SOAT2 p.Ala67=
c.201C>T · rs12317169 · VCV787399
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.234%, 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 1.4 | GERP -0.5, phastCons 0.76 |
| Overall | ||
| CADD | 8.459 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.234%
African / African-American · 174/74,338 alleles
Filtering AF
0.206%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.195%
Overall
0.014%
223/1,587,692 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.234% | 427 |
| Middle Eastern | 0.202% | 496 |
| Admixed American | 0.0285% | 3,509 |
| Remaining individualsnot grpmax-eligible | 0.026% | 3,846 |
| European (non-Finnish) | 0.000428% | 233,414 |
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
- SOAT2
- Protein
- p.Ala67=
- Coding
- c.201C>T
- MANE Select
- NM_003578
- dbSNP
- rs12317169
- Type
- single nucleotide variant
- Location
- chr12:53105169 (GRCh38)
- Gene constraint
- LOEUF 1.403 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 82.59 · 2 PDB
Similar variants
- SOAT2 p.Leu402= Benign ★★ same type
- ACAT2 p.Ala230Pro Uncertain significance ★ ⚠ same type
- ACAT2 p.Ala323Gly Uncertain significance ★ ⚠ same type
- ACAT2 p.Ala330Val Uncertain significance ★ ⚠ same type
- ACAT2 p.Ala348Ser Uncertain significance ★ ⚠ same type
- ACAT2 p.Ala357Gly Uncertain significance ★ ⚠ same type
- ACAT2 p.Arg223His Uncertain significance ★ ⚠ same type
- ACAT2 p.Arg272Cys 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/soat2-p-ala67 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown