BACH2 p.Ser409=
c.1227G>C · rs144958455 · VCV1165150
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.222%, 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 -2.7 | GERP -3.1 |
| Overall | ||
| CADD | 4.354 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.222%
African / African-American · 166/74,892 alleles
Filtering AF
0.194%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.184%
Overall
0.0127%
204/1,606,704 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.222% | 451 |
| Admixed American | 0.0269% | 3,717 |
| Remaining individualsnot grpmax-eligible | 0.0225% | 4,442 |
| South Asian | 0.00111% | 90,304 |
| European (non-Finnish) | 0.000595% | 167,979 |
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.Ser409=
- Coding
- c.1227G>C
- MANE Select
- NM_021813
- dbSNP
- rs144958455
- Type
- single nucleotide variant
- Location
- chr6:89950879 (GRCh38)
- Gene constraint
- LOEUF 0.164 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.66 · 2 PDB
Similar variants
- BACH2 p.Ser409Leu 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-ser409 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown