BAP1 c.*2G>A
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,601,184)
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 | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · C>A here scores Δ0.73 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 2.7 | GERP 1.8, phastCons 1 |
| Non-coding constraint | Z 5.30 | 1 kb window · o/e 0.65 · regional · uncalibrated |
| Overall | ||
| CADD | 15.04 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,601,184). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- BAP1
- Coding
- c.*2G>A
- MANE Select
- NM_007212 · reported on NM_004656
- Type
- single nucleotide variant
- Location
- chr3:52402286 (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-star-2g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown