BAP1 p.Glu652=
c.1956G>A · rs761399207 · VCV485246
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0533%, amr)
Conditions
2
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.365 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -0.84 | GERP -4, phastCons 0.007 |
| Overall | ||
| CADD | 1.847 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0533%
Admixed American · 32/60,008 alleles
Filtering AF
0.0387%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0339%
Overall
0.00198%
32/1,614,118 alleles · ultra-rare
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
- Protein
- p.Glu652=
- Coding
- c.1956G>A
- MANE Select
- NM_007212 · reported on NM_004656
- dbSNP
- rs761399207
- Type
- single nucleotide variant
- Location
- chr3:52402806 (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-p-glu652 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown