BCAR1 p.Val405=
c.1215C>T · rs61729594 · VCV781212
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.38%, afr)
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 -5 | GERP -3.6 |
| Overall | ||
| CADD | 0.032 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.38%
African / African-American · 1,787/75,002 alleles
Filtering AF
2.29%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.25%
Overall
0.125%
2,010/1,611,470 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.38% | 42 |
| Remaining individualsnot grpmax-eligible | 0.175% | 572 |
| Admixed American | 0.125% | 798 |
| Middle Eastern | 0.116% | 864 |
| South Asian | 0.00661% | 15,133 |
| East Asian | 0.00446% | 22,419 |
| European (non-Finnish) | 0.00204% | 49,118 |
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
- BCAR1
- Protein
- p.Val405=
- Coding
- c.1215C>T
- MANE Select
- NM_014567
- dbSNP
- rs61729594
- Type
- single nucleotide variant
- Location
- chr16:75235684 (GRCh38)
- Gene constraint
- LOEUF 0.778 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.07 · 5 PDB
- Residue 405
- the 'substrate for kinases' region
Similar variants
- BCAR1 c.2100+10C>T Benign/Likely benign ★★ same type
- BCAR1 p.Ala411= Benign ★★ same type
- BCAR1 p.Ala514= Benign ★★ same type
- BCAR1 p.Ala590Thr Benign ★★ ⚠ same type
- BCAR1 p.Arg491Leu Benign ★★ same type
- BCAR1 p.Gly450Val Benign ★★ same type
- BCAR1 p.Gly568Ser Benign ★★ same type
- BCAR1 p.His558Arg Benign ★★ 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/bcar1-p-val405 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown