SMARCC2 p.Asp664=
c.1992C>T · VCV4873208
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00401%, 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 -0.4 | GERP -3.4, phastCons 0.001 |
| Overall | ||
| CADD | 12.99 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00401%
African / African-American · 3/74,906 alleles
Filtering AF
0.00106%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000539%
Overall
0.00105%
17/1,613,606 alleles · very rare
exomes 12/1,461,442 · genomes 5/152,164 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00401% | 24,969 |
| European (non-Finnish) | 0.00119% | 84,262 |
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.Asp664=
- Coding
- c.1992C>T
- MANE Select
- NM_001330288
- Type
- single nucleotide variant
- Location
- chr12:56171872 (GRCh38)
- Gene constraint
- LOEUF 0.167 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.89 · 9 PDB
- Residue 664
- 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-asp664 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown