BMP6 p.Ser495=
c.1485C>G · rs149391648 · VCV2673043
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.224%, 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 1.1 | GERP -0.12, phastCons 1 |
| Overall | ||
| CADD | 10.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.224%
African / African-American · 168/75,002 alleles
Filtering AF
0.196%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.186%
Overall
0.012%
193/1,614,104 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.224% | 446 |
| Admixed American | 0.0183% | 5,457 |
| Remaining individualsnot grpmax-eligible | 0.016% | 6,251 |
| European (non-Finnish) | 0.000339% | 295,001 |
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
- BMP6
- Protein
- p.Ser495=
- Coding
- c.1485C>G
- MANE Select
- NM_001718
- dbSNP
- rs149391648
- Type
- single nucleotide variant
- Location
- chr6:7880286 (GRCh38)
- Gene constraint
- LOEUF 0.523 · pLI 0.94 (gnomAD)
- Structure
- AlphaFold pLDDT 69.74 · 5 PDB
- Residue 495
- a disulfide bond; a UniProt-annotated variant site (in io; associated with disease susceptibility)
Similar variants
- BMP6 p.Leu209Pro Uncertain significance ★★ ⚠ same type
- BMP6 p.Ser160= Benign/Likely benign ★★ same type
- BMP6 p.Leu137Met Likely pathogenic ★ ⚠ same type
- BMP6 c.-377G>A Uncertain significance ★ same type
- BMP6 p.Ala142Thr Uncertain significance ★ ⚠ same type
- BMP6 p.Ala152Glu Uncertain significance ★ ⚠ same type
- BMP6 p.Ala203Ser Uncertain significance ★ ⚠ same type
- BMP6 p.Ala254Thr Uncertain significance ★ ⚠ 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/bmp6-p-ser495 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown