dc7ac233e8848cee5087dca606f4d638ca8a3be1
lrnassar
  Tue Apr 14 11:58:42 2026 -0700
Update InSiGHT scripts per v2.0.0 CSpec: fix PMS2 BS1 threshold, add PMS2 PVS1 Moderate region. refs #36582

diff --git src/hg/makeDb/doc/InSiGHT.txt src/hg/makeDb/doc/InSiGHT.txt
index 5e826d5b3bf..1f49a3e32fd 100644
--- src/hg/makeDb/doc/InSiGHT.txt
+++ src/hg/makeDb/doc/InSiGHT.txt
@@ -44,31 +44,31 @@
 
 cd /hive/users/lrnassar/insightHub/clinDomains
 python3 ~/kent/src/hg/makeDb/scripts/insight/insightClinDomains.py
 
 # Output: InSiGHTclinDomainsHg38.bb, InSiGHTclinDomainsHg19.bb
 
 ##############################################################################
 # Track 2: PVS1 Regions
 ##############################################################################
 
 # PVS1 decision tree regions based on NMD predictions and critical functional
 # regions. Gene-specific codon boundaries from the InSiGHT VCEP specs:
 #   MLH1: NMD <=684, CritRegion 685-753, FuncUnknown 754-756, n.a. >756
 #   MSH2: NMD <=861, CritRegion 862-891, FuncUnknown 892-934, n.a. >934
 #   MSH6: NMD <=1317, CritRegion 1318-1341, FuncUnknown 1342-1360, n.a. >1360
-#   PMS2: NMD <=798, n.a. >798
+#   PMS2: NMD <=798, FuncUnknown 799-862, n.a. >862
 # Generates bigBed 9+3 files for hg38 and hg19.
 
 cd /hive/users/lrnassar/insightHub/pvs1
 python3 ~/kent/src/hg/makeDb/scripts/insight/insightPVS1.py
 
 # Output: InSiGHTPVS1Hg38.bb, InSiGHTPVS1Hg19.bb
 
 ##############################################################################
 # Track 3: Allele Frequencies (BA1/BS1/PM2)
 ##############################################################################
 
 # ACMG allele frequency classifications from gnomAD v4.1 exomes.
 # Gene-specific thresholds from the InSiGHT VCEP specs.
 # Requires access to gnomAD v4.1 bigBed files in /gbdb/hg38/gnomAD/v4.1/exomes/
 # Generates bigBed 9+3 files for hg38 and hg19 (hg19 via liftOver).