SMARCA2 p.Glu360=
c.1080A>G · rs138782877 · VCV1265175
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.461%, amr)
Conditions
1
Inborn genetic diseases
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 1.7 | GERP -2.1, phastCons 1 |
| Overall | ||
| CADD | 8.429 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.461%
Admixed American · 277/60,034 alleles
Filtering AF
0.417%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.399%
Overall
0.0193%
311/1,614,146 alleles · rare
exomes 281/1,461,816 · genomes 30/152,330 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.461% | 217 |
| Remaining individualsnot grpmax-eligible | 0.0208% | 4,808 |
| African / African-American | 0.0147% | 6,821 |
| East Asian | 0.00669% | 14,957 |
| European (non-Finnish) | 0.000593% | 168,572 |
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
- SMARCA2
- Protein
- p.Glu360=
- Coding
- c.1080A>G
- MANE Select
- NM_003070
- dbSNP
- rs138782877
- Type
- single nucleotide variant
- Location
- chr9:2054630 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.06 · 32 PDB
Similar variants
- SMARCA2 p.Ala1138Pro Pathogenic/Likely pathogenic ★★ same condition
- SMARCA2 p.Arg505Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- SMARCA2 p.Ala1215Val Uncertain significance ★★ ⚠ same condition
- SMARCA2 p.Ala1389Ser Uncertain significance ★★ ⚠ same condition
- SMARCA2 p.Arg1266Gly Uncertain significance ★★ ⚠ same condition
- SMARCA2 p.Arg427Cys Uncertain significance ★★ ⚠ same condition
- SMARCA2 p.Glu1509Asp Uncertain significance ★★ ⚠ same condition
- SMARCA2 p.Gly304Trp Uncertain significance ★★ same condition
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/smarca2-p-glu360 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown