SMARCA2 p.Pro161=
c.483G>A · rs146359524 · VCV1278061
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.165%, sas)
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 -2.8 | GERP -4.8 |
| Overall | ||
| CADD | 3.321 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.165%
South Asian · 150/91,080 alleles
Filtering AF
0.143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.135%
Overall
0.0174%
281/1,614,128 alleles · rare
exomes 253/1,461,894 · genomes 28/152,234 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.165% | 607 |
| Admixed American | 0.0233% | 4,287 |
| African / African-American | 0.0227% | 4,413 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| Middle Eastern | 0.0165% | 6,062 |
| East Asian | 0.0134% | 7,479 |
| European (non-Finnish) | 0.00686% | 14,568 |
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.Pro161=
- Coding
- c.483G>A
- MANE Select
- NM_003070
- dbSNP
- rs146359524
- Type
- single nucleotide variant
- Location
- chr9:2039593 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.06 · 32 PDB
- Residue 161
- the 'disordered' region
Similar variants
- SMARCA2 p.Pro161Leu Conflicting classifications of pathogenicity ★ ⚠ 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
- SMARCA2 p.Arg1105Pro 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/smarca2-p-pro161 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown