BEND2 p.Glu784=
c.2352G>A · rs141037742 · VCV783905
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 1.67%, 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 0.63 | GERP -1.4, phastCons 0.005 |
| Overall | ||
| CADD | 0.621 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.67%
African / African-American · 950/56,975 alleles
Filtering AF
1.58%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.54%
Overall
0.0979%
1,183/1,207,976 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.67% | 60 |
| Admixed American | 0.134% | 748 |
| Remaining individualsnot grpmax-eligible | 0.126% | 792 |
| Middle Eastern | 0.0634% | 1,578 |
| South Asian | 0.0159% | 6,297 |
| European (non-Finnish) | 0.0112% | 8,951 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00454% | 22,032 |
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
- BEND2
- Protein
- p.Glu784=
- Coding
- c.2352G>A
- MANE Select
- NM_153346
- dbSNP
- rs141037742
- Type
- single nucleotide variant
- Location
- chrX:18165057 (GRCh38)
- Structure
- AlphaFold pLDDT 49.94
- Residue 784
- the 'disordered' region
Similar variants
- BEND2 p.Gln198His Benign ★★ same type
- BEND2 p.Gly580Val Benign ★★ same type
- BEND2 p.Ser183Ile Benign ★★ ⚠ same type
- BEND2 p.Thr367= Likely benign ★★ same type
- BEND2 p.Val261Gly Benign ★★ same type
- BEND2 p.Ala185Gly Uncertain significance ★ ⚠ same type
- BEND2 p.Ala193Thr Uncertain significance ★ ⚠ same type
- BEND2 p.Ala222Ser 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/bend2-p-glu784 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown