BEND7 p.Arg98Cys
c.292C>T · VCV3480450
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0078%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.146 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.50 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 7.5 | GERP 1.9, phastCons 1 |
| Regional constraint | o/e 1.03 | unconstrained · MANE · 48 kb · p 0.55 · regional, not allelic |
| Overall | ||
| CADD | 24.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0078%
European (non-Finnish) · 92/1,180,048 alleles
Filtering AF
0.00647%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.006%
Overall
0.00582%
94/1,614,094 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0078% | 12,827 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
| African / African-American | 0.00133% | 74,944 |
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.Arg98Cys
- Coding
- c.292C>T
- MANE Select
- NM_001369863
- Type
- single nucleotide variant
- Location
- chr10:13499934 (GRCh38)
- Gene constraint
- LOEUF 0.842 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 62.17
- Residue 98
- the 'disordered' region
Similar variants
- BEND7 p.Ala103Val Uncertain significance ★ same type
- BEND7 p.Ala105Asp Uncertain significance ★ same type
- BEND7 p.Ala105Val 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
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-arg98cys (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown