SMARCC2 p.Ala960=
c.2880C>T · rs145178493 · VCV2643074
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.528%, mid)
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 -1.9 | GERP -3.6 |
| Overall | ||
| CADD | 4.398 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.528%
Middle Eastern · 32/6,060 alleles
Filtering AF
0.384%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.335%
Overall
0.0425%
685/1,611,952 alleles · rare
exomes 614/1,459,638 · genomes 71/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.528% | 189 |
| Ashkenazi Jewishnot grpmax-eligible | 0.368% | 272 |
| Remaining individualsnot grpmax-eligible | 0.0848% | 1,179 |
| Admixed American | 0.0683% | 1,464 |
| South Asian | 0.0538% | 1,859 |
| European (non-Finnish) | 0.0322% | 3,105 |
| African / African-American | 0.0227% | 4,415 |
| East Asian | 0.00446% | 22,441 |
| Finnishnot grpmax-eligible | 0.00323% | 30,913 |
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
- SMARCC2
- Protein
- p.Ala960=
- Coding
- c.2880C>T
- MANE Select
- NM_001330288
- dbSNP
- rs145178493
- Type
- single nucleotide variant
- Location
- chr12:56165670 (GRCh38)
- Gene constraint
- LOEUF 0.167 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.89 · 9 PDB
- Residue 960
- the 'disordered' region; a UniProt-annotated variant site (in css8)
Similar variants
- SMARCC2 c.1311-3C>G Pathogenic/Likely pathogenic ★★ same type
- SMARCC2 c.1926+1G>A Pathogenic/Likely pathogenic ★★ same type
- SMARCC2 c.1926+1G>T Pathogenic/Likely pathogenic ★★ same type
- SMARCC2 c.1926+2T>C Pathogenic/Likely pathogenic ★★ same type
- SMARCC2 p.Arg116His Likely pathogenic ★★ same type
- SMARCC2 p.Arg192Ter Pathogenic/Likely pathogenic ★★ same type
- SMARCC2 p.Arg269Ter Pathogenic/Likely pathogenic ★★ same type
- SMARCC2 p.Arg474Ter 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/smarcc2-p-ala960 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown