BEND3 p.Tyr499=
c.1497C>T · VCV4205187
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0213%, 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 -1.3 | GERP -3.5 |
| Overall | ||
| CADD | 7.017 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0213%
African / African-American · 16/75,046 alleles
Filtering AF
0.0133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0109%
Overall
0.00342%
55/1,609,888 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0213% | 4,690 |
| East Asian | 0.00892% | 11,216 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,606 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,236 |
| European (non-Finnish) | 0.00254% | 39,332 |
| Admixed American | 0.00167% | 60,022 |
| South Asian | 0.0011% | 91,072 |
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
- BEND3
- Protein
- p.Tyr499=
- Coding
- c.1497C>T
- MANE Select
- NM_001367314
- Type
- single nucleotide variant
- Location
- chr6:107069694 (GRCh38)
- Gene constraint
- LOEUF 0.339 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 65.11 · 2 PDB
- Residue 499
- the 'disordered' region
Similar variants
- BEND3 p.Ala102Val Uncertain significance ★ ⚠ same type
- BEND3 p.Ala122Gly Uncertain significance ★ ⚠ same type
- BEND3 p.Ala161Thr Uncertain significance ★ ⚠ same type
- BEND3 p.Ala250Val Uncertain significance ★ ⚠ same type
- BEND3 p.Ala251Thr Uncertain significance ★ ⚠ same type
- BEND3 p.Ala28Asp Uncertain significance ★ ⚠ same type
- BEND3 p.Ala355Thr Uncertain significance ★ ⚠ same type
- BEND3 p.Ala387Thr 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/bend3-p-tyr499 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown