BMS1 p.Ser558=
c.1674T>C · rs767774070 · VCV726701
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.158%, amr)
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 0.3 | GERP -2.5 |
| Overall | ||
| CADD | 1.227 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.158%
Admixed American · 95/60,004 alleles
Filtering AF
0.133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.123%
Overall
0.00589%
95/1,613,996 alleles · rare
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.Ser558=
- Coding
- c.1674T>C
- MANE Select
- NM_014753
- dbSNP
- rs767774070
- Type
- single nucleotide variant
- Location
- chr10:42796918 (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-ser558 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown