BMP1 c.2575+150A>G
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 29%, afr) — 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 | ||
| Splice region | donor +150 | deep intronic (+150 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP 0.072 |
| Non-coding constraint | Z 2.87 | 1 kb window · o/e 0.80 · regional · uncalibrated |
| Overall | ||
| CADD | 6.487 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
29%
African / African-American · 17,498/60,416 alleles
Filtering AF
28.6%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 28.5%
Overall
24.1%
222,650/923,786 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 29% | 3 |
| European (non-Finnish) | 27.2% | 4 |
| Middle Eastern | 26.9% | 4 |
| Remaining individualsnot grpmax-eligible | 23.4% | 4 |
| Finnishnot grpmax-eligible | 22.2% | 5 |
| Amishnot grpmax-eligible | 21.2% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 21% | 5 |
| Admixed American | 15.2% | 7 |
| South Asian | 11.2% | 9 |
| East Asian | 0.408% | 245 |
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
- BMP1
- Coding
- c.2575+150A>G
- MANE Select
- NM_006129
- dbSNP
- rs62494057
- Type
- single nucleotide variant
- Location
- chr8:22207666 (GRCh38)
- Gene constraint
- LOEUF 0.648 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 81.89 · 8 PDB
Similar variants
- BMP1 p.Cys183Ter Pathogenic/Likely pathogenic ★★ same type
- BMP1 p.Gln70Ter Pathogenic/Likely pathogenic ★★ same type
- BMP1 c.1443+6T>C Uncertain significance ★★ same type
- BMP1 c.1639+4C>G Uncertain significance ★★ same type
- BMP1 c.2233+4C>T Uncertain significance ★★ same type
- BMP1 c.*452A>C Uncertain significance ★★ same type
- BMP1 p.Ala538Val Uncertain significance ★★ ⚠ same type
- BMP1 p.Ala657Thr 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/bmp1-c-2575-plus-150a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown