BMP15 p.Ser273=
c.819A>C · rs73488038 · VCV259776
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.37%, afr)
Conditions
1
ovarian dysgenesis 2
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 -0.7 | GERP -3.2 |
| Overall | ||
| CADD | 0.313 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.37%
African / African-American · 1,349/56,910 alleles
Filtering AF
2.27%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.22%
Overall
0.131%
1,578/1,208,992 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.37% | 42 |
| Middle Eastern | 0.23% | 435 |
| Remaining individualsnot grpmax-eligible | 0.216% | 462 |
| Admixed American | 0.131% | 761 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0863% | 1,159 |
| South Asian | 0.0053% | 18,885 |
| European (non-Finnish) | 0.0038% | 26,320 |
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
- BMP15
- Protein
- p.Ser273=
- Coding
- c.819A>C
- MANE Select
- NM_005448
- dbSNP
- rs73488038
- Type
- single nucleotide variant
- Location
- chrX:50916247 (GRCh38)
- Structure
- AlphaFold pLDDT 72.64
- Residue 273
- a modified residue (phosphoserine; in p16)
Similar variants
- BMP15 p.Gly271Cys Uncertain significance ★★ ⚠ same condition
- BMP15 c.-9C>G Benign ★★ same condition
- BMP15 c.*13G>A Benign ★★ same condition
- BMP15 p.Asn103Ser Benign ★★ same condition
- BMP15 p.Gly54= Benign/Likely benign ★★ same condition
- BMP15 p.His337= Benign ★★ same condition
- BMP15 p.Leu148Pro Benign/Likely benign ★★ same condition
- BMP15 p.Phe194Ser Benign/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/bmp15-p-ser273 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown