SMARCA2 p.Arg562=
c.1686G>A · rs781391587 · VCV1778015
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0033%, sas)
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 2.2 | GERP 1.5, phastCons 1 |
| Overall | ||
| CADD | 8.17 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0033%
South Asian · 3/90,990 alleles
Filtering AF
0.000876%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000443%
Overall
0.000186%
3/1,613,420 alleles · very rare
exomes 3/1,461,106 · genomes 0/152,314 · joint denominator
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.Arg562=
- Coding
- c.1686G>A
- MANE Select
- NM_003070
- dbSNP
- rs781391587
- Type
- single nucleotide variant
- Location
- chr9:2060980 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.06 · 32 PDB
- Residue 562
- the 'disordered' region
Similar variants
- SMARCA2 p.Arg562Lys Conflicting classifications of pathogenicity ★ ⚠ same residue
- 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
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-arg562 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown