SIN3A p.Ala1032=
c.3096C>T · rs750561401 · VCV2163205
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0467%, 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 1.5 | GERP -3, phastCons 1 |
| Overall | ||
| CADD | 8.947 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0467%
Admixed American · 28/59,976 alleles
Filtering AF
0.0332%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0286%
Overall
0.00248%
40/1,613,494 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0467% | 2,142 |
| Remaining individualsnot grpmax-eligible | 0.0064% | 15,614 |
| African / African-American | 0.00134% | 74,872 |
| European (non-Finnish) | 0.000593% | 168,524 |
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
- SIN3A
- Protein
- p.Ala1032=
- Coding
- c.3096C>T
- MANE Select
- NM_001145358
- dbSNP
- rs750561401
- Type
- single nucleotide variant
- Location
- chr15:75384363 (GRCh38)
- Gene constraint
- LOEUF 0.14 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.67
Similar variants
- SIN3A p.Ala1032Ser Uncertain significance ★ ⚠ same residue
- SIN3A p.Arg1140Ter Pathogenic ★★ same type
- SIN3A p.Arg471Ter Pathogenic ★★ same type
- SIN3A p.Arg537Ter Pathogenic ★★ same type
- SIN3A p.Arg553Ter Pathogenic/Likely pathogenic ★★ same type
- SIN3A p.Arg559Ter Pathogenic/Likely pathogenic ★★ same type
- SIN3A p.Arg718Ter Pathogenic/Likely pathogenic ★★ same type
- SIN3A p.Arg897Ter Pathogenic ★★ 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/sin3a-p-ala1032 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown