BMS1 p.Ala980=
c.2940A>T · rs1370712378 · VCV3053391
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0512%, 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 0.9 | GERP -3.4, phastCons 0.9 |
| Overall | ||
| CADD | 8.536 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0512%
East Asian · 23/44,900 alleles
Filtering AF
0.035%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0296%
Overall
0.0018%
29/1,611,718 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0512% | 1,952 |
| Admixed American | 0.00333% | 29,992 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,146 |
| European (non-Finnish) | 0.00017% | 589,870 |
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.Ala980=
- Coding
- c.2940A>T
- MANE Select
- NM_014753
- dbSNP
- rs1370712378
- Type
- single nucleotide variant
- Location
- chr10:42820678 (GRCh38)
- Gene constraint
- LOEUF 0.507 · pLI 0.50 (gnomAD)
- Structure
- AlphaFold pLDDT 72.04 · 3 PDB
- Residue 980
- a β-strand
Similar variants
- BMS1 p.Ala980Thr Uncertain significance ★ ⚠ same residue
- 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
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-ala980 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown