Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.9%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -3.9 | GERP -3.1 |
| Overall | ||
| CADD | 0.407 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.9%
East Asian · 404/44,880 alleles
Filtering AF
0.828%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.799%
Overall
0.0433%
699/1,614,028 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.9% | 111 |
| Ashkenazi Jewishnot grpmax-eligible | 0.473% | 211 |
| South Asian | 0.0944% | 1,059 |
| Remaining individualsnot grpmax-eligible | 0.0736% | 1,359 |
| Middle Eastern | 0.0165% | 6,060 |
| European (non-Finnish) | 0.00186% | 53,634 |
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
- BRAP
- Protein
- p.Val341=
- Coding
- c.1023C>T
- MANE Select
- NM_006768
- dbSNP
- rs3742002
- Type
- single nucleotide variant
- Location
- chr12:111659295 (GRCh38)
- Gene constraint
- LOEUF 0.766 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 76.92
Similar variants
- BRAP p.Ala42= Benign ★★ same type
- BRAP p.Gly250= Benign ★★ same type
- BRAP p.Ile193= Benign ★★ same type
- BRAP p.Lys451= Benign ★★ same type
- BRAP p.Ala100Val Uncertain significance ★ ⚠ same type
- BRAP p.Ala379Val Uncertain significance ★ same type
- BRAP p.Ala403Ser Uncertain significance ★ ⚠ same type
- BRAP p.Ala481Gly Uncertain significance ★ ⚠ same type
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/brap-p-val341 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown