BAP1 c.*45C>G
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 9.2%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.3 | GERP 1.9, phastCons 1 |
| Non-coding constraint | Z 5.30 | 1 kb window · o/e 0.65 · regional · uncalibrated |
| Overall | ||
| CADD | 12.89 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
9.2%
African / African-American · 6,886/74,884 alleles
Filtering AF
9.01%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 8.94%
Overall
0.877%
13,947/1,589,528 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 9.2% | 11 |
| South Asian | 1.48% | 68 |
| Remaining individualsnot grpmax-eligible | 0.912% | 110 |
| Admixed American | 0.845% | 118 |
| Middle Eastern | 0.534% | 187 |
| European (non-Finnish) | 0.4% | 250 |
| Finnishnot grpmax-eligible | 0.0319% | 3,137 |
| East Asian | 0.0136% | 7,353 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0069% | 14,502 |
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.*45C>G
- MANE Select
- NM_004656
- dbSNP
- rs56898787
- Type
- single nucleotide variant
- Location
- chr3:52402243 (GRCh38)
- Gene constraint
- LOEUF 0.324 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.87 · 4 PDB
Similar variants
- BAP1 c.1117-1G>A Likely pathogenic ★★ same type
- BAP1 c.122+1G>A Pathogenic ★★ same type
- BAP1 c.122+1G>T Pathogenic/Likely pathogenic ★★ same type
- BAP1 c.122+5G>A Pathogenic/Likely pathogenic ★★ same type
- BAP1 c.122+5G>C Likely pathogenic ★★ same type
- BAP1 c.1251-1G>A Likely pathogenic ★★ same type
- BAP1 c.1251-1G>C Likely pathogenic ★★ same type
- BAP1 c.1251-2A>G Likely pathogenic ★★ same type
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-star-45c-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown