BBX p.Ala892=
c.2676C>T · rs140221563 · VCV784014
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.19%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.317 | indeterminate |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -11 | GERP -4.7 |
| Overall | ||
| CADD | 2.276 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.19%
African / African-American · 1,647/75,056 alleles
Filtering AF
2.11%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.07%
Overall
0.117%
1,885/1,614,178 alleles · low-frequency
exomes 934/1,461,870 · genomes 951/152,308 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.19% | 46 |
| Remaining individualsnot grpmax-eligible | 0.154% | 651 |
| Admixed American | 0.14% | 715 |
| Middle Eastern | 0.033% | 3,031 |
| East Asian | 0.00446% | 22,440 |
| South Asian | 0.00439% | 22,769 |
| European (non-Finnish) | 0.00424% | 23,600 |
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
- BBX
- Protein
- p.Ala892=
- Coding
- c.2676C>T
- MANE Select
- NM_001142568
- dbSNP
- rs140221563
- Type
- single nucleotide variant
- Location
- chr3:107801219 (GRCh38)
- Gene constraint
- LOEUF 0.359 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 50.79
Similar variants
- BBX p.Ala892Pro Uncertain significance ★ ⚠ same residue
- BBX p.Ala442Thr Benign ★★ same type
- BBX p.Ala60= Likely benign ★★ same type
- BBX p.Ala139Thr Uncertain significance ★ ⚠ same type
- BBX p.Ala143Gly Uncertain significance ★ ⚠ same type
- BBX p.Ala269Pro Uncertain significance ★ ⚠ same type
- BBX p.Ala354Thr Uncertain significance ★ ⚠ same type
- BBX p.Ala375Thr 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/bbx-p-ala892 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown