BEND7 p.Ala105Asp
c.314C>A · rs147003029 · VCV2261067
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.085%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.067 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 2.8 | GERP -1.4, phastCons 1 |
| Regional constraint | o/e 1.03 | unconstrained · MANE · 48 kb · p 0.55 · regional, not allelic |
| Overall | ||
| CADD | 12.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.085%
Admixed American · 51/60,034 alleles
Filtering AF
0.0663%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0597%
Overall
0.0337%
544/1,614,180 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.085% | 1,177 |
| Finnishnot grpmax-eligible | 0.0672% | 1,489 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,718 |
| European (non-Finnish) | 0.0348% | 2,871 |
| Middle Eastern | 0.0165% | 6,062 |
| African / African-American | 0.016% | 6,253 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0101% | 9,869 |
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
- BEND7
- Protein
- p.Ala105Asp
- Coding
- c.314C>A
- MANE Select
- NM_001369863
- dbSNP
- rs147003029
- Type
- single nucleotide variant
- Location
- chr10:13499912 (GRCh38)
- Gene constraint
- LOEUF 0.842 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.17
- Residue 105
- the 'disordered' region
Similar variants
- BEND7 p.Ala105Val Uncertain significance ★ same residue
- BEND7 p.Ala103Val Uncertain significance ★ same type
- BEND7 p.Ala255Gly Uncertain significance ★ same type
- BEND7 p.Ala397Val Uncertain significance ★ same type
- BEND7 p.Arg114Cys Uncertain significance ★ same type
- BEND7 p.Arg134Cys Uncertain significance ★ same type
- BEND7 p.Arg136Gly Uncertain significance ★ same type
- BEND7 p.Arg265Cys 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/bend7-p-ala105asp (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown