BMP7 p.Ser405=
c.1215C>T · rs141004050 · VCV710157
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2%, 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 -11 | GERP -5.3 |
| Overall | ||
| CADD | 0.522 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2%
African / African-American · 1,503/75,050 alleles
Filtering AF
1.92%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.88%
Overall
0.124%
1,998/1,614,188 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2% | 50 |
| Admixed American | 0.232% | 432 |
| Middle Eastern | 0.231% | 433 |
| Remaining individualsnot grpmax-eligible | 0.154% | 651 |
| European (non-Finnish) | 0.0202% | 4,958 |
| South Asian | 0.00659% | 15,178 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| East Asian | 0.00223% | 44,882 |
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.Ser405=
- Coding
- c.1215C>T
- MANE Select
- NM_001719
- dbSNP
- rs141004050
- Type
- single nucleotide variant
- Location
- chr20:57171040 (GRCh38)
- Gene constraint
- LOEUF 0.523 · pLI 0.96 (gnomAD)
- Structure
- AlphaFold pLDDT 76.50 · 4 PDB
- Residue 405
- a disulfide bond; a β-strand
Similar variants
- 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
- BMP7 p.Thr251Met 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-ser405 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown