SMARCC2 p.Ser115=
c.345A>G · rs770578859 · VCV1675504
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00891%, eas)
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 -0.48, phastCons 1 |
| Overall | ||
| CADD | 10.69 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00891%
East Asian · 4/44,878 alleles
Filtering AF
0.00298%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0018%
Overall
0.000867%
14/1,614,098 alleles · very rare
exomes 10/1,461,854 · genomes 4/152,244 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00891% | 11,220 |
| Remaining individualsnot grpmax-eligible | 0.0048% | 20,837 |
| South Asian | 0.0022% | 45,535 |
| European (non-Finnish) | 0.000424% | 236,000 |
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.Ser115=
- Coding
- c.345A>G
- MANE Select
- NM_001330288
- dbSNP
- rs770578859
- Type
- single nucleotide variant
- Location
- chr12:56185084 (GRCh38)
- Gene constraint
- LOEUF 0.167 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 64.89 · 9 PDB
- Residue 115
- the marr-like domain; the 'marr-like, brct and chromo domains module' region
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-ser115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown