BMS1 p.Ala1108=
c.3324G>A · rs112721376 · VCV779113
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.02%, 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 0.39 | GERP -1.5, phastCons 0.99 |
| Overall | ||
| CADD | 14.02 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.02%
African / African-American · 1,508/74,810 alleles
Filtering AF
1.93%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9%
Overall
0.119%
1,898/1,593,838 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.02% | 50 |
| Middle Eastern | 0.294% | 340 |
| Remaining individualsnot grpmax-eligible | 0.24% | 417 |
| Admixed American | 0.201% | 497 |
| South Asian | 0.0155% | 6,449 |
| European (non-Finnish) | 0.00747% | 13,395 |
| Finnishnot grpmax-eligible | 0.00617% | 16,198 |
| East Asian | 0.00447% | 22,386 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00339% | 29,530 |
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.Ala1108=
- Coding
- c.3324G>A
- MANE Select
- NM_014753
- dbSNP
- rs112721376
- Type
- single nucleotide variant
- Location
- chr10:42823652 (GRCh38)
- Gene constraint
- LOEUF 0.507 · pLI 0.50 (gnomAD)
- Structure
- AlphaFold pLDDT 72.04 · 3 PDB
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-ala1108 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown