BAP1 p.Asp397del
c.1188TGA[1] · rs2471332956 · VCV1744835
Uncertain significance
Multiple submitters
Classification
Uncertain significance
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00167%, amr)
Conditions
2
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 -0.83 | GERP -3.1, phastCons 0.003 |
| Region caveats | ||
| Repeat context | tandem | (TCATCC)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00167%
Admixed American · 1/60,020 alleles
Overall
6.84e-05%
1/1,461,864 alleles · very 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.Asp397del
- Coding
- c.1188TGA[1]
- MANE Select
- NM_004656
- dbSNP
- rs2471332956
- Type
- Microsatellite
- Location
- chr3:52404510 (GRCh38)
- Gene constraint
- LOEUF 0.324 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 63.87 · 4 PDB
- Residue 397
- the 'disordered' region; a UniProt-annotated variant site (in tpds1)
Similar variants
- BAP1 p.Asp397Asn Uncertain significance ★★ ⚠ same residue
- BAP1 p.Asp397= Benign/Likely benign ★★ same residue
- BAP1 p.Asp397Glu Uncertain significance ★ ⚠ same residue
- BAP1 p.Asp397Gly 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
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-asp397del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown