BACH2 p.Ala65=
c.195G>A · rs138881451 · VCV1454433
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0906%, 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 -8.2 | GERP -4.2 |
| Overall | ||
| CADD | 4.731 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0906%
African / African-American · 68/75,058 alleles
Filtering AF
0.0733%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.067%
Overall
0.00688%
111/1,614,190 alleles · ultra-rare
exomes 67/1,461,872 · genomes 44/152,318 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0906% | 1,104 |
| Middle Eastern | 0.0495% | 2,021 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,945 |
| Admixed American | 0.0117% | 8,575 |
| European (non-Finnish) | 0.00203% | 49,168 |
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
- BACH2
- Protein
- p.Ala65=
- Coding
- c.195G>A
- MANE Select
- NM_021813
- dbSNP
- rs138881451
- Type
- single nucleotide variant
- Location
- chr6:90008650 (GRCh38)
- Gene constraint
- LOEUF 0.164 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.66 · 2 PDB
- Residue 65
- the btb domain; an α-helix
Similar variants
- BACH2 p.Ala148Val Uncertain significance ★★ ⚠ same type
- BACH2 p.Ala205Thr Uncertain significance ★★ ⚠ same type
- BACH2 p.Ala304Glu Uncertain significance ★★ ⚠ same type
- BACH2 p.Ala479Val Uncertain significance ★★ ⚠ same type
- BACH2 p.Ala529Val Uncertain significance ★★ same type
- BACH2 p.Ala747Val Uncertain significance ★★ ⚠ same type
- BACH2 p.Ala756Val Uncertain significance ★★ ⚠ same type
- BACH2 p.Ala761Ser 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/bach2-p-ala65 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown