BMP5 p.Val101=
c.303A>G · rs150791548 · VCV3035176
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.092%, afr)
Conditions
1
BMP5-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 0.19 | GERP -2.3, phastCons 0.027 |
| Overall | ||
| CADD | 3.175 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.092%
African / African-American · 69/74,964 alleles
Filtering AF
0.0745%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0682%
Overall
0.00459%
74/1,613,516 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.092% | 1,086 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,822 |
| Admixed American | 0.00334% | 29,953 |
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
- BMP5
- Protein
- p.Val101=
- Coding
- c.303A>G
- MANE Select
- NM_021073
- dbSNP
- rs150791548
- Type
- single nucleotide variant
- Location
- chr6:55874563 (GRCh38)
- Gene constraint
- LOEUF 0.711 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 74.85
Disease context
BMP5-related disorder
Similar variants
- BMP5 p.Ser347Arg Uncertain significance ★ ⚠ same condition
- BMP5 p.Asn282= Benign same condition
- BMP5 p.Gln298= Likely benign same condition
- BMP5 p.Ile127Lys Benign same condition
- BMP5 p.Ser37= Benign same condition
- BMP5 p.Tyr377= Benign same condition
- BMP5 c.1105-29GT[11] Likely benign same condition
- BMP5 c.1105-29GT[15] Likely 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/bmp5-p-val101 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown