BMP15 p.Leu203=
c.607C>T · rs781940193 · VCV208063
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0689%, mid)
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 1.8 | GERP 1.6, phastCons 0.91 |
| Overall | ||
| CADD | 1.773 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0689%
Middle Eastern · 3/4,356 alleles
Filtering AF
0.0187%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00995%
Overall
0.00264%
29/1,098,210 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0689% | 1,452 |
| Remaining individualsnot grpmax-eligible | 0.00839% | 11,913 |
| Admixed American | 0.00651% | 15,352 |
| South Asian | 0.00351% | 28,494 |
| European (non-Finnish) | 0.0019% | 52,681 |
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.Leu203=
- Coding
- c.607C>T
- MANE Select
- NM_005448
- dbSNP
- rs781940193
- Type
- single nucleotide variant
- Location
- chrX:50916035 (GRCh38)
- Structure
- AlphaFold pLDDT 72.64
Similar variants
- BMP15 p.Gly271Cys Uncertain significance ★★ ⚠ same type
- BMP15 c.329-74A>C Benign ★★ same type
- BMP15 c.-9C>G Benign ★★ same type
- BMP15 c.*13G>A Benign ★★ same type
- BMP15 p.Asn103Ser Benign ★★ same type
- BMP15 p.Gly54= Benign/Likely benign ★★ same type
- BMP15 p.His337= Benign ★★ same type
- BMP15 p.Leu148Pro Benign/Likely benign ★★ ⚠ 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/bmp15-p-leu203 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown