SMARCA2 p.Ala9=
c.27G>A · rs149689575 · VCV2708966
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0188%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -5.4 |
| Overall | ||
| CADD | 7.551 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0188%
Middle Eastern · 1/5,328 alleles
Filtering AF
0.00178%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00106%
Overall
0.000643%
10/1,554,132 alleles · ultra-rare
exomes 8/1,401,884 · genomes 2/152,248 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0188% | 5,328 |
| African / African-American | 0.00547% | 18,282 |
| Remaining individualsnot grpmax-eligible | 0.00166% | 60,136 |
| European (non-Finnish) | 0.000348% | 287,171 |
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.Ala9=
- Coding
- c.27G>A
- MANE Select
- NM_003070
- dbSNP
- rs149689575
- Type
- single nucleotide variant
- Location
- chr9:2029049 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.06 · 32 PDB
- Residue 9
- the 'disordered' region
Similar variants
- SMARCA2 p.Ala9Val 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
- 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-ala9 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown