BACH2 p.Pro461=
c.1383G>A · rs569909772 · VCV1660057
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
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 -0.67 | GERP -1.9, phastCons 0.003 |
| Overall | ||
| CADD | 9.953 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,080 alleles
Filtering AF
0.00307%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00275%
Overall
0.00328%
53/1,614,152 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,770 |
| European (non-Finnish) | 0.00398% | 25,107 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,510 |
| African / African-American | 0.00133% | 75,028 |
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.Pro461=
- Coding
- c.1383G>A
- MANE Select
- NM_021813
- dbSNP
- rs569909772
- Type
- single nucleotide variant
- Location
- chr6:89950723 (GRCh38)
- Gene constraint
- LOEUF 0.164 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.66 · 2 PDB
Similar variants
- BACH2 p.Pro461Leu Uncertain significance ★★ ⚠ same residue
- 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
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-pro461 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown