BACH2 p.Ser533=
c.1599C>T · rs574405475 · VCV1590719
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0233%, amr)
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 -3.2 | GERP -2.8 |
| Overall | ||
| CADD | 6.45 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0233%
Admixed American · 14/59,982 alleles
Filtering AF
0.0141%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0112%
Overall
0.00242%
39/1,613,774 alleles · ultra-rare
exomes 23/1,461,614 · genomes 16/152,160 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0233% | 4,284 |
| African / African-American | 0.0174% | 5,762 |
| East Asian | 0.00668% | 14,961 |
| South Asian | 0.0022% | 45,539 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,484 |
| European (non-Finnish) | 0.000509% | 196,644 |
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.Ser533=
- Coding
- c.1599C>T
- MANE Select
- NM_021813
- dbSNP
- rs574405475
- Type
- single nucleotide variant
- Location
- chr6:89950507 (GRCh38)
- Gene constraint
- LOEUF 0.164 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.66 · 2 PDB
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-ser533 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown