diff --git a/seqr/management/commands/check_for_new_samples_from_pipeline.py b/seqr/management/commands/check_for_new_samples_from_pipeline.py
index 2635da91ca..0b4373e94a 100644
--- a/seqr/management/commands/check_for_new_samples_from_pipeline.py
+++ b/seqr/management/commands/check_for_new_samples_from_pipeline.py
@@ -32,7 +32,7 @@
 
 DATASET_TYPE_MAP = {'GCNV': Sample.DATASET_TYPE_SV_CALLS}
 USER_EMAIL = 'manage_command'
-MAX_LOOKUP_VARIANTS = 3000
+MAX_LOOKUP_VARIANTS = 2000
 RELATEDNESS_CHECK_NAME = 'relatedness_check'
 
 PDO_COPY_FIELDS = [