BMPER p.Val56=
c.168C>T · rs112068976 · VCV1645783
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.357%, 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 -0.62 | GERP -5.2, phastCons 0.016 |
| Overall | ||
| CADD | 6.398 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.357%
African / African-American · 268/75,026 alleles
Filtering AF
0.322%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.308%
Overall
0.0202%
326/1,613,904 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.357% | 280 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,083 |
| Admixed American | 0.0267% | 3,751 |
| South Asian | 0.0011% | 91,070 |
| European (non-Finnish) | 0.000932% | 107,265 |
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
- BMPER
- Protein
- p.Val56=
- Coding
- c.168C>T
- MANE Select
- NM_001365308
- dbSNP
- rs112068976
- Type
- single nucleotide variant
- Location
- chr7:33906852 (GRCh38)
- Gene constraint
- LOEUF 0.652 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 80.24
- Residue 56
- the vwfc 1 domain
Similar variants
- BMPER p.Arg241Ter Likely pathogenic ★★ same type
- BMPER p.Gln309Ter Pathogenic ★★ same type
- BMPER p.Ala39Ser Uncertain significance ★★ ⚠ same type
- BMPER p.Ala486Val Uncertain significance ★★ ⚠ same type
- BMPER p.Arg131Cys Uncertain significance ★★ ⚠ same type
- BMPER p.Arg16Ser Uncertain significance ★★ ⚠ same type
- BMPER p.Arg332His Uncertain significance ★★ ⚠ same type
- BMPER p.Arg410His 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/bmper-p-val56 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown