SMARCA2 p.Pro303=
c.909C>T · rs971553304 · VCV1765764
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00604%, afr)
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 -20 | GERP -3.8 |
| Overall | ||
| CADD | 0.877 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00604%
African / African-American · 4/66,236 alleles
Filtering AF
0.00201%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00115%
Overall
0.00154%
22/1,426,072 alleles · very rare
exomes 19/1,277,382 · genomes 3/148,690 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.00604% | 16,559 |
| Remaining individualsnot grpmax-eligible | 0.00572% | 17,494 |
| South Asian | 0.00132% | 75,812 |
| European (non-Finnish) | 0.0013% | 77,130 |
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.Pro303=
- Coding
- c.909C>T
- MANE Select
- NM_003070
- dbSNP
- rs971553304
- Type
- single nucleotide variant
- Location
- chr9:2047347 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.06 · 32 PDB
- Residue 303
- the 'disordered' region
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-pro303 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown