BAP1 c.1729+8T>C
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 22 submitters
gnomAD v4.1
Rare
rare (popmax 0.788%, nfe)
Conditions
4
melanoma, uveal, susceptibility to, 2
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +8 | near-intronic (+8 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.55 | GERP -1.3, phastCons 0.002 |
| Non-coding constraint | Z 4.03 | 1 kb window · o/e 0.76 · regional · uncalibrated |
| Overall | ||
| CADD | 6.649 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.788%
European (non-Finnish) · 9,292/1,179,874 alleles
Filtering AF
0.774%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.769%
Overall
0.626%
10,107/1,613,504 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.788% | 127 |
| Remaining individualsnot grpmax-eligible | 0.475% | 210 |
| South Asian | 0.329% | 304 |
| Middle Eastern | 0.297% | 337 |
| African / African-American | 0.109% | 915 |
| Admixed American | 0.0966% | 1,035 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0743% | 1,346 |
| Finnishnot grpmax-eligible | 0.0582% | 1,717 |
| East Asian | 0.00223% | 44,884 |
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.1729+8T>C
- MANE Select
- NM_007212 · reported on NM_004656
- dbSNP
- rs150945583
- Type
- single nucleotide variant
- Location
- chr3:52403408 (GRCh38)
- Structure
- AlphaFold pLDDT 78.27 · 28 PDB
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-1729-plus-8t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown