BACH2 p.Ser334=
c.1002C>T · rs1029658356 · VCV1898778
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.004%, 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 0.047 | GERP -2.8 |
| Overall | ||
| CADD | 4.186 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.004%
African / African-American · 3/74,978 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000495%
Overall
0.000434%
7/1,612,430 alleles · very rare
exomes 7/1,460,192 · genomes 0/152,238 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.004% | 24,993 |
| East Asian | 0.00223% | 44,830 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,394 |
| Finnishnot grpmax-eligible | 0.00156% | 63,898 |
| European (non-Finnish) | 8.48e-05% | 1,179,322 |
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.Ser334=
- Coding
- c.1002C>T
- MANE Select
- NM_021813
- dbSNP
- rs1029658356
- Type
- single nucleotide variant
- Location
- chr6:89951104 (GRCh38)
- Gene constraint
- LOEUF 0.164 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.66 · 2 PDB
Similar variants
- BACH2 p.Ser334Asn 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-ser334 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown