BMS1 p.Lys399=
c.1197G>A · rs7921071 · VCV3060154
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 16.3%, amr) — too common for a highly-penetrant pathogenic allele
Conditions
1
BMS1-related disorder
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 3.1 | GERP -1.8, phastCons 1 |
| Overall | ||
| CADD | 1.839 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
16.3%
Admixed American · 9,765/59,978 alleles
Filtering AF
16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 15.9%
Overall
4.44%
71,502/1,611,578 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 16.3% | 6 |
| African / African-American | 15% | 7 |
| East Asian | 6.15% | 16 |
| Remaining individualsnot grpmax-eligible | 4.77% | 21 |
| South Asian | 3.64% | 28 |
| Middle Eastern | 3.36% | 30 |
| European (non-Finnish) | 3.31% | 30 |
| Finnishnot grpmax-eligible | 2.66% | 38 |
| Amishnot grpmax-eligible | 2.08% | 48 |
| Ashkenazi Jewishnot grpmax-eligible | 2.03% | 49 |
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.Lys399=
- Coding
- c.1197G>A
- MANE Select
- NM_014753
- dbSNP
- rs7921071
- Type
- single nucleotide variant
- Location
- chr10:42793959 (GRCh38)
- Gene constraint
- LOEUF 0.507 · pLI 0.50 (gnomAD)
- Structure
- AlphaFold pLDDT 72.04 · 3 PDB
- Residue 399
- a cross-link site; the 'disordered' region
Disease context
BMS1-related disorder
Similar variants
- BMS1 c.779+7T>A Likely benign same condition
- BMS1 c.779+8A>G Likely benign same condition
- BMS1 p.Ala549Thr Benign same condition
- BMS1 p.Ala864Thr Benign ⚠ same condition
- BMS1 p.Asp505= Likely benign same condition
- BMS1 p.Gln419Glu Benign same condition
- BMS1 p.Phe1047Leu Benign same condition
- BMS1 p.Thr583= Benign same condition
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-lys399 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown