SMARCA2 p.Val712=
c.2136G>A · rs147739329 · VCV588159
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 6 submitters
gnomAD v4.1
Rare
rare (popmax 0.505%, 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 1.7 | GERP -3.5, phastCons 1 |
| Overall | ||
| CADD | 6.702 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.505%
African / African-American · 379/75,030 alleles
Filtering AF
0.463%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.447%
Overall
0.0314%
506/1,613,912 alleles · rare
exomes 281/1,461,650 · genomes 225/152,262 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.505% | 198 |
| Remaining individualsnot grpmax-eligible | 0.0592% | 1,689 |
| Middle Eastern | 0.0331% | 3,018 |
| Admixed American | 0.0317% | 3,158 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0135% | 7,401 |
| European (non-Finnish) | 0.00542% | 18,436 |
| South Asian | 0.0011% | 91,056 |
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.Val712=
- Coding
- c.2136G>A
- MANE Select
- NM_003070
- dbSNP
- rs147739329
- Type
- single nucleotide variant
- Location
- chr9:2077728 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.06 · 32 PDB
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-val712 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown