,9 0,19 NA 0/1 NA NA NA NA 0,0,18,13 G/A PANCANCER NA FALSE PRKX chrX:3713482:3713483:G:A SNV 4:0 chrX:3612471:11139621:4:0:1 NA NA 0.96 +chrX 5890384 5890385 C T 26 65 0.4 MODIFIER NLGN4X ENSG00000146938 T 3_prime_UTR_variant Transcript ENST00000275857 protein_coding 6/6 ENST00000275857.10:c.*2433G>A NA 5348 rs1473145218 -1 SNV HGNC HGNC:14287 1 P2 CCDS14126.1 ENSP00000275857 Q8N0W4.176 A0A024RBV0.62 UPI0000072EC5 Q8N0W4-1 1 8.976e-06 3.267e-05 0 0 0 0 0 0 0 0 0 3.267e-05 gnomADg_AFR 23 NA NA PASS SITE 65,24|20,6 NA NA 1 93 20,36 174,172 60,60 18 1.55 NA 10.23 NA FALSE 6.00 71 NA NA NA FALSE NA NA 75.04 23 5890384 HCC1395_HCC1395T 39 0.393 65 12,13 21,7 33,21 NA 0/1 NA NA NA NA 32,7,20,6 C/T PANCANCER NA FALSE NLGN4X chrX:5890384:5890385:C:T SNV 4:0 chrX:3612471:11139621:4:0:1 NA NA 0.96 +chrX 6227814 6227815 C G 65 65 1 MODIFIER NLGN4X ENSG00000146938 G 5_prime_UTR_variant Transcript ENST00000275857 protein_coding 1/6 ENST00000275857.10:c.-431G>C NA 34 rs2290488 -1 SNV HGNC HGNC:14287 1 P2 CCDS14126.1 ENSP00000275857 Q8N0W4.176 A0A024RBV0.62 UPI0000072EC5 Q8N0W4-1 1 0.2747 0.1236 0.3874 0.2147 0.3851 0.3496 0.301 0.1401 0.3061 0.3682 0.3936 0.2056 0.3799 0.3106 0.3708 0.3121 0.3385 0.3936 gnomADg_ASJ 23 NA NA PASS SITE 27,33|23,42 NA NA 1 74 20,20 165,159 60,60 33 1.62 NA 12.04 NA FALSE 0.510 93 NA NA NA FALSE NA NA 201.74 23 6227814 HCC1395_HCC1395T 0 0.980 65 0,13 0,27 0,46 NA 0/1 NA NA NA NA 0,0,23,42 C/G PANCANCER NA FALSE NLGN4X chrX:6227814:6227815:C:G SNV 4:0 chrX:3612471:11139621:4:0:1 NA NA 0.96 +chrX 8529469 8529470 C T 52 52 1 MODIFIER ANOS1 ENSG00000011201 T 3_prime_UTR_variant Transcript ENST00000262648 protein_coding 14/14 ENST00000262648.8:c.*3526G>A NA 5670 rs6640166 -1 SNV HGNC HGNC:6211 YES NM_000216.4 1 P1 CCDS14130.1 ENSP00000262648 P23352.212 UPI00001AE843 1 0.4660 0.349 0.4733 0.7605 0.3786 0.4039 0.3829 0.3457 0.3733 0.4701 0.3797 0.7699 0.4331 0.4153 0.3545 0.3981 0.4079 0.7699 gnomADg_EAS 23 NA NA PASS SITE 35,14|46,6 NA NA 1 71 33,36 215,198 60,60 21 1.61 NA 12.04 NA FALSE 0.405 93 NA NA NA FALSE NA NA 193.68 23 8529469 HCC1395_HCC1395T 0 0.980 52 0,16 0,31 0,47 NA 0/1 NA NA NA NA 0,0,46,6 C/T PANCANCER NA FALSE ANOS1 chrX:8529469:8529470:C:T SNV 4:0 chrX:3612471:11139621:4:0:1 NA NA 0.96 +chrX 9025630 9025631 C T 28 28 1 MODIFIER FAM9B ENSG00000177138 T intron_variant Transcript ENST00000327220 protein_coding 7/8 ENST00000327220.10:c.493-47G>A NA rs148142009 -1 SNV HGNC HGNC:18404 YES NM_205849.3 1 P1 CCDS14132.1 ENSP00000318716 Q8IZU0.139 A0A024RBV3.56 UPI000012A419 Q8IZU0-1 0.0082 0 0.0095 0 0.0209 0.0139 0.01793 0.003438 0.006745 0.01118 0 0.02949 0.02572 0.01584 0.01067 0.01774 0.00438 0 0.009283 0.01515 0.000278 0.03445 0 0.02733 0.01602 0.009985 0.03445 gnomADg_FIN 23 NA NA PASS SITE 5,11|4,24 NA NA 1 17 24,37 164,207 60,60 24 1.11 NA 3.61 NA FALSE 1.72 93 NA NA NA FALSE NA NA 99.63 23 9025630 HCC1395_HCC1395T 0 0.962 28 0,9 0,13 0,24 NA 0/1 NA NA NA NA 0,0,4,24 C/T PANCANCER NA FALSE FAM9B chrX:9025630:9025631:C:T SNV 4:0 chrX:3612471:11139621:4:0:1 NA NA 0.96 +chrX 9937279 9937280 G C 384 384 1 MODERATE SHROOM2 ENSG00000146950 C missense_variant Transcript ENST00000380913 protein_coding 7/10 ENST00000380913.8:c.3733G>C ENSP00000370299.3:p.D1245H ENSP00000370299.3 p.D1245H 3850 3733 1245 D/H Gac/Cac rs1033602309&COSV66611380 1 SNV HGNC HGNC:630 YES NM_001649.4 1 P1 CCDS14135.1 ENSP00000370299 Q13796.174 UPI0000125D05 deleterious(0.01) probably_damaging(0.998) PANTHER:PTHR15012&AlphaFold_DB_import:AF-Q13796-F1 0&1 0&1 23 NA NA PASS SITE 153,129|204,180 NA NA 1 93 20,20 162,154 60,60 34 2.28 NA 57.19 NA FALSE 6.00 93 NA NA NA FALSE NA NA 1111.78 23 9937279 HCC1395_HCC1395T 0 0.996 384 0,100 0,131 0,239 NA 0/1 NA NA NA NA 0,0,204,180 G/C PANCANCER NA FALSE SHROOM2_p.D1245H chrX:9937279:9937280:G:C SNV 4:0 chrX:3612471:11139621:4:0:1 NA NA 0.96 +chrX 9967397 9967398 G A 315 315 1 MODERATE CLDN34 ENSG00000234469 A missense_variant Transcript ENST00000445307 protein_coding 1/1 ENST00000445307.4:c.40G>A ENSP00000403980.3:p.V14I ENSP00000403980.3 p.V14I 40 40 14 V/I Gtc/Atc 1 SNV HGNC HGNC:51259 YES NM_001195081.2 P1 CCDS75951.1 ENSP00000403980 H7C241.55 UPI0001A5E8EC deleterious(0.03) possibly_damaging(0.525) Gene3D:1.20.140.150&AlphaFold_DB_import:AF-H7C241-F1&PANTHER:PTHR12002&Transmembrane_helices:TMhelix 23 NA NA PASS SITE 112,90|178,139 NA NA 1 93 20,20 158,157 60,60 37 0.809 NA 35.42 NA FALSE 6.00 93 NA NA NA FALSE NA NA 927.29 23 9967397 HCC1395_HCC1395T 0 0.995 315 0,87 0,111 0,208 NA 0/1 NA NA NA NA 0,0,177,138 G/A PANCANCER NA FALSE CLDN34_p.V14I chrX:9967397:9967398:G:A SNV 4:0 chrX:3612471:11139621:4:0:1 NA NA 0.96 +chrX 10235076 10235077 G C 28 28 1 MODIFIER CLCN4 ENSG00000073464 C downstream_gene_variant Transcript ENST00000380829 protein_coding NA 1379 1 SNV HGNC HGNC:2022 5 ENSP00000370209 G3XAG5.95 UPI000059DAC0 1 23 NA NA PASS SITE 11,11|13,15 NA NA 1 93 20,25 186,168 60,60 31 1.22 NA 4.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 92.86 23 10235076 HCC1395_HCC1395T 0 0.958 28 0,10 0,9 0,21 NA 0/1 NA NA NA NA 0,0,13,15 G/C PANCANCER NA FALSE CLCN4 chrX:10235076:10235077:G:C SNV 4:0 chrX:3612471:11139621:4:0:1 NA NA 0.96 +chrX 10235554 10235555 C T 66 157 0.420382165605096 MODIFIER CLCN4 ENSG00000073464 T downstream_gene_variant Transcript ENST00000380829 protein_coding NA 1857 1 SNV HGNC HGNC:2022 5 ENSP00000370209 G3XAG5.95 UPI000059DAC0 1 23 NA NA PASS SITE 94,67|39,27 NA NA 1 93 20,20 168,184 60,60 26 1.74 NA 15.30 NA FALSE 6.00 93 NA NA NA FALSE NA NA 181.98 23 10235554 HCC1395_HCC1395T 91 0.433 157 21,17 41,30 66,50 NA 0/1 NA NA NA NA 53,38,39,27 C/T PANCANCER NA FALSE CLCN4 chrX:10235554:10235555:C:T SNV 4:0 chrX:3612471:11139621:4:0:1 NA NA 0.96 +chrX 12975392 12975393 C T 70 70 1 MODIFIER TMSB4X ENSG00000205542 T upstream_gene_variant Transcript ENST00000380633 protein_coding NA rs115781169 266 1 SNV HGNC HGNC:11881 3 P1 CCDS35202.1 ENSP00000370007 P62328.171 A2VCK8.141 UPI0000000CD7 1 0.1550 0.1466 0.3187 0.0288 0.2128 0.1198 0.1915 0.1485 0.138 0.2483 0.2271 0.03528 0.2317 0.2552 0.2128 0.2024 0.1286 0.3187 AMR 23 NA NA PASS SITE 21,39|24,46 NA NA 1 93 38,33 191,178 60,60 22 1.71 NA 14.75 NA FALSE 0.695 93 NA NA NA FALSE NA NA 224.18 23 12975392 HCC1395_HCC1395T 0 0.982 70 0,21 0,29 0,54 NA 0/1 NA NA NA NA 0,0,24,46 C/T PANCANCER TRUE FALSE TMSB4X chrX:12975392:12975393:C:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 13044603 13044604 C T 27 27 1 MODIFIER FAM9C ENSG00000187268 T upstream_gene_variant Transcript ENST00000333995 protein_coding NA rs11095602 1 -1 SNV HGNC HGNC:18405 1 P1 CCDS35203.1 ENSP00000334430 Q8IZT9.126 A0A024RBW5.56 UPI000012A41A 0.5605 0.4497 0.7252 0.6348 0.4334 0.6518 0.4909 0.4666 0.3373 0.6433 0.44 0.5987 0.5547 0.4407 0.4587 0.4677 0.6202 0.7252 AMR 23 NA NA PASS SITE 30,30|14,13 NA NA 1 52 20,20 149,171 60,60 41 1.56 NA 10.53 NA FALSE 0.312 93 NA NA NA FALSE NA NA 80.77 23 13044603 HCC1395_HCC1395T 0 0.951 27 0,8 0,9 0,18 NA 0/1 NA NA NA NA 0,0,14,13 C/T PANCANCER NA FALSE FAM9C chrX:13044603:13044604:C:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 15355262 15355263 C T 49 49 1 MODERATE VEGFD ENSG00000165197 T missense_variant Transcript ENST00000297904 protein_coding 4/7 ENST00000297904.4:c.529G>A ENSP00000297904.3:p.E177K ENSP00000297904.3 p.E177K 996 529 177 E/K Gaa/Aaa COSV52912020 -1 SNV HGNC HGNC:3708 YES NM_004469.5 1 P1 CCDS14166.1 ENSP00000297904 O43915.177 UPI00000012B2 tolerated(0.72) probably_damaging(0.964) PDB-ENSP_mappings:2xv7.A&PROSITE_profiles:PS50278&CDD:cd00135&PANTHER:PTHR12025&Gene3D:2.10.90.10&Pfam:PF00341&SMART:SM00141&Superfamily:SSF57501&AlphaFold_DB_import:AF-O43915-F1 1 1 23 NA NA PASS SITE 18,29|21,28 NA NA 1 93 20,20 156,148 60,60 40 1.49 NA 9.03 NA FALSE 6.00 93 NA NA NA FALSE NA NA 124.35 23 15355262 HCC1395_HCC1395T 0 0.969 49 0,14 0,14 0,30 NA 0/1 NA NA NA NA 0,0,21,28 C/T PANCANCER NA FALSE VEGFD_p.E177K chrX:15355262:15355263:C:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 15784677 15784678 C G 187 187 1 MODIFIER CA5B ENSG00000169239 G 3_prime_UTR_variant Transcript ENST00000318636 protein_coding 8/8 ENST00000318636.8:c.*2013C>G NA 3103 rs5980189 1 SNV HGNC HGNC:1378 YES NM_007220.4 1 P1 CCDS14171.1 ENSP00000314099 Q9Y2D0.170 A0A024RBW9.54 UPI0000126D58 0.2177 0.1605 0.2615 0.0249 0.4843 0.1866 0.3667 0.1901 0.545 0.2612 0.5042 0.01586 0.4357 0.487 0.5033 0.3698 0.2211 0.545 gnomADg_AMI 23 NA NA PASS SITE 96,90|90,97 NA NA 1 93 20,20 171,169 60,60 34 2.09 NA 36.54 NA FALSE 0.405 93 NA NA NA FALSE NA NA 573.73 23 15784677 HCC1395_HCC1395T 0 0.992 187 0,47 0,68 0,122 NA 0/1 NA NA NA NA 0,0,90,97 C/G PANCANCER NA FALSE CA5B chrX:15784677:15784678:C:G SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 15785864 15785866 A AT 13 13 1 MODIFIER ZRSR2 ENSG00000169249 T upstream_gene_variant Transcript ENST00000307771 protein_coding NA rs748757429 4619 1 insertion HGNC HGNC:23019 YES NM_005089.4 1 P2 CCDS14172.1 ENSP00000303015 Q15696.189 UPI0000137929 1 0.4455 0.2379 0.501 0.3559 0.5826 0.02174 0.5422 0.5917 0.5922 0.4527 0.253 0.5922 gnomADg_NFE 23 NA NA PASS SITE 8,20|4,9 NA NA 1 4 33,36 196,206 60,60 32 1.41 NA 6.93 NA FALSE 0.317 93 9,10 T NA TRUE NA 66 28.53 23 15785864 HCC1395_HCC1395T 0 0.933 13 0,3 0,3 0,11 NA 0/1 NA NA NA NA 0,0,4,9 A/AT PANCANCER NA FALSE ZRSR2 chrX:15785864:15785866:A:AT indel 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 15786861 15786862 G A 7 7 1 MODIFIER ZRSR2 ENSG00000169249 A upstream_gene_variant Transcript ENST00000307771 protein_coding NA rs10521650 3623 1 SNV HGNC HGNC:23019 YES NM_005089.4 1 P2 CCDS14172.1 ENSP00000303015 Q15696.189 UPI0000137929 1 0.1841 0.0479 0.2347 0.0249 0.4843 0.1866 0.3356 0.08756 0.5435 0.2465 0.496 0.01554 0.4347 0.4678 0.5019 0.3438 0.2183 0.5435 gnomADg_AMI 23 NA NA PASS SITE 14,12|4,3 NA NA 1 18 20,35 178,198 60,60 29 1.30 NA 5.72 NA FALSE 0.434 60 NA NA NA FALSE NA NA 24.51 23 15786861 HCC1395_HCC1395T 0 0.884 7 0,2 0,3 0,6 NA 0/1 NA NA NA NA 0,0,4,3 G/A PANCANCER NA FALSE ZRSR2 chrX:15786861:15786862:G:A SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 15787668 15787669 A G 24 24 1 MODIFIER ZRSR2 ENSG00000169249 G upstream_gene_variant Transcript ENST00000307771 protein_coding NA rs5021752 2816 1 SNV HGNC HGNC:23019 YES NM_005089.4 1 P2 CCDS14172.1 ENSP00000303015 Q15696.189 UPI0000137929 1 0.1846 0.0479 0.2347 0.0249 0.4869 0.1866 0.3355 0.08796 0.5426 0.247 0.4964 0.015 0.4296 0.4596 0.5033 0.34 0.2162 0.5426 gnomADg_AMI 23 NA NA PASS SITE 8,23|3,21 NA NA 1 26 33,39 186,207 60,60 37 1.41 NA 7.48 NA FALSE 0.434 93 NA NA NA FALSE NA NA 91.44 23 15787668 HCC1395_HCC1395T 0 0.957 24 0,8 0,13 0,21 NA 0/1 NA NA NA NA 0,0,3,21 A/G PANCANCER NA FALSE ZRSR2 chrX:15787668:15787669:A:G SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 17726699 17726700 G A 47 47 1 MODERATE NHS ENSG00000188158 A missense_variant Transcript ENST00000380060 protein_coding 6/8 ENST00000380060.7:c.2530G>A ENSP00000369400.3:p.A844T ENSP00000369400.3 p.A844T 2868 2530 844 A/T Gca/Aca rs149609550&COSV66270898 1 SNV HGNC HGNC:7820 1 A2 CCDS14181.1 ENSP00000369400 Q6T4R5.144 UPI00001DFBF3 Q6T4R5-2 1 tolerated(0.87) benign(0.003) AlphaFold_DB_import:AF-Q6T4R5-F1&Pfam:PF15273&PANTHER:PTHR23039&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite 0.0011 0 0.0038 0 0.0026 0 0.001162 0.000228 0.001094 0.001872 0 0.0001874 0.001894 0.001766 0 0.001312 0.0002273 0 0.001888 0.001509 0 0 0 0.002124 0.001982 0 0.0038 AMR benign&likely_benign 0&1 1&1 23 NA NA PASS SITE 28,27|24,23 NA NA 1 93 20,20 148,162 60,60 26 1.57 NA 10.84 NA FALSE 2.96 93 NA NA NA FALSE NA NA 128.25 23 17726699 HCC1395_HCC1395T 0 0.967 47 0,12 0,16 0,28 NA 0/1 NA NA NA NA 0,0,24,23 G/A PANCANCER NA FALSE NHS_p.A844T chrX:17726699:17726700:G:A SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 18247727 18247728 A G 55 55 1 MODIFIER SCML2 ENSG00000102098 G intron_variant Transcript ENST00000251900 protein_coding 12/14 ENST00000251900.9:c.1570+42T>C NA rs73191503 -1 SNV HGNC HGNC:10581 YES NM_006089.3 1 P1 CCDS14185.1 ENSP00000251900 Q9UQR0.184 UPI0000071E54 Q9UQR0-1 0.0199 0.004 0.0229 0 0.0757 0.0014 0.0396 0.01079 0.0145 0.0153 0 0.04014 0.0674 0.04031 0.007973 0.03926 0.009831 0.05263 0.02086 0.01672 0 0.03699 0.03766 0.06532 0.04342 0.004615 0.0757 EUR 23 NA NA PASS SITE 31,34|26,29 NA NA 1 89 20,20 156,150 60,60 40 1.60 NA 11.44 NA FALSE 1.40 93 NA NA NA FALSE NA NA 153.81 23 18247727 HCC1395_HCC1395T 0 0.972 55 0,11 0,18 0,34 NA 0/1 NA NA NA NA 0,0,26,29 A/G PANCANCER NA FALSE SCML2 chrX:18247727:18247728:A:G SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 19535359 19535360 A C 15 31 0.483870967741935 MODIFIER SH3KBP1 ENSG00000147010 C downstream_gene_variant Transcript ENST00000379698 protein_coding NA 334 -1 SNV HGNC HGNC:13867 1 CCDS35213.1 ENSP00000369020 Q96B97.196 UPI0000074456 Q96B97-2 1 23 NA NA PASS SITE 33,7|12,3 NA NA 1 57 36,39 199,201 60,60 28 1.32 NA 6.02 NA FALSE 6.00 81 NA NA NA FALSE NA NA 48.75 23 19535359 HCC1395_HCC1395T 16 0.483 31 3,8 10,5 14,13 NA 0/1 NA NA NA NA 13,3,12,3 A/C PANCANCER NA FALSE SH3KBP1 chrX:19535359:19535360:A:C SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 21561458 21561459 T C 105 105 1 MODIFIER CNKSR2 ENSG00000149970 C intron_variant Transcript ENST00000279451 protein_coding 11/19 ENST00000279451.9:c.1304-1780T>C NA 1 SNV HGNC HGNC:19701 1 CCDS87728.1 ENSP00000279451 A0A2U3TZH5.21 UPI0000418AFA 1 23 NA NA PASS SITE 54,40|56,49 NA NA 1 93 20,20 152,175 60,60 33 1.80 NA 18.60 NA FALSE 6.00 93 NA NA NA FALSE NA NA 323.99 23 21561458 HCC1395_HCC1395T 0 0.987 105 0,19 0,49 0,73 NA 0/1 NA NA NA NA 0,0,56,49 T/C PANCANCER NA FALSE CNKSR2 chrX:21561458:21561459:T:C SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 24311440 24311441 C T 70 70 1 MODERATE SUPT20HL2 ENSG00000223611 T missense_variant Transcript ENST00000486479 protein_coding 1/1 ENST00000486479.3:c.1876G>A ENSP00000503941.1:p.G626S ENSP00000503941.1 p.G626S 2630 1876 626 G/S Ggt/Agt rs190214531 -1 SNV HGNC HGNC:31797 YES NM_001136233.3 P1 CCDS94580.1 ENSP00000503941 P0C7V6.68 UPI000178DED2 tolerated(0.67) benign(0.001) AlphaFold_DB_import:AF-P0C7V6-F1&MobiDB_lite:mobidb-lite 0.0016 0 0 0 0.0065 0.0014 0.003018 0.0009744 0.0006209 0 7.378e-05 0.004334 0.005137 0.00359 0.0008392 0.002339 0.000611 0 0.0001856 0 0 0.003989 0 0.003921 0.003279 0.001448 0.0065 EUR 23 NA NA PASS SITE 37,52|23,47 NA NA 1 93 20,20 161,156 60,60 28 1.79 NA 18.06 NA FALSE 2.63 93 NA NA NA FALSE NA NA 229.21 23 24311440 HCC1395_HCC1395T 0 0.981 70 0,17 0,26 0,50 NA 0/1 NA NA NA NA 0,0,23,47 C/T PANCANCER NA FALSE SUPT20HL2_p.G626S chrX:24311440:24311441:C:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 24365405 24365406 C G 73 73 1 MODERATE SUPT20HL1 ENSG00000223731 G missense_variant Transcript ENST00000436466 protein_coding 2/2 ENST00000436466.2:c.2645C>G ENSP00000502907.1:p.P882R ENSP00000502907.1 p.P882R 2734 2645 882 P/R cCa/cGa 1 SNV HGNC HGNC:30773 P1 CCDS94581.1 ENSP00000502907 A0A7I2YQ69.7 UPI0001837EA1 deleterious_low_confidence(0) unknown(0) AlphaFold_DB_import:AF-A0A7I2YQ69-F1 23 NA NA PASS SITE 34,39|34,39 NA NA 1 93 20,20 166,155 60,60 40 1.69 NA 14.15 NA FALSE 6.00 93 NA NA NA FALSE NA NA 204.67 23 24365405 HCC1395_HCC1395T 0 0.979 73 0,25 0,17 0,44 NA 0/1 NA NA NA NA 0,0,34,39 C/G PANCANCER NA FALSE SUPT20HL1_p.P882R chrX:24365405:24365406:C:G SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 24716286 24716287 A G 78 78 1 MODIFIER POLA1 ENSG00000101868 G intron_variant Transcript ENST00000379059 protein_coding 6/36 ENST00000379059.7:c.508-76A>G NA rs11573323&COSV66884753 1 SNV HGNC HGNC:9173 1 P4 CCDS14214.1 ENSP00000368349 P09884.213 UPI000014D383 1 0.0040 0 0.0019 0 0.0183 0 0.0104 0.002954 0 0.002014 0.004926 0.0002818 0.008586 0 0.01811 0.007373 0.003472 0.0183 EUR 0&1 0&1 23 NA NA PASS SITE 33,19|58,20 NA NA 1 93 20,36 157,169 60,60 34 1.59 NA 10.84 NA FALSE 2.00 93 NA NA NA FALSE NA NA 272.41 23 24716286 HCC1395_HCC1395T 0 0.984 78 0,29 0,32 0,61 NA 0/1 NA NA NA NA 0,0,58,20 A/G PANCANCER NA FALSE POLA1 chrX:24716286:24716287:A:G SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 26194360 26194361 G C 32 32 1 MODERATE MAGEB6 ENSG00000176746 C missense_variant Transcript ENST00000379034 protein_coding 2/2 ENST00000379034.1:c.514G>C ENSP00000368320.1:p.G172R ENSP00000368320.1 p.G172R 663 514 172 G/R Ggt/Cgt rs145782491 1 SNV HGNC HGNC:23796 YES NM_173523.2 1 P1 CCDS14217.1 ENSP00000368320 Q8N7X4.137 UPI00001413F4 tolerated(0.13) possibly_damaging(0.579) Gene3D:1.10.10.1200&AlphaFold_DB_import:AF-Q8N7X4-F1&PANTHER:PTHR11736&SMART:SM01392&MobiDB_lite:mobidb-lite 0.0135 0 0.0095 0 0.0248 0.0376 0.01366 0.001368 0.003027 0.01364 0 0.01194 0.01717 0.01259 0.03397 0.01062 0.001903 0.002903 0.004878 0.01655 0 0.008126 0.004184 0.01679 0.009241 0.02906 0.0376 SAS 23 NA NA PASS SITE 19,23|13,19 NA NA 1 77 20,20 169,177 60,60 23 1.49 NA 9.03 NA FALSE 2.00 93 NA NA NA FALSE NA NA 96.48 23 26194360 HCC1395_HCC1395T 0 0.961 32 0,5 0,16 0,23 NA 0/1 NA NA NA NA 0,0,13,19 G/C PANCANCER NA FALSE MAGEB6_p.G172R chrX:26194360:26194361:G:C SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 27821864 27821865 A C 85 85 1 LOW MAGEB10 ENSG00000177689 C synonymous_variant Transcript ENST00000356790 protein_coding 3/3 ENST00000356790.2:c.558A>C ENSP00000368304.1:p.L186= ENSP00000368304.1 p.L186= 803 558 186 L ctA/ctC rs139940961&COSV63310950 1 SNV HGNC HGNC:25377 YES NM_182506.3 1 P1 CCDS35221.1 ENSP00000368304 Q96LZ2.128 UPI000013F050 Gene3D:1.10.10.1200&AlphaFold_DB_import:AF-Q96LZ2-F1&Pfam:PF01454&PROSITE_profiles:PS50838&PANTHER:PTHR11736&SMART:SM01373 0.0159 0.001 0.0134 0 0.0209 0.0501 0.01967 0.002586 0.00361 0.02595 7.214e-05 0.01999 0.02243 0.01766 0.05468 0.01602 0.002735 0.00292 0.01148 0.02577 0.0002809 0.01822 0.01674 0.02354 0.01398 0.04749 0.05468 gnomADe_SAS 0&1 0&1 23 NA NA PASS SITE 45,40|42,45 NA NA 1 93 20,20 156,167 60,60 32 -1.330e+00 NA 14.02 NA FALSE 1.77 93 NA NA NA FALSE NA NA 271.33 23 27821864 HCC1395_HCC1395T 0 0.985 85 0,21 0,37 0,63 NA 0/1 NA NA NA NA 0,0,41,44 A/C PANCANCER NA FALSE MAGEB10_p.L186= chrX:27821864:27821865:A:C SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 32035545 32035546 G C 80 80 1 MODIFIER DMD ENSG00000198947 C intron_variant Transcript ENST00000357033 protein_coding 44/78 ENST00000357033.9:c.6439-67031C>G NA rs2222852&COSV58893515 -1 SNV HGNC HGNC:2928 YES NM_004006.3 1 P2 CCDS14233.1 ENSP00000354923 A0A075B6G3.66 UPI000049E111 1 0.2408 0.2134 0.2366 0.3613 0.1971 0.2006 0.1799 0.1848 0.1846 0.1769 0.2739 0.1633 0.1668 0.1748 0.1592 0.2071 0.2063 0.313 0.2047 0.2015 0.3271 0.191 0.1838 0.2018 0.1939 0.1991 0.3613 EAS 0&1 0&1 23 NA NA PASS SITE 24,42|29,51 NA NA 1 88 20,20 166,154 60,60 24 1.65 NA 12.94 NA FALSE 0.680 93 NA NA NA FALSE NA NA 251.11 23 32035545 HCC1395_HCC1395T 0 0.983 80 0,22 0,24 0,55 NA 0/1 NA NA NA NA 0,0,29,51 G/C PANCANCER NA FALSE DMD chrX:32035545:32035546:G:C SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 32389610 32389611 C T 94 94 1 MODERATE DMD ENSG00000198947 T missense_variant Transcript ENST00000357033 protein_coding 32/79 ENST00000357033.9:c.4409G>A ENSP00000354923.3:p.R1470H ENSP00000354923.3 p.R1470H 4646 4409 1470 R/H cGt/cAt rs752129019&COSV63749245 -1 SNV HGNC HGNC:2928 YES NM_004006.3 1 P2 CCDS14233.1 ENSP00000354923 A0A075B6G3.66 UPI000049E111 1 deleterious(0.03) probably_damaging(1) CDD:cd00176&PANTHER:PTHR12268&Gene3D:1.20.58.60&PIRSF:PIRSF002341&SMART:SM00150 5.47e-06 0 0 0 0 0 1.228e-05 0 0 1.795e-05 0 0 0 0 0 0 0 1.886e-05 0 0.0003713 0.0003713 gnomADg_SAS uncertain_significance 0&1 1&1 23 NA NA PASS SITE 28,45|35,59 NA NA 1 93 20,20 159,166 60,60 32 1.71 NA 15.05 NA FALSE 6.00 93 NA NA NA FALSE NA NA 296.54 23 32389610 HCC1395_HCC1395T 0 0.985 94 0,21 0,39 0,67 NA 0/1 NA NA NA NA 0,0,35,59 C/T PANCANCER NA FALSE DMD_p.R1470H chrX:32389610:32389611:C:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 37811476 37811477 T G 137 137 1 MODIFIER CYBB ENSG00000165168 G 3_prime_UTR_variant Transcript ENST00000378588 protein_coding 13/13 ENST00000378588.5:c.*559T>G NA 2291 rs5964151 1 SNV HGNC HGNC:2578 YES NM_000397.4 1 P1 CCDS14242.1 ENSP00000367851 P04839.231 A0A0S2Z3S6.38 UPI0000001628 1 0.2040 0.3699 0.1469 0.0668 0.1371 0.2312 0.2121 0.3484 0.09867 0.1938 0.2002 0.0662 0.1307 0.09787 0.1608 0.1871 0.1901 0.3699 AFR 23 NA NA PASS SITE 63,59|87,50 NA NA 1 93 20,29 164,185 60,60 28 1.93 NA 24.68 NA FALSE 0.688 93 NA NA NA FALSE NA NA 463.60 23 37811476 HCC1395_HCC1395T 0 0.991 137 0,39 0,63 0,105 NA 0/1 NA NA NA NA 0,0,87,50 T/G PANCANCER NA FALSE CYBB chrX:37811476:37811477:T:G SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 37839169 37839170 A T 14 14 1 MODIFIER DYNLT3 ENSG00000165169 T 3_prime_UTR_variant Transcript ENST00000378578 protein_coding 5/5 ENST00000378578.9:c.*1406T>A NA 1818 rs12849 -1 SNV HGNC HGNC:11694 YES NM_006520.3 1 P1 CCDS14243.1 ENSP00000367841 P51808.163 UPI0000000C1C 0.1751 0.2532 0.124 0.072 0.1384 0.2521 0.1822 0.2468 0.09545 0.1652 0.1992 0.06931 0.1317 0.09283 0.1618 0.1659 0.2027 0.2532 AFR 23 NA NA PASS SITE 26,11|12,2 NA NA 1 47 36,37 177,243 60,60 21 1.48 NA 8.73 NA FALSE 0.745 93 NA NA NA FALSE NA NA 56.98 23 37839169 HCC1395_HCC1395T 0 0.939 14 0,6 0,7 0,14 NA 0/1 NA NA NA NA 0,0,12,2 A/T PANCANCER NA FALSE DYNLT3 chrX:37839169:37839170:A:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 38408967 38408968 A G 110 110 1 MODERATE OTC ENSG00000036473 G missense_variant Transcript ENST00000039007 protein_coding 8/10 ENST00000039007.5:c.809A>G ENSP00000039007.4:p.Q270R ENSP00000039007.4 p.Q270R 902 809 270 Q/R cAa/cGa rs1800328&CM062960&COSV50005143 1 SNV HGNC HGNC:8512 YES NM_000531.6 1 P1 CCDS14247.1 ENSP00000039007 P00480.240 UPI000013C550 1 deleterious(0.01) possibly_damaging(0.832) PDB-ENSP_mappings:1c9y.A&PDB-ENSP_mappings:1ep9.A&PDB-ENSP_mappings:1fvo.A&PDB-ENSP_mappings:1fvo.B&PDB-ENSP_mappings:1oth.A&PANTHER:PTHR45753&TIGRFAM:TIGR00658&Gene3D:3.40.50.1370&Gene3D:3.40.50.1370&Pfam:PF00185&Superfamily:SSF53671&Prints:PR00102&AlphaFold_DB_import:AF-P00480-F1 0.0167 0 0.0229 0.0013 0.0535 0.0125 0.02946 0.004562 0.01773 0.03186 7.226e-05 0.03604 0.04447 0.03962 0.01174 0.02849 0.005296 0.09692 0.03119 0.03753 0.0002802 0.02933 0.02941 0.04254 0.03407 0.01195 0.09692 gnomADg_AMI benign&benign/likely_benign 0&0&1 1&1&1 23 NA NA PASS SITE 42,53|46,64 NA NA 1 93 20,20 165,166 60,60 28 1.80 NA 18.66 NA FALSE 1.51 93 NA NA NA FALSE NA NA 326.75 23 38408967 HCC1395_HCC1395T 0 0.987 110 0,18 0,44 0,73 NA 0/1 NA NA NA NA 0,0,46,64 A/G PANCANCER NA FALSE OTC_p.Q270R chrX:38408967:38408968:A:G SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 40655058 40655059 G T 41 41 1 MODERATE MED14 ENSG00000180182 T missense_variant&splice_region_variant Transcript ENST00000324817 protein_coding 29/31 ENST00000324817.6:c.3975C>A ENSP00000323720.1:p.F1325L ENSP00000323720.1 p.F1325L 4105 3975 1325 F/L ttC/ttA COSV61358915 -1 SNV HGNC HGNC:2370 YES NM_004229.4 1 P1 CCDS14254.1 ENSP00000323720 O60244.185 UPI00001414B1 deleterious_low_confidence(0) possibly_damaging(0.632) PDB-ENSP_mappings:7emf.N&PDB-ENSP_mappings:7ena.n&PDB-ENSP_mappings:7enc.n&PDB-ENSP_mappings:7enj.N&PDB-ENSP_mappings:7lbm.r&PDB-ENSP_mappings:7nvr.l&PDB-ENSP_mappings:8gxq.n&PDB-ENSP_mappings:8gxs.n&AlphaFold_DB_import:AF-O60244-F1&PANTHER:PTHR12809 1 1 23 NA NA PASS SITE 18,18|17,24 NA NA 1 93 20,20 166,164 60,60 33 1.42 NA 7.52 NA FALSE 6.00 93 NA NA NA FALSE NA NA 109.19 23 40655058 HCC1395_HCC1395T 0 0.962 41 0,5 0,16 0,24 NA 0/1 NA NA NA NA 0,0,17,24 G/T PANCANCER NA FALSE MED14_p.F1325L chrX:40655058:40655059:G:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 41344255 41344256 G C 71 71 1 MODERATE DDX3X ENSG00000215301 C missense_variant Transcript ENST00000399959 protein_coding 10/17 ENST00000399959.7:c.878G>C ENSP00000382840.3:p.R293T ENSP00000382840.3 p.R293T 969 878 293 R/T aGa/aCa COSV67864673 1 SNV HGNC HGNC:2745 1 A1 ENSP00000382840 A0A2U3TZJ9.23 UPI000387C895 1 deleterious_low_confidence(0) benign(0.066) Gene3D:3.40.50.300&AlphaFold_DB_import:AF-A0A2U3TZJ9-F1&Pfam:PF00270&PROSITE_profiles:PS51192&PANTHER:PTHR47958&SMART:SM00487&Superfamily:SSF52540&CDD:cd18051 1 1 23 NA NA PASS SITE 43,45|38,33 NA NA 1 93 20,20 151,157 60,60 31 1.76 NA 16.86 NA FALSE 6.00 93 NA NA NA FALSE NA NA 224.64 23 41344255 HCC1395_HCC1395T 0 0.981 71 0,18 0,30 0,50 NA 0/1 NA NA NA NA 0,0,38,33 G/C PANCANCER TRUE TRUE DDX3X_p.R293T chrX:41344255:41344256:G:C SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 43656386 43656387 C A 88 88 1 MODERATE MAOA ENSG00000189221 A missense_variant Transcript ENST00000338702 protein_coding 1/15 ENST00000338702.4:c.45C>A ENSP00000340684.3:p.D15E ENSP00000340684.3 p.D15E 88 45 15 D/E gaC/gaA COSV100108602&COSV58645801 1 SNV HGNC HGNC:6833 YES NM_000240.4 1 P1 CCDS14260.1 ENSP00000340684 P21397.230 Q53YE7.130 UPI0000125B99 P21397-1 1 deleterious_low_confidence(0.05) possibly_damaging(0.638) PDB-ENSP_mappings:2bxr.A&PDB-ENSP_mappings:2bxr.B&PDB-ENSP_mappings:2bxs.A&PDB-ENSP_mappings:2bxs.B&PDB-ENSP_mappings:2z5x.A&PDB-ENSP_mappings:2z5y.A&PANTHER:PTHR43563&Gene3D:3.50.50.60&Superfamily:SSF51905&Prints:PR00757&AlphaFold_DB_import:AF-P21397-F1 1&1 1&1 23 NA NA PASS SITE 70,54|48,40 NA NA 1 93 20,20 164,158 60,60 34 1.92 NA 24.84 NA FALSE 6.00 93 NA NA NA FALSE NA NA 280.97 23 43656386 HCC1395_HCC1395T 0 0.985 88 0,20 0,38 0,62 NA 0/1 NA NA NA NA 0,0,48,40 C/A PANCANCER NA FALSE MAOA_p.D15E chrX:43656386:43656387:C:A SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 44538732 44538733 T C 36 36 1 MODIFIER FUNDC1 ENSG00000069509 C intron_variant Transcript ENST00000378045 protein_coding 2/4 ENST00000378045.5:c.186-190A>G NA rs41312153 -1 SNV HGNC HGNC:28746 YES NM_173794.4 1 P1 CCDS14263.1 ENSP00000367284 Q8IVP5.142 UPI000004A05A 0.0066 0.001 0.0134 0 0.0196 0.0028 0.009283 0.001892 0 0.005802 0.007181 0 0.02137 0.02119 0.01401 0.008672 0.002619 0.02137 gnomADg_FIN 23 NA NA PASS SITE 9,20|13,23 NA NA 1 48 20,20 176,176 60,60 24 1.35 NA 6.32 NA FALSE 1.92 93 NA NA NA FALSE NA NA 102.40 23 44538732 HCC1395_HCC1395T 0 0.963 36 0,9 0,11 0,25 NA 0/1 NA NA NA NA 0,0,13,23 T/C PANCANCER NA FALSE FUNDC1 chrX:44538732:44538733:T:C SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 47836343 47836344 CT C 85 85 1 MODIFIER ZNF81 ENSG00000197779 - upstream_gene_variant Transcript ENST00000334937 protein_coding NA rs35084954 602 1 deletion HGNC HGNC:13156 1 ENSP00000334641 B1AJV1.88 UPI0000211F7C 1 0.5695 0.6092 0.5992 0.5982 0.5352 0.4986 0.5464 0.6133 0.5685 0.5581 0.616 0.4556 0.5272 0.5432 0.5274 0.5428 0.5949 0.451 0.558 0.5451 0.5994 0.4273 0.6695 0.5221 0.5475 0.4836 0.6695 gnomADg_MID 23 NA NA PASS SITE 31,53|39,46 NA NA 1 93 20,20 170,170 60,60 31 1.77 NA 17.45 NA FALSE 0.275 93 2,1 T NA TRUE NA 93 202.03 23 47836343 HCC1395_HCC1395T 0 0.983 85 0,23 0,19 0,57 NA 0/1 NA NA NA NA 0,0,39,46 CT/C PANCANCER NA FALSE ZNF81 chrX:47836343:47836344:CT:C indel 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 48559322 48559323 C T 13 13 1 LOW TBC1D25 ENSG00000068354 T synonymous_variant Transcript ENST00000376771 protein_coding 5/6 ENST00000376771.9:c.681C>T ENSP00000365962.4:p.G227= ENSP00000365962.4 p.G227= 765 681 227 G ggC/ggT rs146316025&COSV104687888 1 SNV HGNC HGNC:8092 YES NM_002536.4 1 P1 CCDS35242.1 ENSP00000365962 Q3MII6.129 UPI0000160685 Q3MII6-1 AlphaFold_DB_import:AF-Q3MII6-F1&PANTHER:PTHR22957&SMART:SM00164&Superfamily:SSF47923 0.0050 0 0.0038 0 0.0209 0.0014 0.007808 0.001255 0.004672 0.005176 0 0.008428 0.01299 0.007053 0.001327 0.008343 0.001205 0.001477 0.005073 0.008296 0 0.006777 0.02092 0.01424 0.007989 0.001495 0.02092 gnomADg_MID 0&1 0&1 23 NA NA PASS SITE 4,10|5,8 NA NA 1 16 20,20 151,148 60,60 30 1.04 NA 3.01 NA FALSE 2.01 44 NA NA NA FALSE NA NA 34.50 23 48559322 HCC1395_HCC1395T 0 0.906 13 0,1 0,4 0,8 NA 0/1 NA NA NA NA 0,0,5,8 C/T PANCANCER NA FALSE TBC1D25_p.G227= chrX:48559322:48559323:C:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 48831165 48831166 G A 67 67 1 MODIFIER PCSK1N ENSG00000102109 A 3_prime_UTR_variant Transcript ENST00000218230 protein_coding 3/3 ENST00000218230.6:c.*95C>T NA 956 rs56338702 -1 SNV HGNC HGNC:17301 YES NM_013271.5 1 P1 CCDS14307.1 ENSP00000218230 Q9UHG2.151 UPI000003778D 0.0177 0.001 0.0286 0 0.0587 0.0084 0.02983 0.004911 0.001464 0.03035 0.03516 0.0005618 0.01821 0.04603 0.04847 0.03517 0.009919 0.0587 EUR 23 NA NA PASS SITE 62,61|30,37 NA NA 1 93 20,20 152,152 60,60 39 1.90 NA 23.13 NA FALSE 1.48 93 NA NA NA FALSE NA NA 175.06 23 48831165 HCC1395_HCC1395T 0 0.976 67 0,17 0,17 0,40 NA 0/1 NA NA NA NA 0,0,30,37 G/A PANCANCER NA FALSE PCSK1N chrX:48831165:48831166:G:A SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 48903090 48903091 C T 104 104 1 MODIFIER PQBP1 ENSG00000102103 T 3_prime_UTR_variant Transcript ENST00000218224 protein_coding 6/6 ENST00000218224.9:c.*6C>T NA 1376 rs181088115 1 SNV HGNC HGNC:9330 1 P1 CCDS14309.1 ENSP00000218224 O60828.193 A0A0S2Z4V5.49 UPI0000073DB7 O60828-1 1 0.0011 0 0.0019 0 0.0039 0 0.0005535 0 0.0001559 0.0008617 0 0.001304 0.0007901 0.0004973 0.0002413 0.0006509 9.718e-05 0 0.0001893 0.0003768 0 0.0009801 0.004167 0.001109 0 0.0003623 0.004167 gnomADg_MID uncertain_significance&conflicting_interpretations_of_pathogenicity 1 23 NA NA PASS SITE 57,52|55,49 NA NA 1 93 20,20 162,155 60,60 29 1.91 NA 23.42 NA FALSE 3.46 93 NA NA NA FALSE NA NA 320.85 23 48903090 HCC1395_HCC1395T 0 0.987 104 0,26 0,42 0,73 NA 0/1 NA NA NA NA 0,0,55,49 C/T PANCANCER NA FALSE PQBP1 chrX:48903090:48903091:C:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 48967569 48967570 C T 22 22 1 MODIFIER KCND1 ENSG00000102057 T intron_variant Transcript ENST00000218176 protein_coding 1/5 ENST00000218176.4:c.1122-463G>A NA rs2064034 -1 SNV HGNC HGNC:6237 YES NM_004979.6 1 P1 CCDS14314.1 ENSP00000218176 Q9NSA2.179 UPI000000DB05 Q9NSA2-1 0.2511 0.0189 0.4561 0.2395 0.4843 0.1894 0.3187 0.06263 0.247 0.4083 0.4593 0.2565 0.425 0.4915 0.4405 0.36 0.1852 0.4915 gnomADg_MID 23 NA NA PASS SITE 15,6|12,10 NA NA 1 93 32,20 165,178 60,60 42 1.26 NA 5.11 NA FALSE 6.00 93 NA NA NA FALSE NA NA 65.70 23 48967569 HCC1395_HCC1395T 0 0.941 22 0,4 0,10 0,15 NA 0/1 NA NA NA NA 0,0,12,10 C/T PANCANCER NA FALSE KCND1 chrX:48967569:48967570:C:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 48977739 48977740 G A 28 28 1 MODIFIER GRIPAP1 ENSG00000068400 A intron_variant Transcript ENST00000376423 protein_coding 22/25 ENST00000376423.8:c.2061+566C>T NA rs45462097 -1 SNV HGNC HGNC:18706 YES NM_020137.5 1 P2 CCDS35248.1 ENSP00000365606 Q4V328.146 UPI0004620CB8 Q4V328-1 0.2524 0.0189 0.4561 0.2408 0.483 0.1964 0.3223 0.06342 0.2557 0.4095 0.4642 0.2576 0.4226 0.5152 0.4441 0.3625 0.2009 0.5152 gnomADg_MID 23 NA NA PASS SITE 7,18|7,21 NA NA 1 93 20,34 167,185 60,60 29 1.34 NA 5.93 NA FALSE 6.00 93 NA NA NA FALSE NA NA 91.41 23 48977739 HCC1395_HCC1395T 0 0.961 28 0,12 0,8 0,24 NA 0/1 NA NA NA NA 0,0,7,21 G/A PANCANCER NA FALSE GRIPAP1 chrX:48977739:48977740:G:A SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 48981275 48981276 G T 40 40 1 LOW GRIPAP1 ENSG00000068400 T synonymous_variant Transcript ENST00000376423 protein_coding 21/26 ENST00000376423.8:c.1870C>A ENSP00000365606.5:p.R624= ENSP00000365606.5 p.R624= 1905 1870 624 R Cgg/Agg rs368055066&COSV64551154&COSV64551750 -1 SNV HGNC HGNC:18706 YES NM_020137.5 1 P2 CCDS35248.1 ENSP00000365606 Q4V328.146 UPI0004620CB8 Q4V328-1 AlphaFold_DB_import:AF-Q4V328-F1&Coiled-coils_(Ncoils):Coil&PANTHER:PTHR18978 2.765e-05 0 0 0 0 0 4.955e-05 0.0002223 0 8.894e-05 0 0 0 0 0 0 0 0.000188 0 0 0.0002223 gnomADe_OTH 0&1&1 0&1&1 23 NA NA PASS SITE 29,11|26,14 NA NA 1 93 29,20 176,162 60,60 27 1.51 NA 9.33 NA FALSE 6.00 93 NA NA NA FALSE NA NA 123.44 23 48981275 HCC1395_HCC1395T 0 0.968 40 0,10 0,17 0,28 NA 0/1 NA NA NA NA 0,0,26,14 G/T PANCANCER NA FALSE GRIPAP1_p.R624= chrX:48981275:48981276:G:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 49190868 49190869 G A 15 15 1 MODIFIER SYP ENSG00000102003 A intron_variant Transcript ENST00000263233 protein_coding 6/6 ENST00000263233.9:c.*4+565C>T NA rs3817678 -1 SNV HGNC HGNC:11506 YES NM_003179.3 1 P1 CCDS14321.1 ENSP00000263233 P08247.194 UPI0000117AEC P08247-1 1 0.4281 0.1715 0.3989 0.3141 0.6854 0.6546 0.5146 0.2422 0.6051 0.4258 0.775 0.3393 0.6083 0.658 0.6703 0.5467 0.6215 0.775 gnomADg_ASJ 23 NA NA PASS SITE 20,10|10,5 NA NA 1 93 34,20 192,192 60,60 35 1.44 NA 7.47 NA FALSE 6.00 90 NA NA NA FALSE NA NA 46.77 23 49190868 HCC1395_HCC1395T 0 0.923 15 0,8 0,3 0,11 NA 0/1 NA NA NA NA 0,0,10,5 G/A PANCANCER NA FALSE SYP chrX:49190868:49190869:G:A SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 53556270 53556271 C A 42 42 1 MODIFIER HUWE1 ENSG00000086758 A intron_variant Transcript ENST00000262854 protein_coding 60/83 ENST00000262854.11:c.8206+1112G>T NA -1 SNV HGNC HGNC:30892 YES NM_031407.7 1 P2 CCDS35301.1 ENSP00000262854 Q7Z6Z7.199 A0A024R9W5.65 UPI00004A0DAC Q7Z6Z7-1 1 23 NA NA PASS SITE 26,32|20,22 NA NA 1 93 20,20 156,162 60,60 27 1.62 NA 12.04 NA FALSE 6.00 93 NA NA NA FALSE NA NA 129.42 23 53556270 HCC1395_HCC1395T 0 0.969 42 0,11 0,18 0,30 NA 0/1 NA NA NA NA 0,0,20,22 C/A PANCANCER NA FALSE HUWE1 chrX:53556270:53556271:C:A SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 63754668 63754669 G A 32 32 1 MODIFIER ARHGEF9 ENSG00000131089 A 5_prime_UTR_variant Transcript ENST00000253401 protein_coding 1/10 ENST00000253401.10:c.-356C>T NA 446 -1 SNV HGNC HGNC:14561 1 P4 CCDS35315.1 ENSP00000253401 O43307.176 UPI000006F940 O43307-1 1 23 NA NA PASS SITE 17,16|16,16 NA NA 1 93 36,20 160,153 60,60 40 1.40 NA 7.22 NA FALSE 6.00 93 NA NA NA FALSE NA NA 93.16 23 63754668 HCC1395_HCC1395T 0 0.957 32 0,9 0,11 0,21 NA 0/1 NA NA NA NA 0,0,16,16 G/A PANCANCER NA FALSE ARHGEF9 chrX:63754668:63754669:G:A SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 68043451 68043452 A G 35 35 1 MODIFIER OPHN1 ENSG00000079482 G 3_prime_UTR_variant Transcript ENST00000355520 protein_coding 25/25 ENST00000355520.6:c.*3721T>C NA 6462 rs7888212 -1 SNV HGNC HGNC:8148 YES NM_002547.3 1 P1 CCDS14388.1 ENSP00000347710 O60890.177 UPI000003319E O60890-1 1 0.5189 0.9621 0.3874 0.356 0.3486 0.351 0.4807 0.8881 0.3911 0.3773 0.3163 0.3388 0.2305 0.3879 0.3242 0.4654 0.3311 0.9621 AFR 23 NA NA PASS SITE 24,20|21,14 NA NA 1 39 20,20 150,147 60,60 36 1.50 NA 9.03 NA FALSE 0.350 93 NA NA NA FALSE NA NA 96.65 23 68043451 HCC1395_HCC1395T 0 0.958 35 0,7 0,14 0,22 NA 0/1 NA NA NA NA 0,0,21,14 A/G PANCANCER NA FALSE OPHN1 chrX:68043451:68043452:A:G SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 68046073 68046075 C CT 63 63 1 MODIFIER OPHN1 ENSG00000079482 T 3_prime_UTR_variant Transcript ENST00000355520 protein_coding 25/25 ENST00000355520.6:c.*1098_*1099insA NA 3839-3840 rs200336978 -1 insertion HGNC HGNC:8148 YES NM_002547.3 1 P1 CCDS14388.1 ENSP00000347710 O60890.177 UPI000003319E O60890-1 1 0.1823 0.3071 0.1622 0.0052 0.2676 0.1198 0.2389 0.2732 0.3928 0.1614 0.2684 0.00338 0.2159 0.2773 0.256 0.2249 0.1104 0.3928 gnomADg_AMI 23 NA NA PASS SITE 24,30|33,30 NA NA 1 57 20,20 184,186 60,60 38 1.60 NA 11.60 NA FALSE 0.625 93 6,7 T NA TRUE NA 93 124.69 23 68046073 HCC1395_HCC1395T 0 0.979 63 0,16 0,20 0,46 NA 0/1 NA NA NA NA 0,0,33,30 C/CT PANCANCER NA FALSE OPHN1 chrX:68046073:68046075:C:CT indel 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 68532334 68532335 C T 61 61 1 MODIFIER YIPF6 ENSG00000181704 T 3_prime_UTR_variant Transcript ENST00000374622 protein_coding 6/6 ENST00000374622.3:c.*335C>T NA 1202 rs1012089086 1 SNV HGNC HGNC:28304 2 CCDS56604.1 ENSP00000363751 Q96EC8.145 UPI00002122B7 Q96EC8-2 2.682e-05 0 0 0 0 0 0 0 5.638e-05 0 0 5.638e-05 gnomADg_NFE 23 NA NA PASS SITE 38,30|37,24 NA NA 1 93 20,20 170,166 60,60 38 1.67 NA 13.85 NA FALSE 6.00 93 NA NA NA FALSE NA NA 172.45 23 68532334 HCC1395_HCC1395T 0 0.975 61 0,10 0,28 0,38 NA 0/1 NA NA NA NA 0,0,37,24 C/T PANCANCER NA FALSE YIPF6 chrX:68532334:68532335:C:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 68717716 68717717 G A 34 34 1 MODERATE STARD8 ENSG00000130052 A missense_variant Transcript ENST00000252336 protein_coding 5/14 ENST00000252336.10:c.562G>A ENSP00000252336.6:p.G188S ENSP00000252336.6 p.G188S 934 562 188 G/S Ggt/Agt rs139380533&COSV52933985 1 SNV HGNC HGNC:19161 1 CCDS14390.1 ENSP00000252336 Q92502.165 UPI000016A011 Q92502-1 tolerated(0.63) benign(0) AlphaFold_DB_import:AF-Q92502-F1&PANTHER:PTHR12659&Low_complexity_(Seg):seg 0.0003 0.001 0 0 0 0 0.0003228 0.0001527 7.297e-05 0 0 0 0.000651 0.0004432 0 0.0005498 0.0003864 0.01316 0 0 0 0 0 0.0007694 0 0 0.01316 gnomADg_AMI 0&1 0&1 23 NA NA PASS SITE 26,32|17,17 NA NA 1 93 20,28 169,186 60,60 28 1.63 NA 12.64 NA FALSE 3.57 93 NA NA NA FALSE NA NA 112.30 23 68717716 HCC1395_HCC1395T 0 0.964 34 0,6 0,18 0,26 NA 0/1 NA NA NA NA 0,0,17,17 G/A PANCANCER NA FALSE STARD8_p.G188S chrX:68717716:68717717:G:A SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 70038122 70038123 G C 12 12 1 MODIFIER AWAT2 ENSG00000147160 C downstream_gene_variant Transcript ENST00000276101 protein_coding NA rs3764746 2420 -1 SNV HGNC HGNC:23251 YES NM_001002254.1 5 P1 CCDS35320.1 ENSP00000421172 Q6E213.131 UPI00001D7BE0 0.1730 0.1675 0.2557 0.195 0.0183 0.2618 0.08397 0.1357 0.1721 0.2058 0.01927 0.1813 0.02863 0.03782 0.02589 0.09066 0.2164 0.2618 SAS 23 NA NA PASS SITE 3,10|2,10 NA NA 1 5 39,40 174,208 60,60 31 1.08 NA 3.31 NA FALSE 1.19 93 NA NA NA FALSE NA NA 44.53 23 70038122 HCC1395_HCC1395T 0 0.917 12 0,4 0,5 0,10 NA 0/1 NA NA NA NA 0,0,2,10 G/C PANCANCER NA FALSE AWAT2 chrX:70038122:70038123:G:C SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 71378281 71378282 GAGATAT G 106 106 1 MODERATE TAF1 ENSG00000147133 - inframe_deletion Transcript ENST00000276072 protein_coding 2/34 ENST00000276072.9:c.272_277del ENSP00000276072.5:p.ID91del ENSP00000276072.5 p.ID91del 267-272 267-272 89-91 GDI/G ggAGATATa/gga rs1131691413 1 cds_start_NF deletion HGNC HGNC:11535 5 ENSP00000276072 P21675.234 UPI001B8967DD 1 PDB-ENSP_mappings:5fur.G&PDB-ENSP_mappings:6mzd.A&AlphaFold_DB_import:AF-P21675-F1&PIRSF:PIRSF003047&PANTHER:PTHR13900 5 2.686e-05 0 0 0 0 0.0002809 0 0 3.763e-05 0 0 0.0002809 gnomADg_EAS uncertain_significance 1 23 NA NA PASS SITE 39,54|46,60 NA NA 1 93 20,20 170,172 60,60 39 1.85 NA 20.08 NA FALSE 4.31 93 NA NA NA FALSE NA NA 474.34 23 71378281 HCC1395_HCC1395T 0 0.987 106 0,29 0,23 0,75 NA 0/1 NA NA NA NA 0,0,46,60 GAGATAT/G PANCANCER NA FALSE TAF1_p.ID91del chrX:71378281:71378282:GAGATAT:G indel 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 71544434 71544435 A C 9 9 1 MODIFIER OGT ENSG00000147162 C intron_variant Transcript ENST00000373701 protein_coding 3/21 ENST00000373701.7:c.433-133A>C NA rs773975440 1 SNV HGNC HGNC:8127 1 A1 CCDS35502.1 ENSP00000362805 O15294.234 UPI0000130C59 O15294-3 1 0.001534 0.0004536 0 0.0002857 0.0003768 0 0.001322 0 0.002723 0.0006662 0 0.002723 gnomADg_NFE 23 NA NA PASS SITE 8,1|8,1 NA NA 1 15 36,38 179,186 60,60 8 0.974 NA 2.41 NA FALSE 2.81 93 NA NA NA FALSE NA NA 34.09 23 71544434 HCC1395_HCC1395T 0 0.912 9 0,4 0,3 0,9 NA 0/1 NA NA NA NA 0,0,8,1 A/C PANCANCER NA FALSE OGT chrX:71544434:71544435:A:C SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 72569035 72569036 C T 7 7 1 MODIFIER HDAC8 ENSG00000147099 T intron_variant Transcript ENST00000373554 protein_coding 2/3 ENST00000373554.6:c.165-151G>A NA rs12156784 -1 SNV HGNC HGNC:13315 2 CCDS55450.1 ENSP00000362655 Q9BY41.188 UPI000059DB58 Q9BY41-8 1 0.0154 0.002 0.0153 0.0013 0.0274 0.0362 0.02729 0.005207 0 0.01369 0.02443 0.0002769 0.03507 0.07113 0.04328 0.02512 0.04356 0.07113 gnomADg_MID likely_benign 1 23 NA NA PASS SITE 5,13|1,6 NA NA 1 13 20,39 205,156 60,60 24 1.16 NA 3.91 NA FALSE 1.48 40 NA NA NA FALSE NA NA 25.83 23 72569035 HCC1395_HCC1395T 0 0.875 7 0,0 0,5 0,6 NA 0/1 NA NA NA NA 0,0,1,6 C/T PANCANCER NA FALSE HDAC8 chrX:72569035:72569036:C:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 72635090 72635091 T A 41 41 1 MODIFIER PHKA1 ENSG00000067177 A intron_variant Transcript ENST00000339490 protein_coding 16/30 ENST00000339490.7:c.1714+65A>T NA rs782303224 -1 SNV HGNC HGNC:8925 1 CCDS48137.1 ENSP00000342469 P46020.192 UPI0000212364 P46020-2 1 0.0007925 0.0002914 0 9.439e-05 0.0007524 0 0 0 0.001445 0 0 0.001445 gnomADg_NFE 23 NA NA PASS SITE 21,19|22,19 NA NA 1 82 20,20 162,173 60,60 34 1.40 NA 7.22 NA FALSE 3.16 93 NA NA NA FALSE NA NA 122.75 23 72635090 HCC1395_HCC1395T 0 0.968 41 0,9 0,17 0,28 NA 0/1 NA NA NA NA 0,0,22,19 T/A PANCANCER NA FALSE PHKA1 chrX:72635090:72635091:T:A SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 73005492 73005493 A C 88 88 1 MODIFIER PABPC1L2B ENSG00000184388 C 3_prime_UTR_variant Transcript ENST00000373521 protein_coding 1/1 ENST00000373521.4:c.*1247A>C NA 2554 rs1330356366&COSV65174838 1 SNV HGNC HGNC:31852 YES NM_001042506.2 P1 CCDS43972.1 ENSP00000362621 Q5JQF8.137 UPI00001C207A 0.001431 0.0009761 0 0.0006672 0.001132 0.0008364 0 0 0.002161 0.001332 0 0.002161 gnomADg_NFE 0&1 0&1 23 NA NA PASS SITE 20,37|35,53 NA NA 1 93 20,20 164,164 60,60 32 1.59 NA 11.44 NA FALSE 2.88 93 NA NA NA FALSE NA NA 249.49 23 73005492 HCC1395_HCC1395T 0 0.983 88 0,23 0,23 0,55 NA 0/1 NA NA NA NA 0,0,35,53 A/C PANCANCER NA FALSE PABPC1L2B chrX:73005492:73005493:A:C SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 73563683 73563684 G C 10 10 1 MODIFIER CHIC1 ENSG00000204116 C intron_variant Transcript ENST00000373502 protein_coding 1/5 ENST00000373502.10:c.296+103G>C NA 1 SNV HGNC HGNC:1934 YES NM_001039840.4 1 P1 CCDS35335.2 ENSP00000362601 Q5VXU3.129 UPI0000160F74 Q5VXU3-1 23 NA NA PASS SITE 1,14|1,9 NA NA 1 68 38,40 199,234 60,60 46 1.19 NA 4.21 NA FALSE 6.00 93 NA NA NA FALSE NA NA 39.24 23 73563683 HCC1395_HCC1395T 0 0.909 10 0,4 0,4 0,9 NA 0/1 NA NA NA NA 0,0,1,9 G/C PANCANCER NA FALSE CHIC1 chrX:73563683:73563684:G:C SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 75369246 75369247 G T 48 48 1 MODIFIER ZDHHC15 ENSG00000102383 T 3_prime_UTR_variant Transcript ENST00000373367 protein_coding 12/12 ENST00000373367.8:c.*3732C>A NA 4759 -1 SNV HGNC HGNC:20342 YES NM_144969.3 1 P1 CCDS14430.1 ENSP00000362465 Q96MV8.157 UPI000006DB5A Q96MV8-1 1 23 NA NA PASS SITE 28,30|29,19 NA NA 1 93 20,20 169,184 60,60 35 1.61 NA 11.74 NA FALSE 6.00 93 NA NA NA FALSE NA NA 140.30 23 75369246 HCC1395_HCC1395T 0 0.971 48 0,9 0,22 0,33 NA 0/1 NA NA NA NA 0,0,29,19 G/T PANCANCER NA FALSE ZDHHC15 chrX:75369246:75369247:G:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 77456823 77456824 G T 10 10 1 MODIFIER FGF16 ENSG00000196468 T 3_prime_UTR_variant Transcript ENST00000439435 protein_coding 3/3 ENST00000439435.3:c.*301G>T NA 1211 rs41300245 1 SNV HGNC HGNC:3672 YES NM_003868.3 1 P1 CCDS75996.1 ENSP00000399324 O43320.162 A0A7U3L5H2.5 UPI00000374B2 1 0.0074 0 0.0095 0 0.0235 0.007 0.01937 0.004534 0.00146 0.01436 0.0144 0.0002814 0.01958 0.008475 0.03136 0.02129 0.004949 0.03136 gnomADg_NFE likely_benign 1 23 NA NA PASS SITE 10,15|4,6 NA NA 1 34 20,20 184,156 60,60 18 1.26 NA 5.12 NA FALSE 1.66 68 NA NA NA FALSE NA NA 30.50 23 77456823 HCC1395_HCC1395T 0 0.893 10 0,5 0,2 0,7 NA 0/1 NA NA NA NA 0,0,4,6 G/T PANCANCER NA FALSE FGF16 chrX:77456823:77456824:G:T SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 77681733 77681734 T C 45 45 1 MODERATE ATRX ENSG00000085224 C missense_variant Transcript ENST00000373344 protein_coding 9/35 ENST00000373344.11:c.3523A>G ENSP00000362441.4:p.K1175E ENSP00000362441.4 p.K1175E 3738 3523 1175 K/E Aaa/Gaa rs1252599533&COSV64887089 -1 SNV HGNC HGNC:886 YES NM_000489.6 1 P2 CCDS14434.1 ENSP00000362441 P46100.236 A4LAA3.95 UPI00001B644E P46100-1 1 deleterious_low_confidence(0.02) AlphaFold_DB_import:AF-P46100-F1&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg 8.962e-06 0 0 0 0 0 0 0 1.886e-05 0 0 1.886e-05 gnomADg_NFE 0&1 0&1 23 NA NA PASS SITE 27,36|17,28 NA NA 1 93 20,20 158,167 60,60 33 1.63 NA 12.34 NA FALSE 6.00 93 NA NA NA FALSE NA NA 132.17 23 77681733 HCC1395_HCC1395T 0 0.968 45 0,11 0,14 0,29 NA 0/1 NA NA NA NA 0,0,17,28 T/C PANCANCER TRUE TRUE ATRX_p.K1175E chrX:77681733:77681734:T:C SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 78015863 78015864 G C 59 59 1 MODERATE ATP7A ENSG00000165240 C missense_variant Transcript ENST00000341514 protein_coding 12/23 ENST00000341514.11:c.2608G>C ENSP00000345728.6:p.D870H ENSP00000345728.6 p.D870H 2772 2608 870 D/H Gat/Cat 1 SNV HGNC HGNC:869 YES NM_000052.7 1 P1 CCDS35339.1 ENSP00000345728 Q04656.240 UPI000044D414 Q04656-1 1 deleterious_low_confidence(0) probably_damaging(0.997) Gene3D:2.70.150.10&PDB-ENSP_mappings:2kij.A&AlphaFold_DB_import:AF-Q04656-F1&Pfam:PF00122&Prints:PR00119&Superfamily:SSF81653&Superfamily:SSF81665&TIGRFAM:TIGR01494&TIGRFAM:TIGR01525&CDD:cd02094 23 NA NA PASS SITE 15,24|20,39 NA NA 1 93 20,20 165,179 60,60 35 1.16 NA 7.78 NA FALSE 6.00 93 NA NA NA FALSE NA NA 180.38 23 78015863 HCC1395_HCC1395T 0 0.977 59 0,14 0,23 0,41 NA 0/1 NA NA NA NA 0,0,20,39 G/C PANCANCER NA FALSE ATP7A_p.D870H chrX:78015863:78015864:G:C SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 78947904 78947905 C A 52 52 1 MODIFIER P2RY10 ENSG00000078589 A intron_variant Transcript ENST00000171757 protein_coding 2/3 ENST00000171757.3:c.-157+41C>A NA rs2251819 1 SNV HGNC HGNC:19906 YES NM_014499.4 1 P1 CCDS14442.1 ENSP00000171757 O00398.176 UPI0000050471 0.7817 0.6032 0.7462 0.9961 0.7781 0.8329 0.7296 0.6216 0.7259 0.7557 0.7654 0.9958 0.7585 0.7426 0.7599 0.7572 0.7905 0.9961 EAS 23 NA NA PASS SITE 41,65|19,33 NA NA 1 93 23,37 185,206 60,60 24 1.91 NA 24.08 NA FALSE 0.131 93 NA NA NA FALSE NA NA 184.28 23 78947904 HCC1395_HCC1395T 0 0.977 52 0,12 0,27 0,42 NA 0/1 NA NA NA NA 0,0,19,33 C/A PANCANCER NA FALSE P2RY10 chrX:78947904:78947905:C:A SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 80682179 80682180 T A 8 8 1 MODIFIER BRWD3 ENSG00000165288 A intron_variant Transcript ENST00000373275 protein_coding 38/40 ENST00000373275.5:c.4398-85A>T NA -1 SNV HGNC HGNC:17342 YES NM_153252.5 1 P1 CCDS14447.1 ENSP00000362372 Q6RI45.149 UPI000045785B Q6RI45-1 1 23 NA NA PASS SITE 1,13|0,8 NA NA 1 60 35,35 203,233 60,60 36 1.15 NA 3.91 NA FALSE 6.00 76 NA NA NA FALSE NA NA 30.40 23 80682179 HCC1395_HCC1395T 0 0.903 8 0,2 0,5 0,8 NA 0/1 NA NA NA NA 0,0,0,8 T/A PANCANCER NA FALSE BRWD3 chrX:80682179:80682180:T:A SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 81298099 81298100 A G 180 180 1 MODIFIER SH3BGRL ENSG00000131171 G 3_prime_UTR_variant Transcript ENST00000373212 protein_coding 4/4 ENST00000373212.6:c.*872A>G NA 1316 rs41300896 1 SNV HGNC HGNC:10823 YES NM_003022.3 1 P1 CCDS14449.1 ENSP00000362308 O75368.182 V9HW48.66 UPI0000135938 0.0077 0 0.0076 0 0.0235 0.0097 0.0133 0.002103 0 0.0092 0.01511 0 0.03314 0.004219 0.01967 0.01334 0.007994 0.03314 gnomADg_FIN 23 NA NA PASS SITE 69,80|72,108 NA NA 1 93 20,20 172,176 60,60 40 2.01 NA 30.01 NA FALSE 1.80 93 NA NA NA FALSE NA NA 582.01 23 81298099 HCC1395_HCC1395T 0 0.992 180 0,46 0,68 0,127 NA 0/1 NA NA NA NA 0,0,72,108 A/G PANCANCER NA FALSE SH3BGRL chrX:81298099:81298100:A:G SNV 2:0 chrX:11664955:86739680:2:0:1 TRUE NA 0.96 +chrX 100350874 100350875 C T 35 35 1 MODIFIER PCDH19 ENSG00000165194 T intron_variant Transcript ENST00000255531 protein_coding 2/4 ENST00000255531.8:c.2476-170G>A NA rs972472566 -1 SNV HGNC HGNC:14270 1 P4 CCDS43976.1 ENSP00000255531 Q8TAB3.177 UPI0000232D09 Q8TAB3-2 1 2.667e-05 6.469e-05 0 0 0 0 0 0 1.876e-05 0 0 6.469e-05 gnomADg_AFR 23 NA NA PASS SITE 4,10|9,26 NA NA 1 69 20,20 153,177 60,60 24 1.04 NA 3.01 NA FALSE 4.61 93 NA NA NA FALSE NA NA 114.26 23 100350874 HCC1395_HCC1395T 0 0.965 35 0,11 0,12 0,26 NA 0/1 NA NA NA NA 0,0,9,26 C/T PANCANCER NA FALSE PCDH19 chrX:100350874:100350875:C:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 100585422 100585423 G C 32 32 1 MODIFIER TNMD ENSG00000000005 C intron_variant Transcript ENST00000373031 protein_coding 2/6 ENST00000373031.5:c.180+60G>C NA rs56242689 1 SNV HGNC HGNC:17757 YES NM_022144.3 1 P1 CCDS14469.1 ENSP00000362122 Q9H2S6.151 UPI0000001042 Q9H2S6-1 0.0127 0.007 0.0286 0 0.0326 0.0014 0.02275 0.01141 0.105 0.02843 0.03446 0 0.01824 0.02929 0.02944 0.03061 0.0007502 0.105 gnomADg_AMI 23 NA NA PASS SITE 3,15|3,29 NA NA 1 28 40,39 174,185 60,60 17 1.23 NA 4.81 NA FALSE 1.66 93 NA NA NA FALSE NA NA 122.99 23 100585422 HCC1395_HCC1395T 0 0.968 32 0,8 0,17 0,29 NA 0/1 NA NA NA NA 0,0,3,29 G/C PANCANCER NA FALSE TNMD chrX:100585422:100585423:G:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 100665498 100665499 C G 40 84 0.476190476190476 MODIFIER SRPX2 ENSG00000102359 G intron_variant Transcript ENST00000373004 protein_coding 6/10 ENST00000373004.5:c.660-38C>G NA 1 SNV HGNC HGNC:30668 YES NM_014467.3 1 P1 CCDS14471.1 ENSP00000362095 O60687.165 UPI000006CCC6 1 23 NA NA PASS SITE 49,36|25,15 NA NA 1 92 30,39 183,195 60,60 30 1.52 NA 9.63 NA FALSE 6.00 93 NA NA NA FALSE NA NA 137.58 23 100665498 HCC1395_HCC1395T 44 0.515 84 12,16 21,19 34,36 NA 0/1 NA NA NA NA 22,22,25,15 C/G PANCANCER NA FALSE SRPX2 chrX:100665498:100665499:C:G SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 100731629 100731630 GA G 13 13 1 MODIFIER SYTL4 ENSG00000102362 - intron_variant Transcript ENST00000263033 protein_coding 1/16 ENST00000263033.9:c.-71+374del NA rs34576016 -1 deletion HGNC HGNC:15588 2 P1 CCDS14472.1 ENSP00000263033 Q96C24.191 A0A024RCF8.69 UPI00001AE9F2 Q96C24-1 0.5821 0.6469 0.4069 0.5967 0.4661 0.472 0.5363 0.5665 0.5615 0.5712 0.5998 0.6469 gnomADg_AFR 23 NA NA PASS SITE 5,14|3,10 NA NA 1 67 38,38 175,176 60,60 33 1.25 NA 4.79 NA FALSE 6.00 93 5,4 A NA TRUE NA 93 32.24 23 100731629 HCC1395_HCC1395T 0 0.927 13 0,0 0,3 0,11 NA 0/1 NA NA NA NA 0,0,3,10 GA/G PANCANCER NA FALSE SYTL4 chrX:100731629:100731630:GA:G indel 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 101051864 101051865 C T 62 62 1 MODIFIER TRMT2B ENSG00000188917 T 5_prime_UTR_variant Transcript ENST00000372935 protein_coding 1/14 ENST00000372935.5:c.-161G>A NA 207 rs113780984 -1 SNV HGNC HGNC:25748 1 P1 CCDS14477.1 ENSP00000362026 Q96GJ1.171 A0A024RCF5.54 UPI0000070468 Q96GJ1-1 0.0570 0.005 0.1336 0.017 0.111 0.0585 0.08244 0.01548 0.2436 0.1347 0.0919 0.01441 0.1527 0.09787 0.1058 0.09505 0.05932 0.2436 gnomADg_AMI 23 NA NA PASS SITE 15,26|24,39 NA NA 1 19 20,20 170,192 60,60 31 -1.069e+00 NA 5.25 NA FALSE 1.05 93 NA NA NA FALSE NA NA 198.46 23 101051864 HCC1395_HCC1395T 0 0.980 62 0,13 0,30 0,46 NA 0/1 NA NA NA NA 0,0,24,38 C/T PANCANCER NA FALSE TRMT2B chrX:101051864:101051865:C:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 101390487 101390488 G A 147 147 1 MODIFIER BTK ENSG00000010671 A upstream_gene_variant Transcript ENST00000308731 protein_coding NA rs141862637&COSV58117587 4296 -1 SNV HGNC HGNC:1133 YES NM_000061.3 1 P2 CCDS14482.1 ENSP00000308176 Q06187.259 UPI0000126B16 Q06187-1 1 0.0087 0.001 0.0172 0 0.0274 0.0028 0.01683 0.004294 0.01012 0.02136 0.0001278 0.02824 0.0274 0.01827 0.005499 0.01861 0.003594 0.04246 0.02145 0.01995 0 0.02229 0 0.02793 0.0213 0.004762 0.04246 gnomADg_AMI benign 0&1 1&1 23 NA NA PASS SITE 54,29|91,56 NA NA 1 93 20,20 165,164 60,60 33 1.75 NA 16.55 NA FALSE 1.68 93 NA NA NA FALSE NA NA 436.01 23 101390487 HCC1395_HCC1395T 0 0.990 147 0,35 0,57 0,96 NA 0/1 NA NA NA NA 0,0,91,56 G/A PANCANCER NA FALSE BTK chrX:101390487:101390488:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 101656080 101656081 T C 131 131 1 LOW ARMCX2 ENSG00000184867 C synonymous_variant Transcript ENST00000328766 protein_coding 5/5 ENST00000328766.9:c.1509A>G ENSP00000331662.5:p.Q503= ENSP00000331662.5 p.Q503= 1963 1509 503 Q caA/caG rs3850315 -1 SNV HGNC HGNC:16869 1 P1 CCDS14490.1 ENSP00000331662 Q7L311.146 A0A024RCG7.61 UPI0000071305 Gene3D:1.25.10.10&AlphaFold_DB_import:AF-Q7L311-F1&Pfam:PF04826&PANTHER:PTHR15712&Superfamily:SSF48371 0.0331 0.012 0.0458 0 0.0953 0.0223 0.05606 0.01598 0.09412 0.05641 0.0885 0 0.04532 0.1314 0.08317 0.07005 0.01996 0.1314 gnomADg_MID 23 NA NA PASS SITE 32,29|60,71 NA NA 1 93 33,37 182,181 60,60 24 1.69 NA 14.45 NA FALSE 6.00 93 NA NA NA FALSE NA NA 466.95 23 101656080 HCC1395_HCC1395T 0 0.991 131 0,32 0,67 0,105 NA 0/1 NA NA NA NA 0,0,60,71 T/C PANCANCER NA FALSE ARMCX2_p.Q503= chrX:101656080:101656081:T:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 102156023 102156024 T C 45 45 1 MODIFIER BEX5 ENSG00000184515 C upstream_gene_variant Transcript ENST00000333643 protein_coding NA rs6621362 46 -1 SNV HGNC HGNC:27990 YES NM_001012978.3 1 P1 CCDS35350.1 ENSP00000328030 Q5H9J7.125 UPI00001998F9 0.7404 0.6481 0.75 0.9908 0.5666 0.7813 0.6161 0.6533 0.2722 0.68 0.528 0.9863 0.6271 0.6681 0.5584 0.6364 0.7711 0.9908 EAS 23 NA NA PASS SITE 12,23|13,33 NA NA 1 14 20,20 144,168 60,60 29 1.40 NA 7.18 NA FALSE 0.208 93 NA NA NA FALSE NA NA 142.27 23 102156023 HCC1395_HCC1395T 0 0.972 45 0,16 0,12 0,32 NA 0/1 NA NA NA NA 0,0,13,32 T/C PANCANCER NA FALSE BEX5 chrX:102156023:102156024:T:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 103502863 103502864 C T 22 40 0.55 MODIFIER RAB40A ENSG00000172476 T intron_variant Transcript ENST00000304236 protein_coding 2/2 ENST00000304236.2:c.-70-2037G>A NA -1 SNV HGNC HGNC:18283 YES NM_080879.3 2 P1 CCDS35357.1 ENSP00000305648 Q8WXH6.177 UPI000013E953 23 NA NA PASS SITE 16,25|9,13 NA NA 1 38 20,20 145,145 60,60 30 1.18 NA 4.21 NA FALSE 6.00 48 NA NA NA FALSE NA NA 56.09 23 103502863 HCC1395_HCC1395T 18 0.556 40 2,3 9,9 11,14 NA 0/1 NA NA NA NA 7,11,9,13 C/T PANCANCER NA FALSE RAB40A chrX:103502863:103502864:C:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 104193582 104193586 T TTGG 393 393 1 MODIFIER FAM199X ENSG00000123575 TGG downstream_gene_variant Transcript ENST00000299906 protein_coding_CDS_not_defined NA rs113076514 2136 1 insertion HGNC HGNC:25195 1 0.6212 0.7876 0.4198 0.6296 0.6005 0.5487 0.6148 0.7764 0.5945 0.4608 0.6089 0.6357 0.5493 0.7064 0.562 0.5982 0.5413 0.7876 AFR 23 NA NA PASS SITE 80,101|161,232 NA NA 2 93 20,20 157,165 60,60 35 2.08 NA 34.97 NA FALSE 0.218 93 NA NA NA FALSE NA NA 1758.26 23 104193582 HCC1395_HCC1395T 0 0.996 393 0,68 0,108 0,267 NA 0|1 0|1 104193582_T_TTGG NA 104193582 0,0,161,232 T|TTGG PANCANCER NA FALSE FAM199X chrX:104193582:104193586:T:TTGG indel 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 104193585 104193586 A G 390 390 1 MODIFIER FAM199X ENSG00000123575 G downstream_gene_variant Transcript ENST00000299906 protein_coding_CDS_not_defined NA rs72616862 2139 1 SNV HGNC HGNC:25195 1 0.6215 0.7886 0.4198 0.6296 0.6005 0.5487 0.6158 0.7771 0.596 0.4612 0.6109 0.6389 0.5535 0.7094 0.5624 0.5981 0.5467 0.7886 AFR 23 NA NA PASS SITE 80,102|161,229 NA NA 2 93 20,20 158,165 60,60 34 2.08 NA 34.96 NA FALSE 0.218 93 NA NA NA FALSE NA NA 1748.13 23 104193585 HCC1395_HCC1395T 0 0.996 390 0,64 0,108 0,264 NA 0|1 0|1 104193582_T_TTGG NA 104193582 0,0,161,229 A|G PANCANCER NA FALSE FAM199X chrX:104193585:104193586:A:G SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 105219811 105219812 C T 22 22 1 MODIFIER IL1RAPL2 ENSG00000189108 T intron_variant Transcript ENST00000372582 protein_coding 3/10 ENST00000372582.6:c.357-14007C>T NA rs782658900 1 SNV HGNC HGNC:5997 YES NM_017416.2 1 P1 CCDS14517.1 ENSP00000361663 Q9NP60.166 UPI0000073DF7 0.0005811 0.0002649 0 0 0 0 0.002047 0 0.0008361 0 0 0.002047 gnomADg_FIN 23 NA NA PASS SITE 7,11|8,14 NA NA 1 47 31,36 183,170 60,60 23 1.21 NA 4.21 NA FALSE 2.93 93 NA NA NA FALSE NA NA 76.75 23 105219811 HCC1395_HCC1395T 0 0.950 22 0,7 0,9 0,18 NA 0/1 NA NA NA NA 0,0,8,14 C/T PANCANCER NA FALSE IL1RAPL2 chrX:105219811:105219812:C:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 107601386 107601387 G T 73 176 0.414772727272727 MODERATE FRMPD3 ENSG00000147234 T missense_variant Transcript ENST00000276185 protein_coding 16/16 ENST00000276185.9:c.3347G>T ENSP00000276185.5:p.S1116I ENSP00000276185.5 p.S1116I 3446 3347 1116 S/I aGc/aTc COSV52199335 1 SNV HGNC HGNC:29382 5 P1 CCDS94646.1 ENSP00000276185 Q5JV73.132 UPI000387B8F4 tolerated_low_confidence(0.18) benign(0.017) AlphaFold_DB_import:AF-Q5JV73-F1&PANTHER:PTHR46221&MobiDB_lite:mobidb-lite 1 1 23 NA NA PASS SITE 111,135|38,35 NA NA 1 93 20,20 169,165 60,60 30 2.01 NA 30.10 NA FALSE 6.00 93 NA NA NA FALSE NA NA 189.32 23 107601386 HCC1395_HCC1395T 103 0.420 176 31,23 37,28 71,51 NA 0/1 NA NA NA NA 45,58,38,35 G/T PANCANCER NA FALSE FRMPD3_p.S1116I chrX:107601386:107601387:G:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 107603968 107603969 C T 54 54 1 MODIFIER FRMPD3 ENSG00000147234 T 3_prime_UTR_variant Transcript ENST00000276185 protein_coding 16/16 ENST00000276185.9:c.*595C>T NA 6028 rs41304066&COSV52190975 1 SNV HGNC HGNC:29382 5 P1 CCDS94646.1 ENSP00000276185 Q5JV73.132 UPI000387B8F4 0.0456 0.005 0.042 0 0.1567 0.0348 0.112 0.02158 0.1295 0.0627 0.1323 0.0008616 0.256 0.05932 0.1687 0.1066 0.03113 0.256 gnomADg_FIN 0&1 0&1 23 NA NA PASS SITE 19,21|24,30 NA NA 1 47 20,26 165,176 60,60 26 1.47 NA 8.43 NA FALSE 0.863 93 NA NA NA FALSE NA NA 178.39 23 107603968 HCC1395_HCC1395T 0 0.977 54 0,18 0,20 0,41 NA 0/1 NA NA NA NA 0,0,24,30 C/T PANCANCER NA FALSE FRMPD3 chrX:107603968:107603969:C:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 108156191 108156192 T C 68 68 1 MODIFIER COL4A6 ENSG00000197565 C 3_prime_UTR_variant Transcript ENST00000334504 protein_coding 45/45 ENST00000334504.12:c.*809A>G NA 6108 rs5973850 -1 SNV HGNC HGNC:2208 YES NM_033641.4 5 P4 CCDS14542.1 ENSP00000334733 Q14031.215 UPI000015FFB9 Q14031-2 1 0.3823 0.676 0.2099 0.1571 0.436 0.2799 0.4926 0.6596 0.8044 0.262 0.3453 0.1622 0.589 0.3745 0.4692 0.4281 0.3016 0.8044 gnomADg_AMI 23 NA NA PASS SITE 23,34|33,35 NA NA 1 69 20,37 175,187 60,60 21 1.63 NA 12.34 NA FALSE 0.284 93 NA NA NA FALSE NA NA 241.81 23 108156191 HCC1395_HCC1395T 0 0.983 68 0,21 0,33 0,56 NA 0/1 NA NA NA NA 0,0,33,35 T/C PANCANCER NA FALSE COL4A6 chrX:108156191:108156192:T:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 108156283 108156284 A G 91 91 1 MODIFIER COL4A6 ENSG00000197565 G 3_prime_UTR_variant Transcript ENST00000334504 protein_coding 45/45 ENST00000334504.12:c.*717T>C NA 6016 rs1042071 -1 SNV HGNC HGNC:2208 YES NM_033641.4 5 P4 CCDS14542.1 ENSP00000334733 Q14031.215 UPI000015FFB9 Q14031-2 1 0.3823 0.677 0.2099 0.1571 0.436 0.2786 0.4938 0.6602 0.8041 0.2632 0.348 0.1647 0.5931 0.3814 0.4699 0.4281 0.2987 0.8041 gnomADg_AMI 23 NA NA PASS SITE 33,28|45,46 NA NA 1 63 20,20 152,172 60,60 37 1.62 NA 11.69 NA FALSE 0.284 93 NA NA NA FALSE NA NA 279.04 23 108156283 HCC1395_HCC1395T 0 0.985 91 0,20 0,37 0,64 NA 0/1 NA NA NA NA 0,0,45,46 A/G PANCANCER NA FALSE COL4A6 chrX:108156283:108156284:A:G SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 108161585 108161586 G A 21 21 1 MODIFIER COL4A6 ENSG00000197565 A intron_variant Transcript ENST00000334504 protein_coding 42/44 ENST00000334504.12:c.4333+34C>T NA rs749072437&COSV57871202 -1 SNV HGNC HGNC:2208 YES NM_033641.4 5 P4 CCDS14542.1 ENSP00000334733 Q14031.215 UPI000015FFB9 Q14031-2 1 1.061e-05 0 0 0 0 0 2.114e-05 0 0 2.907e-05 0 0 0 0 0 0 0 5.559e-05 0 0 5.559e-05 gnomADg_NFE 0&1 1&1 23 NA NA PASS SITE 13,8|16,5 NA NA 1 93 20,29 177,152 60,60 26 1.19 NA 4.21 NA FALSE 6.00 93 NA NA NA FALSE NA NA 67.52 23 108161585 HCC1395_HCC1395T 0 0.944 21 0,6 0,10 0,16 NA 0/1 NA NA NA NA 0,0,16,5 G/A PANCANCER NA FALSE COL4A6 chrX:108161585:108161586:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 109481907 109481908 G A 164 164 1 MODIFIER GUCY2F ENSG00000101890 A 5_prime_UTR_variant Transcript ENST00000218006 protein_coding 1/20 ENST00000218006.3:c.-127C>T NA 180 rs494589 -1 SNV HGNC HGNC:4691 YES NM_001522.3 1 P1 CCDS14545.1 ENSP00000218006 P51841.205 UPI000013C740 0.2162 0.1476 0.1851 0.1728 0.3512 0.2368 0.2933 0.1987 0.1647 0.212 0.3398 0.1673 0.4269 0.25 0.3613 0.2803 0.2217 0.4269 gnomADg_FIN 23 NA NA PASS SITE 49,24|109,56 NA NA 1 73 20,20 158,173 60,60 29 -4.080e-01 NA 12.03 NA FALSE 0.493 93 NA NA NA FALSE NA NA 525.94 23 109481907 HCC1395_HCC1395T 0 0.992 164 0,39 0,75 0,119 NA 0/1 NA NA NA NA 0,0,108,56 G/A PANCANCER NA FALSE GUCY2F chrX:109481907:109481908:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 109543085 109543086 G A 59 59 1 MODIFIER NXT2 ENSG00000101888 A 3_prime_UTR_variant Transcript ENST00000218004 protein_coding 5/5 ENST00000218004.5:c.*397G>A NA 1093 rs5943382 1 SNV HGNC HGNC:18151 1 CCDS14546.1 ENSP00000218004 Q9NPJ8.178 UPI000013C73F Q9NPJ8-3 0.3563 0.6261 0.2271 0.1872 0.3734 0.2354 0.4211 0.6034 0.1627 0.2683 0.3438 0.1722 0.4622 0.2564 0.3768 0.3853 0.2413 0.6261 AFR 23 NA NA PASS SITE 41,44|26,33 NA NA 1 93 20,37 179,190 60,60 31 1.80 NA 18.36 NA FALSE 0.367 93 NA NA NA FALSE NA NA 208.25 23 109543085 HCC1395_HCC1395T 0 0.980 59 0,14 0,31 0,49 NA 0/1 NA NA NA NA 0,0,26,33 G/A PANCANCER NA FALSE NXT2 chrX:109543085:109543086:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 109543785 109543786 T C 680 680 1 MODIFIER NXT2 ENSG00000101888 C 3_prime_UTR_variant Transcript ENST00000218004 protein_coding 5/5 ENST00000218004.5:c.*1097T>C NA 1793 rs3204027 1 SNV HGNC HGNC:18151 1 CCDS14546.1 ENSP00000218004 Q9NPJ8.178 UPI000013C73F Q9NPJ8-3 0.1608 0.0289 0.1298 0.0903 0.3668 0.2228 0.2614 0.08193 0.1657 0.1796 0.3411 0.08163 0.456 0.2265 0.3725 0.26 0.2221 0.456 gnomADg_FIN 23 NA NA PASS SITE 143,149|334,346 NA NA 1 93 20,20 148,160 60,60 35 2.24 NA 51.77 NA FALSE 0.527 93 NA NA NA FALSE NA NA 1936.44 23 109543785 HCC1395_HCC1395T 0 0.998 680 0,154 0,244 0,419 NA 0/1 NA NA NA NA 0,0,334,346 T/C PANCANCER NA FALSE NXT2 chrX:109543785:109543786:T:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 112382201 112382202 A G 111 111 1 MODIFIER RTL4 ENSG00000187823 G intron_variant Transcript ENST00000340433 protein_coding 2/3 ENST00000340433.4:c.-285+39084A>G NA rs188300399 1 SNV HGNC HGNC:25214 P1 CCDS35369.1 ENSP00000340590 Q6ZR62.129 UPI00001975B5 0.0011 0.001 0 0 0.0013 0.0028 0.00176 0.0006186 0 0.002079 0 0 0 0 0.002838 0.0006649 0.001509 0.002838 gnomADg_NFE 23 NA NA PASS SITE 18,30|40,71 NA NA 1 93 20,20 164,175 60,60 27 1.52 NA 9.63 NA FALSE 2.81 93 NA NA NA FALSE NA NA 343.32 23 112382201 HCC1395_HCC1395T 0 0.988 111 0,45 0,27 0,77 NA 0/1 NA NA NA NA 0,0,40,71 A/G PANCANCER NA FALSE RTL4 chrX:112382201:112382202:A:G SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 115191630 115191631 G A 290 291 0.996563573883162 MODIFIER LRCH2 ENSG00000130224 A intron_variant Transcript ENST00000317135 protein_coding 1/20 ENST00000317135.13:c.350-3260C>T NA rs186877600 -1 SNV HGNC HGNC:29292 YES NM_020871.4 1 P2 CCDS48155.1 ENSP00000325091 Q5VUJ6.152 UPI000022DB30 Q5VUJ6-1 0.0257 0.002 0.0305 0 0.0875 0.0167 0.04834 0.009605 0.02931 0.04447 0.0003685 0.07383 0.07456 0.05152 0.01554 0.04728 0.01026 0.08169 0.03914 0.04749 0.0008678 0.05822 0.02643 0.07311 0.0473 0.01545 0.0875 EUR 23 NA NA PASS SITE 142,126|153,137 NA NA 1 93 20,20 166,165 60,60 36 2.28 NA 56.46 NA FALSE 1.28 93 NA NA NA FALSE NA NA 911.23 23 115191630 HCC1395_HCC1395T 1 0.995 291 0,87 0,89 1,203 NA 0/1 NA NA NA NA 0,1,153,137 G/A PANCANCER NA FALSE LRCH2 chrX:115191630:115191631:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 116170939 116170940 G A 154 154 1 MODIFIER AGTR2 ENSG00000180772 A intron_variant Transcript ENST00000371906 protein_coding 1/2 ENST00000371906.5:c.-95-29G>A NA rs1403543&CS052026&COSV64156521 1 SNV HGNC HGNC:338 YES NM_000686.5 1 P1 CCDS14569.1 ENSP00000360973 P50052.192 UPI0000125687 1 0.5038 0.337 0.7061 0.5694 0.564 0.4554 0.4811 0.3465 0.5332 0.6272 0.542 0.5684 0.4493 0.5085 0.5245 0.5044 0.4608 0.7061 AMR 0&0&1 1&1&1 23 NA NA PASS SITE 43,43|86,68 NA NA 1 93 20,20 175,160 60,60 37 1.76 NA 16.86 NA FALSE 0.329 93 NA NA NA FALSE NA NA 419.50 23 116170939 HCC1395_HCC1395T 0 0.990 154 0,36 0,55 0,94 NA 0/1 NA NA NA NA 0,0,86,68 G/A PANCANCER NA FALSE AGTR2 chrX:116170939:116170940:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 116174557 116174558 G T 102 102 1 MODIFIER AGTR2 ENSG00000180772 T 3_prime_UTR_variant Transcript ENST00000371906 protein_coding 3/3 ENST00000371906.5:c.*1185G>T NA 2445 rs17231478 1 SNV HGNC HGNC:338 YES NM_000686.5 1 P1 CCDS14569.1 ENSP00000360973 P50052.192 UPI0000125687 1 0.0244 0.001 0.0496 0 0.0705 0.0153 0.0343 0.006293 0.01023 0.0326 0.03792 0 0.04757 0.03797 0.05266 0.03787 0.01466 0.0705 EUR 23 NA NA PASS SITE 32,40|40,62 NA NA 1 93 20,34 180,182 60,60 30 1.73 NA 15.95 NA FALSE 1.44 93 NA NA NA FALSE NA NA 335.69 23 116174557 HCC1395_HCC1395T 0 0.988 102 0,29 0,43 0,80 NA 0/1 NA NA NA NA 0,0,40,62 G/T PANCANCER NA FALSE AGTR2 chrX:116174557:116174558:G:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 118824239 118824240 C T 34 34 1 MODIFIER ZCCHC12 ENSG00000174460 T intron_variant Transcript ENST00000310164 protein_coding 1/3 ENST00000310164.3:c.-291-100C>T NA 1 SNV HGNC HGNC:27273 YES NM_173798.4 1 P1 CCDS14574.1 ENSP00000308921 Q6PEW1.141 UPI00000373C7 23 NA NA PASS SITE 9,5|21,13 NA NA 1 93 27,20 157,178 60,60 24 1.08 NA 3.31 NA FALSE 6.00 93 NA NA NA FALSE NA NA 105.43 23 118824239 HCC1395_HCC1395T 0 0.964 34 0,9 0,16 0,25 NA 0/1 NA NA NA NA 0,0,21,13 C/T PANCANCER NA FALSE ZCCHC12 chrX:118824239:118824240:C:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 119588394 119588396 A AT 83 95 0.873684210526316 MODIFIER NKRF ENSG00000186416 T 3_prime_UTR_variant Transcript ENST00000304449 protein_coding 3/3 ENST00000304449.8:c.*957_*958insA NA 3759-3760 rs374040551 -1 insertion HGNC HGNC:19374 1 ENSP00000304803 O15226.210 A3F769.118 UPI00001BBB5F O15226-1 0.004437 0.003185 0.006024 0.001843 0 0.06281 0.0006314 0 0.002473 0.001419 0.002371 0.06281 gnomADg_EAS 23 NA NA PASS SITE 29,41|42,41 NA NA 1 93 20,20 181,183 60,60 35 1.19 NA 11.81 NA FALSE 2.14 93 12,13 T NA TRUE NA 93 81.55 23 119588394 HCC1395_HCC1395T 12 0.868 95 3,14 4,38 9,58 NA 0/1 NA NA NA NA 6,6,42,41 A/AT PANCANCER NA FALSE NKRF chrX:119588394:119588396:A:AT indel 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 119617244 119617246 A AT 38 39 0.974358974358974 MODIFIER SEPTIN6 ENSG00000125354 T downstream_gene_variant Transcript ENST00000343984 protein_coding NA rs533552227 394 -1 insertion HGNC HGNC:15848 1 P4 CCDS14584.1 ENSP00000341524 Q14141.197 UPI0000001C54 Q14141-1 1 0.03653 0.01142 0.01057 0.01985 0.01605 0.003515 0.01808 0.05357 0.05684 0.02048 0.09709 0.09709 gnomADg_SAS 23 NA NA PASS SITE 15,11|17,21 NA NA 1 23 33,35 229,252 60,60 30 1.34 NA 6.27 NA FALSE 1.48 93 10,11 T NA TRUE NA 93 97.94 23 119617244 HCC1395_HCC1395T 1 0.952 39 0,10 0,14 1,37 NA 0/1 NA NA NA NA 0,1,17,21 A/AT PANCANCER NA FALSE SEPTIN6 chrX:119617244:119617246:A:AT indel 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 120441683 120441684 G A 15 15 1 MODIFIER LAMP2 ENSG00000005893 A intron_variant Transcript ENST00000200639 protein_coding 8/8 ENST00000200639.9:c.1093+47C>T NA -1 SNV HGNC HGNC:6501 YES NM_002294.3 1 A1 CCDS14599.1 ENSP00000200639 P13473.225 UPI000012E789 P13473-1 1 23 NA NA PASS SITE 10,1|14,1 NA NA 1 68 39,35 195,220 60,60 22 1.04 NA 3.01 NA FALSE 6.00 93 NA NA NA FALSE NA NA 57.88 23 120441683 HCC1395_HCC1395T 0 0.944 15 0,6 0,9 0,15 NA 0/1 NA NA NA NA 0,0,14,1 G/A PANCANCER NA FALSE LAMP2 chrX:120441683:120441684:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 120875377 120875378 TTCC T 181 181 1 MODERATE CT47B1 ENSG00000236446 - inframe_deletion Transcript ENST00000371311 protein_coding 1/3 ENST00000371311.5:c.291_293del ENSP00000360360.3:p.E99del ENSP00000360360.3 p.E99del 487-489 291-293 97-98 EE/E gaGGAa/gaa rs746257210 -1 deletion HGNC HGNC:33293 YES NM_001145718.3 5 P1 CCDS48161.1 ENSP00000360360 P0C2W7.90 UPI000036776D AlphaFold_DB_import:AF-P0C2W7-F1&Pfam:PF15623&PANTHER:PTHR32157&MobiDB_lite:mobidb-lite&MobiDB_lite:mobidb-lite&Low_complexity_(Seg):seg 0.01582 0.002348 0.008864 0.01563 7.543e-05 0.02553 0.02358 0.02082 0.004352 0.01646 0.00366 0.001466 0.01109 0.0147 0.0002812 0.01882 0.02521 0.02658 0.01991 0.005785 0.02658 gnomADg_NFE 23 NA NA PASS SITE 41,82|51,130 NA NA 2 93 20,20 161,178 60,60 36 2.00 NA 26.64 NA FALSE 1.72 93 4,3 TCC NA TRUE NA 93 636.95 23 120875377 HCC1395_HCC1395T 0 0.993 181 0,30 0,43 0,135 NA 0/1 NA NA NA NA 0,0,51,130 TTCC/T PANCANCER NA FALSE CT47B1_p.E99del chrX:120875377:120875378:TTCC:T indel 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 124022741 124022742 C T 7 7 1 MODIFIER STAG2 ENSG00000101972 T intron_variant Transcript ENST00000218089 protein_coding 3/34 ENST00000218089.13:c.44+70C>T NA rs191443586 1 SNV HGNC HGNC:11355 1 P1 CCDS43990.1 ENSP00000218089 Q8N3U4.186 UPI00004A3A8A Q8N3U4-2 1 0.0003 0 0 0 0.0013 0 0.0005793 9.705e-05 0 0.0003789 0 0 0.0001647 0 0.001052 0.0006605 0 0.0013 EUR 23 NA NA PASS SITE 0,8|0,7 NA NA 1 13 40,34 229,257 60,60 17 0.954 NA 2.41 NA FALSE 3.03 86 NA NA NA FALSE NA NA 25.11 23 124022741 HCC1395_HCC1395T 0 0.893 7 0,4 0,3 0,7 NA 0/1 NA NA NA NA 0,0,0,7 C/T PANCANCER TRUE FALSE STAG2 chrX:124022741:124022742:C:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 124371677 124371678 C T 4 9 0.444444444444444 MODIFIER SH2D1A ENSG00000183918 T 3_prime_UTR_variant Transcript ENST00000360027 protein_coding 4/4 ENST00000360027.5:c.*286C>T NA 891 1 SNV HGNC HGNC:10820 1 A1 CCDS48162.1 ENSP00000353126 O60880.187 UPI000002B38A O60880-4 1 23 NA NA PASS SITE 5,9|2,2 NA NA 1 27 40,35 237,248 60,60 12 1.02 NA 2.71 NA FALSE 6.00 31 NA NA NA FALSE NA NA 12.59 23 124371677 HCC1395_HCC1395T 5 0.454 9 3,1 2,3 5,4 NA 0/1 NA NA NA NA 1,4,2,2 C/T PANCANCER NA FALSE SH2D1A chrX:124371677:124371678:C:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 129794256 129794257 A G 49 49 1 MODIFIER SASH3 ENSG00000122122 G 3_prime_UTR_variant Transcript ENST00000356892 protein_coding 8/8 ENST00000356892.4:c.*424A>G NA 1716 rs34813627 1 SNV HGNC HGNC:15975 YES NM_018990.4 1 P1 CCDS14614.1 ENSP00000349359 O75995.156 UPI000006EC21 1 0.0220 0.001 0.0286 0 0.0822 0.0056 0.05936 0.01175 0.1487 0.03221 0.02112 0.0005556 0.1262 0.01255 0.0929 0.04494 0.007939 0.1487 gnomADg_AMI 23 NA NA PASS SITE 8,13|22,27 NA NA 1 16 31,24 185,181 60,60 30 1.23 NA 4.82 NA FALSE 1.11 93 NA NA NA FALSE NA NA 156.57 23 129794256 HCC1395_HCC1395T 0 0.975 49 0,12 0,21 0,38 NA 0/1 NA NA NA NA 0,0,22,27 A/G PANCANCER NA FALSE SASH3 chrX:129794256:129794257:A:G SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 129842033 129842034 C G 11 51 0.215686274509804 MODIFIER ZDHHC9 ENSG00000188706 G 5_prime_UTR_variant Transcript ENST00000357166 protein_coding 3/11 ENST00000357166.11:c.-88G>C NA 307 COSV100852261 -1 SNV HGNC HGNC:18475 YES NM_016032.4 1 P1 CCDS35395.1 ENSP00000349689 Q9Y397.176 UPI0000048EB7 1 1 1 23 NA NA PASS SITE 22,61|4,7 NA NA 1 93 38,20 196,165 60,60 29 1.55 NA 10.44 NA FALSE 6.00 56 NA NA NA FALSE NA NA 25.55 23 129842033 HCC1395_HCC1395T 40 0.214 51 13,2 15,4 32,8 NA 0/1 NA NA NA NA 12,28,4,7 C/G PANCANCER NA FALSE ZDHHC9 chrX:129842033:129842034:C:G SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 130129650 130129651 T C 133 133 1 MODIFIER AIFM1 ENSG00000156709 C intron_variant Transcript ENST00000287295 protein_coding 15/15 ENST00000287295.8:c.1771-22A>G NA rs187604646 -1 SNV HGNC HGNC:8768 YES NM_004208.4 1 CCDS14618.1 ENSP00000287295 O95831.221 UPI00001313DB O95831-1 1 0.0013 0 0.0038 0 0.0039 0 0.001609 0.0008359 0.00175 0 0.001804 6.277e-05 0.002327 0.002652 0.0004194 0.001605 0.0004923 0 0.003282 0 0.0005653 0 0 0.002341 0.00133 0.0003843 0.0039 EUR 23 NA NA PASS SITE 34,51|50,83 NA NA 1 93 20,20 159,165 60,60 33 1.74 NA 16.25 NA FALSE 2.87 93 NA NA NA FALSE NA NA 403.05 23 130129650 HCC1395_HCC1395T 0 0.989 133 0,33 0,49 0,89 NA 0/1 NA NA NA NA 0,0,50,83 T/C PANCANCER NA FALSE AIFM1 chrX:130129650:130129651:T:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 130145300 130145301 G C 76 76 1 MODIFIER AIFM1 ENSG00000156709 C intron_variant Transcript ENST00000287295 protein_coding 6/15 ENST00000287295.8:c.696+179C>G NA -1 SNV HGNC HGNC:8768 YES NM_004208.4 1 CCDS14618.1 ENSP00000287295 O95831.221 UPI00001313DB O95831-1 1 23 NA NA PASS SITE 34,23|51,26 NA NA 1 93 20,20 149,169 60,60 24 1.14 NA 8.98 NA FALSE 6.00 93 NA NA NA FALSE NA NA 237.66 23 130145300 HCC1395_HCC1395T 0 0.982 76 0,22 0,30 0,52 NA 0/1 NA NA NA NA 0,0,50,26 G/C PANCANCER NA FALSE AIFM1 chrX:130145300:130145301:G:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 131284719 131284721 G GT 72 73 0.986301369863014 MODIFIER IGSF1 ENSG00000147255 T intron_variant Transcript ENST00000361420 protein_coding 5/19 ENST00000361420.8:c.667+459_667+460insA NA rs201348749 -1 insertion HGNC HGNC:5948 YES NM_001555.5 1 P4 CCDS14629.1 ENSP00000355010 Q8N6C5.166 UPI0000227E76 Q8N6C5-1 1 0.2705 0.1825 0.2328 0.1924 0.346 0.4234 0.2844 0.1856 0.324 0.2487 0.4046 0.1722 0.2415 0.4936 0.3471 0.2871 0.405 0.4936 gnomADg_MID 23 NA NA PASS SITE 26,28|23,49 NA NA 1 70 38,36 198,196 60,60 37 1.21 NA 13.05 NA FALSE 0.554 93 9,10 T NA TRUE NA 93 140.18 23 131284719 HCC1395_HCC1395T 1 0.985 73 0,11 0,20 1,61 NA 0/1 NA NA NA NA 0,1,23,49 G/GT PANCANCER NA FALSE IGSF1 chrX:131284719:131284721:G:GT indel 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 132205182 132205183 G A 31 31 1 MODIFIER RAP2C ENSG00000123728 A 3_prime_UTR_variant Transcript ENST00000342983 protein_coding 4/4 ENST00000342983.6:c.*440C>T NA 1739 rs917113580 -1 SNV HGNC HGNC:21165 1 P1 CCDS14632.1 ENSP00000340274 Q9Y3L5.180 UPI00000236AB 0.0006017 0 0 0 0.0219 0 0 0 0.0001509 0.0006693 0 0.0219 gnomADg_ASJ 23 NA NA PASS SITE 17,37|5,26 NA NA 1 93 31,36 181,184 60,60 25 1.63 NA 12.34 NA FALSE 3.31 93 NA NA NA FALSE NA NA 108.90 23 132205182 HCC1395_HCC1395T 0 0.964 31 0,9 0,13 0,26 NA 0/1 NA NA NA NA 0,0,5,26 G/A PANCANCER NA FALSE RAP2C chrX:132205182:132205183:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 135286075 135286076 G C 47 47 1 MODIFIER ZNF75D ENSG00000186376 C 3_prime_UTR_variant Transcript ENST00000370764 protein_coding 4/4 ENST00000370764.1:c.*1062C>G NA 2694 rs7042 -1 SNV HGNC HGNC:13145 2 A2 CCDS55503.1 ENSP00000359800 P51815.192 UPI000013DAB4 P51815-2 0.1677 0.1017 0.1927 0.0628 0.282 0.2312 0.2135 0.1208 0.107 0.1837 0.2898 0.05486 0.282 0.3675 0.271 0.251 0.2307 0.3675 gnomADg_MID 23 NA NA PASS SITE 5,22|8,39 NA NA 2 26 35,40 201,200 60,60 26 1.39 NA 6.88 NA FALSE 0.644 93 NA NA NA FALSE NA NA 185.43 23 135286075 HCC1395_HCC1395T 0 0.977 47 0,12 0,23 0,41 NA 0/1 NA NA NA NA 0,0,8,39 G/C PANCANCER NA FALSE ZNF75D chrX:135286075:135286076:G:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 135286096 135286097 T G 31 31 1 MODIFIER ZNF75D ENSG00000186376 G 3_prime_UTR_variant Transcript ENST00000370764 protein_coding 4/4 ENST00000370764.1:c.*1041A>C NA 2673 rs4589 -1 SNV HGNC HGNC:13145 2 A2 CCDS55503.1 ENSP00000359800 P51815.192 UPI000013DAB4 P51815-2 0.1677 0.1017 0.1927 0.0628 0.282 0.2312 0.2134 0.1208 0.1067 0.184 0.2893 0.05552 0.2816 0.3729 0.2711 0.2502 0.2277 0.3729 gnomADg_MID 23 NA NA PASS SITE 4,15|4,27 NA NA 2 4 33,40 201,223 60,60 21 1.22 NA 4.51 NA FALSE 0.644 93 NA NA NA FALSE NA NA 127.21 23 135286096 HCC1395_HCC1395T 0 0.967 31 0,6 0,14 0,28 NA 0/1 NA NA NA NA 0,0,4,27 T/G PANCANCER NA FALSE ZNF75D chrX:135286096:135286097:T:G SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 135907576 135907577 C A 56 56 1 MODIFIER SAGE1 ENSG00000181433 A intron_variant Transcript ENST00000324447 protein_coding 9/19 ENST00000324447.8:c.1018+123C>A NA rs141186388 1 SNV HGNC HGNC:30369 5 P1 CCDS14652.1 ENSP00000323191 Q9NXZ1.117 UPI00001413AB 0.0021 0 0.0038 0.0013 0.0026 0.0042 0.004668 0.0007211 0 0.003445 0.02387 0.0005672 0.01456 0.004273 0.005398 0.002668 0.006498 0.02387 gnomADg_ASJ 23 NA NA PASS SITE 10,16|18,38 NA NA 1 59 40,27 196,173 60,60 27 1.38 NA 6.92 NA FALSE 2.14 93 NA NA NA FALSE NA NA 180.41 23 135907576 HCC1395_HCC1395T 0 0.977 56 0,15 0,22 0,42 NA 0/1 NA NA NA NA 0,0,18,38 C/A PANCANCER NA FALSE SAGE1 chrX:135907576:135907577:C:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 136210923 136210924 G A 288 288 1 MODIFIER MAP7D3 ENSG00000129680 A downstream_gene_variant Transcript ENST00000370661 protein_coding NA rs9018 2297 -1 SNV HGNC HGNC:25742 1 A2 CCDS55508.1 ENSP00000359695 Q8IWC1.147 UPI000013C756 Q8IWC1-3 0.5068 0.3858 0.4618 0.712 0.4974 0.5 0.5128 0.384 0.5426 0.4353 0.71 0.6244 0.4889 0.4762 0.4774 0.4743 0.3865 0.479 0.476 0.4432 0.6964 0.6107 0.3432 0.4978 0.4307 0.4735 0.712 EAS 23 NA NA PASS SITE 53,78|122,166 NA NA 1 93 20,20 169,166 60,60 39 1.96 NA 26.79 NA FALSE 0.298 93 NA NA NA FALSE NA NA 886.85 23 136210923 HCC1395_HCC1395T 0 0.995 288 0,64 0,116 0,198 NA 0/1 NA NA NA NA 0,0,122,166 G/A PANCANCER NA FALSE MAP7D3 chrX:136210923:136210924:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 136217452 136217453 T C 225 225 1 MODIFIER MAP7D3 ENSG00000129680 C 3_prime_UTR_variant Transcript ENST00000316077 protein_coding 19/19 ENST00000316077.14:c.*1074A>G NA 3747 rs3788953 -1 SNV HGNC HGNC:25742 YES NM_024597.4 1 P5 CCDS44004.1 ENSP00000318086 Q8IWC1.147 UPI00001C207C Q8IWC1-1 0.4882 0.2772 0.4637 0.716 0.5352 0.5084 0.4797 0.2882 0.5082 0.4804 0.4931 0.7051 0.6375 0.3782 0.5588 0.4265 0.4761 0.716 EAS 23 NA NA PASS SITE 39,47|121,104 NA NA 1 93 20,20 172,178 60,60 34 1.77 NA 17.37 NA FALSE 0.286 93 NA NA NA FALSE NA NA 684.36 23 136217452 HCC1395_HCC1395T 0 0.994 225 0,40 0,98 0,152 NA 0/1 NA NA NA NA 0,0,121,104 T/C PANCANCER NA FALSE MAP7D3 chrX:136217452:136217453:T:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 136217699 136217700 C A 57 57 1 MODIFIER MAP7D3 ENSG00000129680 A 3_prime_UTR_variant Transcript ENST00000316077 protein_coding 19/19 ENST00000316077.14:c.*827G>T NA 3500 rs11538745 -1 SNV HGNC HGNC:25742 YES NM_024597.4 1 P5 CCDS44004.1 ENSP00000318086 Q8IWC1.147 UPI00001C207C Q8IWC1-1 0.5142 0.3709 0.4695 0.716 0.5366 0.5084 0.5024 0.3711 0.5104 0.4947 0.4941 0.7056 0.6352 0.3866 0.5554 0.4456 0.4765 0.716 EAS 23 NA NA PASS SITE 9,25|16,41 NA NA 1 21 20,35 160,198 60,60 39 1.42 NA 7.53 NA FALSE 0.271 93 NA NA NA FALSE NA NA 193.47 23 136217699 HCC1395_HCC1395T 0 0.979 57 0,12 0,24 0,46 NA 0/1 NA NA NA NA 0,0,16,41 C/A PANCANCER NA FALSE MAP7D3 chrX:136217699:136217700:C:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 140091769 140091770 G C 110 110 1 MODERATE ENSG00000230707 C missense_variant Transcript ENST00000453380 protein_coding 1/1 ENST00000453380.3:c.27G>C ENSP00000506518.1:p.E9D ENSP00000506518.1 p.E9D 92 27 9 E/D gaG/gaC rs768519967 1 SNV YES NM_001271560.3 P1 CCDS94678.1 ENSP00000506518 A0A7P0TBJ1.7 UPI000023775D tolerated(0.33) benign(0.003) AlphaFold_DB_import:AF-A0A7P0TBJ1-F1&PANTHER:PTHR31624 0.0001872 3.236e-05 0 9.312e-05 0 0 0 0 0.0003575 0 0 0.0003575 gnomADg_NFE 23 NA NA PASS SITE 56,41|66,44 NA NA 1 93 20,20 161,166 60,60 33 1.83 NA 19.56 NA FALSE 3.61 93 NA NA NA FALSE NA NA 333.31 23 140091769 HCC1395_HCC1395T 0 0.987 110 0,30 0,44 0,74 NA 0/1 NA NA NA NA 0,0,66,44 G/C PANCANCER NA FALSE _p.E9D chrX:140091769:140091770:G:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 146001097 146001098 G C 176 176 1 MODIFIER MIR892A ENSG00000215943 C upstream_gene_variant Transcript ENST00000401124 miRNA NA rs143246735 4354 -1 SNV HGNC HGNC:33639 YES 0.0029 0 0.0019 0 0.0091 0.0042 0.005869 0.001366 0.001347 0.002109 0 0.002592 0.01073 0.005296 0.003045 0.005873 0.001042 0.00436 0.001723 0.002645 0 0.002164 0 0.01067 0.002656 0.004501 0.01073 gnomADe_NFE 23 NA NA PASS SITE 37,50|67,109 NA NA 1 93 20,20 166,171 60,60 32 1.75 NA 16.21 NA FALSE 2.24 93 NA NA NA FALSE NA NA 521.73 23 146001097 HCC1395_HCC1395T 0 0.991 176 0,41 0,58 0,113 NA 0/1 NA NA NA NA 0,0,67,109 G/C PANCANCER NA FALSE MIR892A chrX:146001097:146001098:G:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 148886022 148886023 G T 54 54 1 MODIFIER AFF2 ENSG00000155966 T intron_variant Transcript ENST00000286437 protein_coding 5/17 ENST00000286437.7:c.282+37G>T NA rs41299108 1 SNV HGNC HGNC:3776 2 CCDS55521.1 ENSP00000286437 P51816.172 UPI00017A80C4 P51816-7 1 0.0294 0.005 0.0057 0 0.0718 0.0669 0.05284 0.007627 0.01507 0.0551 0.00029 0.09827 0.07148 0.06135 0.05801 0.04558 0.008148 0.1083 0.01935 0.05251 0.0008569 0.09045 0.09013 0.06833 0.04287 0.0603 0.1083 gnomADg_AMI 23 NA NA PASS SITE 5,20|5,49 NA NA 1 34 39,38 190,188 60,60 26 1.35 NA 6.32 NA FALSE 1.26 93 NA NA NA FALSE NA NA 199.43 23 148886022 HCC1395_HCC1395T 0 0.981 54 0,13 0,29 0,49 NA 0/1 NA NA NA NA 0,0,5,49 G/T PANCANCER NA FALSE AFF2 chrX:148886022:148886023:G:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 148997705 148997706 ATTACAC A 64 64 1 MODIFIER AFF2 ENSG00000155966 - 3_prime_UTR_variant Transcript ENST00000286437 protein_coding 18/18 ENST00000286437.7:c.*6380_*6385del NA 9323-9328 rs201762227 1 deletion HGNC HGNC:3776 2 CCDS55521.1 ENSP00000286437 P51816.172 UPI00017A80C4 P51816-7 1 6 0.0265 0.004821 0.005822 0.0134 0.0367 0.0002802 0.0455 0.04219 0.04122 0.0253 0.02139 0.0455 gnomADg_FIN 23 NA NA PASS SITE 15,14|40,24 NA NA 1 18 20,32 151,190 60,60 37 1.34 NA 6.32 NA FALSE 1.48 93 2,1 TTACAC NA TRUE NA 93 286.71 23 148997705 HCC1395_HCC1395T 0 0.980 64 0,16 0,27 0,48 NA 0/1 NA NA NA NA 0,0,40,24 ATTACAC/A PANCANCER NA FALSE AFF2 chrX:148997705:148997706:ATTACAC:A indel 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 149479801 149479802 T C 59 60 0.983333333333333 MODIFIER IDS ENSG00000010404 C 3_prime_UTR_variant Transcript ENST00000340855 protein_coding 9/9 ENST00000340855.11:c.*2945A>G NA 4767 rs8965 -1 SNV HGNC HGNC:5389 YES NM_000202.8 1 P1 CCDS14685.1 ENSP00000339801 P22304.218 UPI000012D213 P22304-1 1 0.6135 0.4666 0.7042 0.8442 0.3916 0.7437 0.4671 0.4792 0.4726 0.5973 0.4371 0.8485 0.4414 0.2839 0.4016 0.4528 0.7199 0.8485 gnomADg_EAS 23 NA NA PASS SITE 23,5|48,11 NA NA 1 93 35,37 196,203 60,60 31 1.36 NA 6.62 NA FALSE 6.00 93 NA NA NA FALSE NA NA 208.93 23 149479801 HCC1395_HCC1395T 1 0.964 60 0,14 0,33 1,48 NA 0/1 NA NA NA NA 1,0,48,11 T/C PANCANCER NA FALSE IDS chrX:149479801:149479802:T:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 150767630 150767631 C A 49 49 1 MODIFIER CD99L2 ENSG00000102181 A 3_prime_UTR_variant&NMD_transcript_variant Transcript ENST00000346693 nonsense_mediated_decay 12/12 ENST00000346693.8:c.*3162G>T NA 3642 rs9866 -1 SNV HGNC HGNC:18237 1 ENSP00000489222 Q8TCZ2.155 UPI000007145B Q8TCZ2-4 0.2509 0.1615 0.3874 0.1924 0.248 0.3412 0.2078 0.153 0.3655 0.3521 0.3031 0.1922 0.1264 0.3974 0.2069 0.2589 0.3111 0.3974 gnomADg_MID 23 NA NA PASS SITE 13,10|23,26 NA NA 1 10 20,20 166,161 60,60 28 1.25 NA 5.07 NA FALSE 0.726 93 NA NA NA FALSE NA NA 142.98 23 150767630 HCC1395_HCC1395T 0 0.971 49 0,10 0,20 0,32 NA 0/1 NA NA NA NA 0,0,23,26 C/A PANCANCER NA FALSE CD99L2 chrX:150767630:150767631:C:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 150768275 150768276 C G 50 50 1 MODIFIER CD99L2 ENSG00000102181 G 3_prime_UTR_variant&NMD_transcript_variant Transcript ENST00000346693 nonsense_mediated_decay 12/12 ENST00000346693.8:c.*2517G>C NA 2997 rs5925425 -1 SNV HGNC HGNC:18237 1 ENSP00000489222 Q8TCZ2.155 UPI000007145B Q8TCZ2-4 0.3261 0.2253 0.4237 0.2238 0.3003 0.532 0.2705 0.2079 0.367 0.3941 0.411 0.2233 0.1763 0.5579 0.2716 0.3322 0.5318 0.5579 gnomADg_MID 23 NA NA PASS SITE 16,13|24,26 NA NA 1 22 30,20 167,157 60,60 34 1.37 NA 6.62 NA FALSE 0.597 93 NA NA NA FALSE NA NA 153.90 23 150768275 HCC1395_HCC1395T 0 0.973 50 0,10 0,22 0,35 NA 0/1 NA NA NA NA 0,0,24,26 C/G PANCANCER NA FALSE CD99L2 chrX:150768275:150768276:C:G SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 150983362 150983363 T A 49 49 1 MODIFIER HMGB3 ENSG00000029993 A 5_prime_UTR_variant Transcript ENST00000325307 protein_coding 1/5 ENST00000325307.12:c.-20T>A NA 28 rs187742210 1 SNV HGNC HGNC:5004 YES NM_005342.4 1 P1 CCDS35428.1 ENSP00000359393 O15347.185 UPI00000362ED 1 0.1709 0.0518 0.2767 0.2552 0.2298 0.1072 0.175 0.07314 0.2188 0.2727 0.1618 0.2555 0.1525 0.1579 0.2148 0.1989 0.1092 0.2767 AMR 23 NA NA PASS SITE 19,31|21,28 NA NA 2 54 20,20 153,179 60,60 36 1.51 NA 9.33 NA FALSE 0.764 93 NA NA NA FALSE NA NA 146.31 23 150983362 HCC1395_HCC1395T 0 0.973 49 0,14 0,11 0,34 NA 0/1 NA NA NA NA 0,0,21,28 T/A PANCANCER NA FALSE HMGB3 chrX:150983362:150983363:T:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 151407126 151407127 C A 342 342 1 MODIFIER VMA21 ENSG00000160131 A 3_prime_UTR_variant Transcript ENST00000330374 protein_coding 3/3 ENST00000330374.7:c.*2068C>A NA 2477 rs35860657 1 SNV HGNC HGNC:22082 YES NM_001017980.4 1 P1 CCDS35430.1 ENSP00000333255 Q3ZAQ7.129 UPI00000467E2 Q3ZAQ7-1 1 0.1571 0.3898 0.0477 0.0366 0.0718 0.1309 0.1393 0.3379 0.04978 0.06636 0.08791 0.03082 0.04673 0.1459 0.06251 0.119 0.1351 0.3898 AFR 23 NA NA PASS SITE 104,74|226,116 NA NA 1 93 20,20 166,169 60,60 27 2.09 NA 36.72 NA FALSE 0.903 93 NA NA NA FALSE NA NA 1104.90 23 151407126 HCC1395_HCC1395T 0 0.996 342 0,82 0,160 0,248 NA 0/1 NA NA NA NA 0,0,226,116 C/A PANCANCER NA FALSE VMA21 chrX:151407126:151407127:C:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 151408567 151408568 C A 101 101 1 MODIFIER VMA21 ENSG00000160131 A 3_prime_UTR_variant Transcript ENST00000330374 protein_coding 3/3 ENST00000330374.7:c.*3509C>A NA 3918 rs41314149 1 SNV HGNC HGNC:22082 YES NM_001017980.4 1 P1 CCDS35430.1 ENSP00000333255 Q3ZAQ7.129 UPI00000467E2 Q3ZAQ7-1 1 0.0058 0 0.0076 0 0.0235 0 0.01546 0.002467 0.0438 0.01543 0.03855 0 0.02655 0.03361 0.02204 0.01123 0.0007386 0.0438 gnomADg_AMI 23 NA NA PASS SITE 9,19|27,74 NA NA 2 47 36,35 186,197 60,60 22 1.38 NA 6.58 NA FALSE 1.74 93 NA NA NA FALSE NA NA 351.62 23 151408567 HCC1395_HCC1395T 0 0.989 101 0,28 0,45 0,86 NA 0|1 0|1 151408567_C_A NA 151408567 0,0,27,74 C|A PANCANCER NA FALSE VMA21 chrX:151408567:151408568:C:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 151648728 151648729 A T 19 82 0.231707317073171 MODIFIER PASD1 ENSG00000166049 T intron_variant Transcript ENST00000370357 protein_coding 9/15 ENST00000370357.5:c.717+26A>T NA 1 SNV HGNC HGNC:20686 YES NM_173493.3 1 P1 CCDS35431.1 ENSP00000359382 Q8IV76.137 UPI0000074686 Q8IV76-1 23 NA NA PASS SITE 44,61|6,13 NA NA 1 93 20,20 161,180 60,60 30 1.45 NA 8.12 NA FALSE 6.00 53 NA NA NA FALSE NA NA 46.50 23 151648728 HCC1395_HCC1395T 63 0.254 82 18,4 24,6 43,14 NA 0/1 NA NA NA NA 24,39,6,13 A/T PANCANCER NA FALSE PASD1 chrX:151648728:151648729:A:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 151702497 151702498 T C 42 42 1 MODIFIER PRRG3 ENSG00000130032 C 3_prime_UTR_variant Transcript ENST00000370353 protein_coding 4/4 ENST00000370353.3:c.*1464T>C NA 2550 rs45494598 1 SNV HGNC HGNC:30798 1 P1 CCDS14699.1 ENSP00000359378 Q9BZD7.153 UPI00004578A5 0.4183 0.1346 0.5973 0.5079 0.3668 0.6435 0.3145 0.1529 0.3579 0.4875 0.3349 0.4606 0.3449 0.2869 0.3429 0.3318 0.6482 0.6482 gnomADg_SAS 23 NA NA PASS SITE 16,21|20,22 NA NA 1 32 20,20 187,168 60,60 30 1.43 NA 7.83 NA FALSE 0.499 93 NA NA NA FALSE NA NA 134.88 23 151702497 HCC1395_HCC1395T 0 0.970 42 0,11 0,18 0,30 NA 0/1 NA NA NA NA 0,0,20,22 T/C PANCANCER NA FALSE PRRG3 chrX:151702497:151702498:T:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 151703263 151703264 G A 45 45 1 MODIFIER PRRG3 ENSG00000130032 A 3_prime_UTR_variant Transcript ENST00000370353 protein_coding 4/4 ENST00000370353.3:c.*2230G>A NA 3316 rs45505195 1 SNV HGNC HGNC:30798 1 P1 CCDS14699.1 ENSP00000359378 Q9BZD7.153 UPI00004578A5 0.0016 0 0 0 0.0078 0 0.005437 0.001365 0 0.00169 0.0003779 0 0.02052 0 0.007843 0.003316 0.0003733 0.02052 gnomADg_FIN 23 NA NA PASS SITE 19,18|24,21 NA NA 1 65 20,20 173,167 60,60 37 1.42 NA 7.52 NA FALSE 2.14 93 NA NA NA FALSE NA NA 135.98 23 151703263 HCC1395_HCC1395T 0 0.970 45 0,12 0,18 0,31 NA 0/1 NA NA NA NA 0,0,24,21 G/A PANCANCER NA FALSE PRRG3 chrX:151703263:151703264:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 151704416 151704417 G A 70 70 1 MODIFIER PRRG3 ENSG00000130032 A 3_prime_UTR_variant Transcript ENST00000370353 protein_coding 4/4 ENST00000370353.3:c.*3383G>A NA 4469 rs10521893 1 SNV HGNC HGNC:30798 1 P1 CCDS14699.1 ENSP00000359378 Q9BZD7.153 UPI00004578A5 0.3971 0.0947 0.5897 0.4817 0.3668 0.6212 0.3006 0.1221 0.3498 0.4792 0.32 0.4237 0.3416 0.2851 0.3378 0.3251 0.6265 0.6265 gnomADg_SAS 23 NA NA PASS SITE 16,19|25,45 NA NA 1 23 20,20 149,176 60,60 23 1.38 NA 6.92 NA FALSE 0.520 93 NA NA NA FALSE NA NA 222.44 23 151704416 HCC1395_HCC1395T 0 0.982 70 0,24 0,22 0,53 NA 0/1 NA NA NA NA 0,0,25,45 G/A PANCANCER NA FALSE PRRG3 chrX:151704416:151704417:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 151745003 151745004 T A 119 119 1 MODIFIER CNGA2 ENSG00000183862 A 3_prime_UTR_variant Transcript ENST00000329903 protein_coding 7/7 ENST00000329903.5:c.*505T>A NA 2724 rs879371 1 SNV HGNC HGNC:2149 YES NM_005140.3 5 P1 CCDS14701.1 ENSP00000328478 Q16280.172 UPI000003E7AE 1 0.2511 0.5563 0.1183 0.0838 0.1567 0.2006 0.2408 0.4919 0.1795 0.1593 0.1694 0.08975 0.08035 0.2949 0.1492 0.2413 0.1734 0.5563 AFR 23 NA NA PASS SITE 27,17|62,57 NA NA 1 57 20,20 182,161 60,60 30 1.54 NA 9.93 NA FALSE 0.658 93 NA NA NA FALSE NA NA 356.26 23 151745003 HCC1395_HCC1395T 0 0.988 119 0,41 0,37 0,79 NA 0/1 NA NA NA NA 0,0,62,57 T/A PANCANCER NA FALSE CNGA2 chrX:151745003:151745004:T:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 152138640 152138641 C T 33 33 1 MODIFIER MAGEA10 ENSG00000124260 T upstream_gene_variant Transcript ENST00000244096 protein_coding NA rs186687937 62 -1 SNV HGNC HGNC:6797 2 P1 CCDS14705.1 ENSP00000244096 P43363.156 UPI00001AE6DA 0.0106 0.001 0.0095 0 0.0366 0.0084 0.0443 0.009374 0.008511 0.02395 0.05031 0 0.07189 0.05042 0.06406 0.03291 0.02279 0.07189 gnomADg_FIN 23 NA NA PASS SITE 8,18|7,26 NA NA 1 31 20,36 159,155 60,60 12 1.32 NA 5.72 NA FALSE 1.40 93 NA NA NA FALSE NA NA 115.00 23 152138640 HCC1395_HCC1395T 0 0.966 33 0,7 0,12 0,27 NA 0/1 NA NA NA NA 0,0,7,26 C/T PANCANCER NA FALSE MAGEA10 chrX:152138640:152138641:C:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 152700708 152700709 G A 90 97 0.927835051546392 MODIFIER MAGEA3 ENSG00000221867 A intron_variant Transcript ENST00000370278 protein_coding 2/2 ENST00000370278.4:c.-66+21G>A NA rs782686156 1 SNV HGNC HGNC:6801 YES NM_005362.4 1 P1 CCDS76045.1 ENSP00000359301 P43357.170 UPI0000062194 0.00672 0.0007941 0.002478 0.02802 0 0.01351 0.01265 0.002762 0.001209 0.009182 0.002265 0 0.003631 0.02 0 0.003906 0.008547 0.0151 0.006228 0.001868 0.02802 gnomADe_ASJ 23 NA NA PASS SITE 52,55|43,47 NA NA 1 93 20,20 173,173 53,45 43 1.81 NA 18.96 NA FALSE 2.33 93 NA NA NA FALSE NA NA 220.04 23 152700708 HCC1395_HCC1395T 7 0.916 97 2,19 1,29 4,53 NA 0/1 NA NA NA NA 4,3,43,47 G/A PANCANCER NA FALSE MAGEA3 chrX:152700708:152700709:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 152827019 152827020 G A 61 61 1 MODIFIER NSDHL ENSG00000147383 A upstream_gene_variant Transcript ENST00000370274 protein_coding NA rs6627689 4044 1 SNV HGNC HGNC:13398 YES NM_015922.3 1 P1 CCDS14717.1 ENSP00000359297 Q15738.190 A0A384NPZ7.20 UPI0000000C8A 1 0.2850 0.5354 0.1718 0.1963 0.1997 0.2033 0.2763 0.5047 0.0614 0.2098 0.1492 0.1827 0.1852 0.2658 0.1894 0.2631 0.1873 0.5354 AFR 23 NA NA PASS SITE 16,8|50,11 NA NA 1 13 30,37 188,205 60,60 25 1.32 NA 5.72 NA FALSE 0.569 93 NA NA NA FALSE NA NA 218.80 23 152827019 HCC1395_HCC1395T 0 0.981 61 0,16 0,34 0,50 NA 0/1 NA NA NA NA 0,0,50,11 G/A PANCANCER NA FALSE NSDHL chrX:152827019:152827020:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 152827242 152827243 G T 205 205 1 MODIFIER NSDHL ENSG00000147383 T upstream_gene_variant Transcript ENST00000370274 protein_coding NA rs3088344 3821 1 SNV HGNC HGNC:13398 YES NM_015922.3 1 P1 CCDS14717.1 ENSP00000359297 Q15738.190 A0A384NPZ7.20 UPI0000000C8A 1 0.1868 0.4417 0.0878 0.0929 0.1345 0.0585 0.2022 0.399 0.04203 0.1095 0.08415 0.08401 0.1444 0.1702 0.1379 0.1856 0.06579 0.4417 AFR 23 NA NA PASS SITE 56,48|108,97 NA NA 1 93 20,20 162,182 60,60 35 1.87 NA 21.97 NA FALSE 0.693 93 NA NA NA FALSE NA NA 664.14 23 152827242 HCC1395_HCC1395T 0 0.994 205 0,58 0,83 0,152 NA 0/1 NA NA NA NA 0,0,108,97 G/T PANCANCER NA FALSE NSDHL chrX:152827242:152827243:G:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 152963989 152963990 G A 191 191 1 MODIFIER ZNF185 ENSG00000147394 A intron_variant Transcript ENST00000318504 protein_coding 16/20 ENST00000318504.12:c.1538+40G>A NA rs5925265 1 SNV HGNC HGNC:12976 5 A2 CCDS55531.1 ENSP00000312782 O15231.176 UPI0001895B93 O15231-4 0.0262 0.005 0.0324 0 0.0927 0.0084 0.06635 0.0106 0.02889 0.07171 0.0001509 0.1295 0.09671 0.073 0.01771 0.0658 0.01281 0.1931 0.03965 0.0683 0.000558 0.1246 0.1004 0.1007 0.0632 0.01126 0.1931 gnomADg_AMI 23 NA NA PASS SITE 52,63|91,100 NA NA 1 93 20,20 148,164 60,60 34 1.90 NA 23.18 NA FALSE 1.10 93 NA NA NA FALSE NA NA 559.74 23 152963989 HCC1395_HCC1395T 0 0.992 191 0,56 0,58 0,125 NA 0/1 NA NA NA NA 0,0,91,100 G/A PANCANCER NA FALSE ZNF185 chrX:152963989:152963990:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 153471228 153471229 C G 126 126 1 MODIFIER TREX2 ENSG00000183479 G upstream_gene_variant Transcript ENST00000330912 protein_coding NA rs2980037&COSV57849681 641 -1 SNV HGNC HGNC:12270 1 P1 CCDS35437.1 ENSP00000333441 Q9BQ50.160 UPI000006F0D9 Q9BQ50-2 0.3897 0.1944 0.5363 0.3259 0.6789 0.3148 0.5125 0.2585 0.6388 0.585 0.663 0.3266 0.6472 0.6525 0.6419 0.5355 0.3176 0.6789 EUR 0&1 0&1 23 NA NA PASS SITE 32,49|60,66 NA NA 1 93 20,20 162,154 60,60 30 1.74 NA 15.95 NA FALSE 0.273 93 NA NA NA FALSE NA NA 365.42 23 153471228 HCC1395_HCC1395T 0 0.988 126 0,30 0,47 0,82 NA 0/1 NA NA NA NA 0,0,60,66 C/G PANCANCER NA FALSE TREX2 chrX:153471228:153471229:C:G SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 153508965 153508966 C A 37 37 1 MODIFIER BGN ENSG00000182492 A 3_prime_UTR_variant Transcript ENST00000331595 protein_coding 8/8 ENST00000331595.9:c.*520C>A NA 1772 rs11538656 1 SNV HGNC HGNC:1044 YES NM_001711.6 1 P1 CCDS14721.1 ENSP00000327336 P21810.213 UPI000003BDBA 1 0.1931 0.0528 0.1889 0.0759 0.4661 0.2256 0.2974 0.08828 0.351 0.2141 0.341 0.06854 0.4478 0.2895 0.4387 0.2741 0.1838 0.4661 EUR 23 NA NA PASS SITE 18,24|12,25 NA NA 1 30 20,20 147,173 60,60 27 1.44 NA 7.83 NA FALSE 0.462 93 NA NA NA FALSE NA NA 112.28 23 153508965 HCC1395_HCC1395T 0 0.966 37 0,7 0,7 0,27 NA 0/1 NA NA NA NA 0,0,12,25 C/A PANCANCER NA FALSE BGN chrX:153508965:153508966:C:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 153533273 153533274 C T 32 32 1 MODIFIER ATP2B3 ENSG00000067842 T intron_variant Transcript ENST00000263519 protein_coding 2/21 ENST00000263519.5:c.-126-2849C>T NA rs989258279 1 SNV HGNC HGNC:816 YES NM_001001344.3 1 P1 CCDS35440.1 ENSP00000263519 Q16720.210 UPI00001AE881 Q16720-1 1 2.687e-05 0 0 0 0 0 0 0 5.647e-05 0 0 5.647e-05 gnomADg_NFE 23 NA NA PASS SITE 5,16|8,24 NA NA 1 93 25,21 179,159 60,60 20 1.24 NA 4.81 NA FALSE 6.00 93 NA NA NA FALSE NA NA 99.81 23 153533273 HCC1395_HCC1395T 0 0.962 32 0,7 0,14 0,24 NA 0/1 NA NA NA NA 0,0,8,24 C/T PANCANCER NA FALSE ATP2B3 chrX:153533273:153533274:C:T SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 153643593 153643594 G C 183 183 1 MODIFIER DUSP9 ENSG00000130829 C upstream_gene_variant Transcript ENST00000342782 protein_coding NA rs72616448 3610 1 SNV HGNC HGNC:3076 YES NM_001318503.2 1 P1 CCDS14724.1 ENSP00000345853 Q99956.184 UPI0000049C1B 0.1285 0.1356 0.1298 0.051 0.2742 0.0446 0.1961 0.1549 0.1133 0.3678 0.0703 0.2234 0.2716 0.2164 0.07875 0.2034 0.1508 0.2437 0.1619 0.3274 0.04883 0.197 0.3305 0.2536 0.1987 0.06701 0.3678 gnomADe_ASJ 23 NA NA PASS SITE 38,57|73,110 NA NA 1 93 20,20 165,163 60,60 24 1.79 NA 17.76 NA FALSE 0.674 93 NA NA NA FALSE NA NA 491.31 23 153643593 HCC1395_HCC1395T 0 0.992 183 0,40 0,62 0,116 NA 0/1 NA NA NA NA 0,0,73,110 G/C PANCANCER NA FALSE DUSP9 chrX:153643593:153643594:G:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 153648360 153648361 C A 129 129 1 MODIFIER DUSP9 ENSG00000130829 A intron_variant Transcript ENST00000342782 protein_coding 2/3 ENST00000342782.4:c.373+34C>A NA rs7882888 1 SNV HGNC HGNC:3076 YES NM_001318503.2 1 P1 CCDS14724.1 ENSP00000345853 Q99956.184 UPI0000049C1B 0.0964 0.0548 0.1107 0.0327 0.2559 0.0418 0.1697 0.08007 0.09341 0.3171 0.04785 0.2059 0.2572 0.2012 0.07517 0.1638 0.0694 0.24 0.1434 0.2865 0.02834 0.1745 0.2974 0.2286 0.1689 0.0622 0.3171 gnomADe_ASJ 23 NA NA PASS SITE 39,52|59,70 NA NA 1 93 20,20 160,160 60,60 33 1.82 NA 18.96 NA FALSE 0.757 93 NA NA NA FALSE NA NA 387.13 23 153648360 HCC1395_HCC1395T 0 0.989 129 0,46 0,35 0,89 NA 0/1 NA NA NA NA 0,0,59,70 C/A PANCANCER NA FALSE DUSP9 chrX:153648360:153648361:C:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 154349377 154349378 C G 130 130 1 MODERATE FLNA ENSG00000196924 G missense_variant Transcript ENST00000360319 protein_coding 45/46 ENST00000360319.9:c.7717G>C ENSP00000353467.4:p.D2573H ENSP00000353467.4 p.D2573H 7755 7717 2573 D/H Gac/Cac COSV61041394 -1 SNV HGNC HGNC:3754 1 P1 CCDS44021.1 ENSP00000353467 P21333.263 UPI00004B2C00 P21333-2 1 deleterious_low_confidence(0) PROSITE_profiles:PS50194&Gene3D:2.60.40.10&Pfam:PF00630&SMART:SM00557&Superfamily:SSF81296&AlphaFold_DB_import:AF-P21333-F1 1 1 23 NA NA PASS SITE 59,25|86,44 NA NA 1 93 30,20 166,167 60,60 33 1.82 NA 19.22 NA FALSE 6.00 93 NA NA NA FALSE NA NA 412.39 23 154349377 HCC1395_HCC1395T 0 0.990 130 0,35 0,51 0,92 NA 0/1 NA NA NA NA 0,0,86,44 C/G PANCANCER NA FALSE FLNA_p.D2573H chrX:154349377:154349378:C:G SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 154401198 154401199 TG T 100 100 1 MODIFIER DNASE1L1 ENSG00000013563 - downstream_gene_variant Transcript ENST00000014935 protein_coding NA 559 -1 deletion HGNC HGNC:2957 2 P1 CCDS14747.1 ENSP00000014935 P49184.190 UPI0000129891 23 NA NA PASS SITE 20,11|65,35 NA NA 1 93 20,20 161,175 60,60 22 1.41 NA 6.91 NA FALSE 6.00 93 NA NA NA FALSE NA NA 287.97 23 154401198 HCC1395_HCC1395T 0 0.987 100 0,25 0,42 0,72 NA 0/1 NA NA NA NA 0,0,65,35 TG/T PANCANCER NA FALSE DNASE1L1 chrX:154401198:154401199:TG:T indel 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 154402199 154402200 A G 61 61 1 MODIFIER DNASE1L1 ENSG00000013563 G 3_prime_UTR_variant Transcript ENST00000014935 protein_coding 9/9 ENST00000014935.7:c.*508T>C NA 2211 rs138408303 -1 SNV HGNC HGNC:2957 2 P1 CCDS14747.1 ENSP00000014935 P49184.190 UPI0000129891 0.0005 0.001 0 0 0.0013 0 0.003764 0.0009079 0 0.001793 0.005279 0 0.004892 0.004202 0.006099 0.003945 0 0.006099 gnomADg_NFE 23 NA NA PASS SITE 26,23|28,33 NA NA 1 93 20,20 165,174 60,60 24 1.54 NA 10.23 NA FALSE 2.29 93 NA NA NA FALSE NA NA 203.53 23 154402199 HCC1395_HCC1395T 0 0.978 61 0,14 0,29 0,44 NA 0/1 NA NA NA NA 0,0,28,33 A/G PANCANCER NA FALSE DNASE1L1 chrX:154402199:154402200:A:G SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 154405616 154405617 G A 54 54 1 MODIFIER DNASE1L1 ENSG00000013563 A 5_prime_UTR_variant Transcript ENST00000014935 protein_coding 3/9 ENST00000014935.7:c.-48C>T NA 747 rs782227237 -1 SNV HGNC HGNC:2957 2 P1 CCDS14747.1 ENSP00000014935 P49184.190 UPI0000129891 0.000414 0 0 0 0 0.002356 0.0001721 0.000999 0 0.0002505 3.254e-05 0 0 0 0 0.002438 0 0.0002266 0 0 0.002438 gnomADg_FIN 23 NA NA PASS SITE 25,31|21,33 NA NA 1 93 20,20 154,183 60,60 33 1.58 NA 11.14 NA FALSE 3.18 93 NA NA NA FALSE NA NA 173.02 23 154405616 HCC1395_HCC1395T 0 0.976 54 0,8 0,29 0,39 NA 0/1 NA NA NA NA 0,0,21,33 G/A PANCANCER NA FALSE DNASE1L1 chrX:154405616:154405617:G:A SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 155057576 155057577 C G 113 113 1 MODIFIER CMC4 ENSG00000182712 G downstream_gene_variant Transcript ENST00000369479 protein_coding NA rs2051161 4052 -1 SNV HGNC HGNC:35428 3 P1 CCDS14764.1 ENSP00000358491 P56277.181 UPI0000000C43 P56277-1 0.5240 0.9292 0.4466 0.3325 0.3225 0.4331 0.5097 0.8766 0.2969 0.4419 0.4081 0.3136 0.3088 0.3544 0.361 0.4748 0.4542 0.9292 AFR 23 NA NA PASS SITE 46,36|66,47 NA NA 1 93 20,20 161,166 60,60 36 1.71 NA 15.05 NA FALSE 0.312 93 NA NA NA FALSE NA NA 364.56 23 155057576 HCC1395_HCC1395T 0 0.988 113 0,33 0,44 0,80 NA 0/1 NA NA NA NA 0,0,66,47 C/G PANCANCER NA FALSE CMC4 chrX:155057576:155057577:C:G SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 155057768 155057769 G C 177 178 0.99438202247191 MODIFIER CMC4 ENSG00000182712 C downstream_gene_variant Transcript ENST00000369479 protein_coding NA rs4898408 3860 -1 SNV HGNC HGNC:35428 3 P1 CCDS14764.1 ENSP00000358491 P56277.181 UPI0000000C43 P56277-1 0.2403 0.1555 0.3073 0.2539 0.1671 0.3733 0.2261 0.1835 0.2493 0.2961 0.2612 0.2537 0.1794 0.2405 0.23 0.2291 0.3873 0.3873 gnomADg_SAS 23 NA NA PASS SITE 41,45|75,102 NA NA 1 93 20,20 146,163 60,60 33 1.77 NA 16.85 NA FALSE 0.648 93 NA NA NA FALSE NA NA 499.76 23 155057768 HCC1395_HCC1395T 1 0.984 178 1,45 0,62 1,118 NA 0/1 NA NA NA NA 1,0,75,102 G/C PANCANCER NA FALSE CMC4 chrX:155057768:155057769:G:C SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96 +chrX 155276345 155276346 A G 86 86 1 MODIFIER CLIC2 ENSG00000155962 G downstream_gene_variant Transcript ENST00000321926 protein_coding NA rs56223905 2861 -1 cds_end_NF SNV HGNC HGNC:2063 3 ENSP00000318558 A6PVS0.100 UPI000155D6E5 1 0.0925 0.2562 0.0611 0.0039 0.0379 0.039 0.09533 0.243 0.06158 0.05521 0.06833 0.005537 0.0431 0.05063 0.03548 0.09224 0.03188 0.2562 AFR 23 NA NA PASS SITE 23,17|60,26 NA NA 1 45 20,20 180,176 60,60 34 1.44 NA 7.78 NA FALSE 1.06 93 NA NA NA FALSE NA NA 262.49 23 155276345 HCC1395_HCC1395T 0 0.985 86 0,20 0,39 0,63 NA 0/1 NA NA NA NA 0,0,60,26 A/G PANCANCER NA FALSE CLIC2 chrX:155276345:155276346:A:G SNV 2:2 chrX:86816148:155613005:2:2:1 FALSE NA 0.96