BAP1 c.37+31G>C
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.138%, sas)
Conditions
1
BAP1-related tumor predisposition syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +31 | near-intronic (+31 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.2 | GERP -2.3, phastCons 0.35 |
| Non-coding constraint | Z 2.71 | 1 kb window · o/e 0.83 · regional · uncalibrated |
| Overall | ||
| CADD | 12.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.138%
South Asian · 126/91,070 alleles
Filtering AF
0.119%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.111%
Overall
0.0162%
261/1,613,050 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.138% | 723 |
| Remaining individualsnot grpmax-eligible | 0.0272% | 3,674 |
| European (non-Finnish) | 0.00983% | 10,172 |
| Admixed American | 0.00167% | 60,012 |
| African / African-American | 0.00133% | 75,054 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- BAP1
- Coding
- c.37+31G>C
- MANE Select
- NM_007212 · reported on NM_004656
- dbSNP
- rs200628603
- Type
- single nucleotide variant
- Location
- chr3:52409811 (GRCh38)
- Structure
- AlphaFold pLDDT 78.27 · 28 PDB
Disease context
BAP1-related tumor predisposition syndrome — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor BAP1-related tumor predisposition syndrome (Orphanet):
- Inheritance
- Autosomal dominant
- Onset
- Adult
Similar variants
- BAP1 c.1117-1G>A Likely pathogenic ★★ same condition
- BAP1 c.122+1G>A Pathogenic ★★ same condition
- BAP1 c.122+1G>T Pathogenic/Likely pathogenic ★★ same condition
- BAP1 c.122+5G>A Pathogenic/Likely pathogenic ★★ same condition
- BAP1 c.122+5G>C Likely pathogenic ★★ same condition
- BAP1 c.1251-1G>A Likely pathogenic ★★ same condition
- BAP1 c.1251-1G>C Likely pathogenic ★★ same condition
- BAP1 c.1251-2A>G Likely pathogenic ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bap1-c-37-plus-31g-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown