BMP7 p.Arg289=
c.867C>T · rs762182367 · VCV2900742
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, 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 0.17 | GERP -2.3, phastCons 0.85 |
| Overall | ||
| CADD | 7.7 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/60,012 alleles
Filtering AF
0.00543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.00112%
18/1,614,098 alleles · ultra-rare
exomes 14/1,461,856 · genomes 4/152,242 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,573 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,622 |
| European (non-Finnish) | 0.000593% | 168,580 |
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
- BMP7
- Protein
- p.Arg289=
- Coding
- c.867C>T
- MANE Select
- NM_001719
- dbSNP
- rs762182367
- Type
- single nucleotide variant
- Location
- chr20:57183813 (GRCh38)
- Gene constraint
- LOEUF 0.523 · pLI 0.96 (gnomAD)
- Structure
- AlphaFold pLDDT 76.50 · 4 PDB
Similar variants
- BMP7 p.Arg289His Uncertain significance ★ same residue
- BMP7 p.Arg150His Uncertain significance ★★ ⚠ same type
- BMP7 p.Arg267Gln Uncertain significance ★★ ⚠ same type
- BMP7 p.His241Tyr Uncertain significance ★★ ⚠ same type
- BMP7 p.Ile386Val Uncertain significance ★★ ⚠ same type
- BMP7 p.Leu160Phe Uncertain significance ★★ same type
- BMP7 p.Pro116Ser Uncertain significance ★★ ⚠ same type
- BMP7 p.Ser248Leu 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/bmp7-p-arg289 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown