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/scripts/insight/insightPVS1.py src/hg/makeDb/scripts/insight/insightPVS1.py
index 5b2ab040a43..6cd94fcceee 100644
--- src/hg/makeDb/scripts/insight/insightPVS1.py
+++ src/hg/makeDb/scripts/insight/insightPVS1.py
@@ -61,31 +61,32 @@
 
     # MSH2
     ('MSH2', 'NMD', 1, 861, '180,0,0', '≤ codon 861', 'PVS1'),
     ('MSH2', 'CritRegion', 862, 891, '180,0,0', '> codon 861 ≤ codon 891', 'PVS1'),
     ('MSH2', 'FuncUnknown', 892, 934, '204,102,0', '> codon 891 ≤ codon 934', 'PVS1_Moderate'),
     ('MSH2', 'PVS1_n.a.', 935, None, '128,128,128', '> codon 934', 'PVS1_n.a.'),
 
     # MSH6
     ('MSH6', 'NMD', 1, 1317, '180,0,0', '≤ codon 1317', 'PVS1'),
     ('MSH6', 'CritRegion', 1318, 1341, '180,0,0', '> codon 1317 ≤ codon 1341', 'PVS1'),
     ('MSH6', 'FuncUnknown', 1342, 1360, '204,102,0', '> codon 1341 ≤ codon 1360', 'PVS1_Moderate'),
     ('MSH6', 'PVS1_n.a.', 1361, None, '128,128,128', '> codon 1360', 'PVS1_n.a.'),
 
     # PMS2
     ('PMS2', 'NMD', 1, 798, '180,0,0', '≤ codon 798', 'PVS1'),
-    ('PMS2', 'PVS1_n.a.', 799, None, '128,128,128', '> codon 798', 'PVS1_n.a.'),
+    ('PMS2', 'FuncUnknown', 799, 862, '204,102,0', '> codon 798 ≤ codon 862', 'PVS1_Moderate'),
+    ('PMS2', 'PVS1_n.a.', 863, None, '128,128,128', '> codon 862', 'PVS1_n.a.'),
 ]
 
 # AutoSQL definition for the BED9+3 format
 AUTOSQL = """table InSiGHTPVS1
 "InSiGHT VCEP PVS1 decision regions for Lynch syndrome genes (MLH1, MSH2, MSH6, PMS2)"
    (
    string chrom;       "Reference sequence chromosome or scaffold"
    uint   chromStart;  "Start position in chromosome"
    uint   chromEnd;    "End position in chromosome"
    string name;        "Region name (NMD, CritRegion, FuncUnknown, PVS1_n.a.)"
    uint score;         "Not used, all 0"
    char[1] strand;     "Not used, all ."
    uint thickStart;    "Same as chromStart"
    uint thickEnd;      "Same as chromEnd"
    uint reserved;      "RGB value (use R,G,B string in input file)"