BMS1 p.Ala289=
c.867A>G · rs1177497889 · VCV3025776
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0121%, 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 -0.35 | GERP 0.78 |
| Overall | ||
| CADD | 6.824 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0121%
African / African-American · 9/74,614 alleles
Filtering AF
0.00626%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00469%
Overall
0.000994%
16/1,609,478 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0121% | 8,290 |
| East Asian | 0.00447% | 22,383 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,122 |
| Admixed American | 0.00167% | 59,908 |
| South Asian | 0.0011% | 90,870 |
| European (non-Finnish) | 8.48e-05% | 1,179,434 |
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
- BMS1
- Protein
- p.Ala289=
- Coding
- c.867A>G
- MANE Select
- NM_014753
- dbSNP
- rs1177497889
- Type
- single nucleotide variant
- Location
- chr10:42792580 (GRCh38)
- Gene constraint
- LOEUF 0.507 · pLI 0.50 (gnomAD)
- Structure
- AlphaFold pLDDT 72.04 · 3 PDB
- Residue 289
- a β-strand
Similar variants
- BMS1 p.Ala214Val Benign/Likely benign ★★ same type
- BMS1 p.Ala500= Benign/Likely benign ★★ same type
- BMS1 p.Arg237His Benign ★★ same type
- BMS1 p.Arg38Trp Benign/Likely benign ★★ ⚠ same type
- BMS1 p.Arg863= Benign ★★ same type
- BMS1 p.Asp768Asn Benign ★★ same type
- BMS1 p.Glu1278= Likely benign ★★ same type
- BMS1 p.Ile942= Benign/Likely 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/bms1-p-ala289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown