BMP2 p.Asp387=
c.1161C>T · rs13037675 · VCV257620
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 15.8%, amr) — too common for a highly-penetrant pathogenic allele
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 0.6 | GERP 2.8, phastCons 1 |
| Overall | ||
| CADD | 7.937 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
15.8%
Admixed American · 9,476/59,894 alleles
Filtering AF
15.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 15.4%
Overall
6.67%
107,339/1,610,308 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 15.8% | 6 |
| European (non-Finnish) | 7.05% | 14 |
| Remaining individualsnot grpmax-eligible | 6.33% | 16 |
| Finnishnot grpmax-eligible | 5.98% | 17 |
| African / African-American | 4.82% | 21 |
| Middle Eastern | 3.85% | 26 |
| Ashkenazi Jewishnot grpmax-eligible | 3.32% | 30 |
| South Asian | 2.52% | 40 |
| Amishnot grpmax-eligible | 2.09% | 48 |
| East Asian | 0.0268% | 3,738 |
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
- BMP2
- Protein
- p.Asp387=
- Coding
- c.1161C>T
- MANE Select
- NM_001200
- dbSNP
- rs13037675
- Type
- single nucleotide variant
- Location
- chr20:6779059 (GRCh38)
- Gene constraint
- LOEUF 0.213 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 80.37 · 21 PDB
- Residue 387
- a disulfide bond; a UniProt-annotated variant site (in ssfsc1); a UniProt-annotated variant site (in); a β-strand
Similar variants
- BMP2 p.Asp387Asn Uncertain significance ★ ⚠ same residue
- BMP2 p.Arg154Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Arg170Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Cys329Ter Likely pathogenic ★★ same type
- BMP2 p.Gln89Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Glu229Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Ser92Ter Pathogenic/Likely pathogenic ★★ same type
- BMP2 p.Ala103Thr 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/bmp2-p-asp387 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown