SMARCA2 p.Arg1503=
c.4509G>A · rs751453496 · VCV1328668
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0126%, nfe)
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 10 | GERP 2.1, phastCons 1 |
| Overall | ||
| CADD | 13.64 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0126%
European (non-Finnish) · 149/1,179,816 alleles
Filtering AF
0.011%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0103%
Overall
0.00967%
156/1,613,782 alleles · ultra-rare
exomes 149/1,461,636 · genomes 7/152,146 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0126% | 7,918 |
| Remaining individualsnot grpmax-eligible | 0.0096% | 10,414 |
| African / African-American | 0.00134% | 74,892 |
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.Arg1503=
- Coding
- c.4509G>A
- MANE Select
- NM_003070
- dbSNP
- rs751453496
- Type
- single nucleotide variant
- Location
- chr9:2186143 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.06 · 32 PDB
- Residue 1503
- an α-helix; the bromo domain
Similar variants
- SMARCA2 p.Arg1503Gln Conflicting classifications of pathogenicity ★ ⚠ same residue
- SMARCA2 p.Arg1503Trp Uncertain significance ★ ⚠ same residue
- SMARCA2 p.Ala1138Pro Pathogenic/Likely pathogenic ★★ same type
- SMARCA2 p.Ala1160Gly Pathogenic ★★ same type
- SMARCA2 p.Ala1201Glu Pathogenic/Likely pathogenic ★★ same type
- SMARCA2 p.Ala1201Val Pathogenic/Likely pathogenic ★★ same type
- SMARCA2 p.Arg1105Cys Pathogenic ★★ same type
- SMARCA2 p.Arg1105His 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/smarca2-p-arg1503 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown