BAP1 p.Asp75del
c.217GAT[2] · VCV4842551
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, eas)
Conditions
1
hereditary neoplastic syndrome
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · substitutions only |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 7.9 | GERP 1.8, phastCons 1 |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,878 alleles
Overall
6.2e-05%
1/1,612,266 alleles · very rare
exomes 1/1,459,976 · genomes 0/152,290 · joint denominator
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.Asp75del
- Coding
- c.217GAT[2]
- MANE Select
- NM_004656
- Type
- Microsatellite
- Location
- chr3:52408504 (GRCh38)
- Gene constraint
- LOEUF 0.324 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.87 · 4 PDB
- Residue 75
- the uch catalytic domain; an α-helix
Similar variants
- BAP1 p.Asp75Asn Uncertain significance ★★ ⚠ same residue
- BAP1 p.Gln267fs Pathogenic ★★ same condition
- BAP1 p.Glu611fs Pathogenic ★★ same condition
- BAP1 p.His481fs Pathogenic ★★ same condition
- BAP1 p.Ser492fs Pathogenic ★★ same condition
- BAP1 p.Val639fs Pathogenic ★★ same condition
- BAP1 p.Asp397del Uncertain significance ★★ same condition
- BAP1 c.1984-18TCT[2] Likely benign ★★ 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-asp75del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown