SIN3A p.Asp1022=
c.3066C>T · rs145667799 · VCV2163320
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.055%, 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 3.9 | GERP -0.34, phastCons 1 |
| Overall | ||
| CADD | 9.745 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.055%
Admixed American · 33/59,998 alleles
Filtering AF
0.0402%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0351%
Overall
0.00998%
161/1,613,814 alleles · ultra-rare
exomes 127/1,461,528 · genomes 34/152,286 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.055% | 1,818 |
| Remaining individualsnot grpmax-eligible | 0.0288% | 3,471 |
| South Asian | 0.0231% | 4,337 |
| European (non-Finnish) | 0.00687% | 14,565 |
| East Asian | 0.00668% | 14,961 |
| African / African-American | 0.00533% | 18,756 |
| Finnishnot grpmax-eligible | 0.00156% | 64,022 |
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.Asp1022=
- Coding
- c.3066C>T
- MANE Select
- NM_001145358
- dbSNP
- rs145667799
- Type
- single nucleotide variant
- Location
- chr15:75384393 (GRCh38)
- Gene constraint
- LOEUF 0.14 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 69.67
Similar variants
- 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
- SIN3A p.Arg935Ter Pathogenic/Likely 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-asp1022 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown