SMARCA2 p.Pro17=
c.51G>C · rs148865068 · VCV1245835
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.12%, 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 -0.73 | GERP -5.4 |
| Overall | ||
| CADD | 1.32 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.12%
African / African-American · 88/73,602 alleles
Filtering AF
0.0994%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0919%
Overall
0.00593%
93/1,568,920 alleles · rare
exomes 53/1,416,700 · genomes 40/152,220 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.12% | 836 |
| Admixed American | 0.00741% | 13,493 |
| European (non-Finnish) | 8.65e-05% | 1,155,735 |
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.Pro17=
- Coding
- c.51G>C
- MANE Select
- NM_003070
- dbSNP
- rs148865068
- Type
- single nucleotide variant
- Location
- chr9:2029073 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.06 · 32 PDB
- Residue 17
- the 'disordered' region
Similar variants
- SMARCA2 p.Pro17Leu Likely benign ★★ same residue
- SMARCA2 p.Pro17Arg Uncertain significance ★ ⚠ 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
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-pro17 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown