44b6d9c6ca033c3f613b336cdc52b9a938e1a8e1
lrnassar
  Fri Aug 14 12:58:26 2026 -0700
Drop dead synonymous_variant from TP53 FLOSSIES coding set; fix comment. refs #37399

Per CR feedback: CODING_CONSEQUENCES listed 'synonymous_variant', but the FLOSSIES
export labels synonymous variants 'silent', so they correctly fall to
Informational (not BS2) as documented. The dead entry contradicted the comment
and would have tiered synonymous as BS2 if the label ever changed. Remove it and
correct the comment. Output is unchanged (no synonymous_variant-labeled variant
exists in the data).

diff --git src/hg/makeDb/scripts/tp53/tp53Flossies.py src/hg/makeDb/scripts/tp53/tp53Flossies.py
index d3bcc7b1363..8498bdb2571 100644
--- src/hg/makeDb/scripts/tp53/tp53Flossies.py
+++ src/hg/makeDb/scripts/tp53/tp53Flossies.py
@@ -25,37 +25,38 @@
 
 DEFAULT_OUTDIR = "/hive/users/lrnassar/claude/RM37399/flossies"
 DEFAULT_SRC = "/hive/users/lrnassar/claude/RM37399/flossies_tp53.json"
 
 COLORS = {
     'BS2':            '23,124,106',  # dark teal   - BS2 (8+ carriers)
     'BS2_Moderate':   '46,157,138',  # medium teal - BS2_Moderate (4-7)
     'BS2_Supporting': '138,201,189', # light teal  - BS2_Supporting (2-3)
     'Observed':       '201,201,201', # light gray  - coding, <2 carriers (below BS2)
     'Informational':  '180,180,180', # gray        - non-coding observations
 }
 
 # Per CSpec GN009 v2.4.0 §BS2: variant observed in a cohort of healthy
 # adult women >70 weakens disease-causation evidence. The VCEP weights BS2
 # by the number of carriers in the cohort: 2-3 -> BS2_Supporting, 4-7 ->
-# BS2_Moderate, 8+ -> BS2. In the FLOSSIES TP53 export the coding
-# observations that carry a consequence in CODING_CONSEQUENCES are all
-# missense; those with a single carrier are shown but do not meet BS2. All
-# other observations (synonymous, labeled "silent" here, plus UTR / deep
-# intronic) are flagged "Informational" since BS2 is not applied to them.
+# BS2_Moderate, 8+ -> BS2. The carrier tiers apply to the protein-altering
+# coding consequences in CODING_CONSEQUENCES below; a coding observation with a
+# single carrier is shown but does not meet BS2. Synonymous (labeled "silent"
+# in this export), UTR, and intronic observations are not protein-altering and
+# are flagged "Informational" (BS2 is not applied to them). In the current
+# FLOSSIES TP53 export the only coding consequence present is missense.
 CODING_CONSEQUENCES = {
-    'missense_variant', 'synonymous_variant', 'splice_donor_variant',
+    'missense_variant', 'splice_donor_variant',
     'splice_acceptor_variant', 'splice_region_variant', 'stop_gained',
     'stop_lost', 'start_lost', 'frameshift_variant',
     'inframe_insertion', 'inframe_deletion',
 }
 
 AUTOSQL = """table TP53Flossies
 "TP53 VCEP BS2 evidence: observations in the FLOSSIES healthy-women-over-70 cohort"
    (
    string chrom;        "Reference sequence chromosome or scaffold"
    uint   chromStart;   "Start position in chromosome"
    uint   chromEnd;     "End position in chromosome"
    string name;         "Variant display name"
    uint   score;        "Not used, all 0"
    char[1] strand;      "Not used, all ."
    uint   thickStart;   "Same as chromStart"