SMARCA2 p.Val850=
c.2550G>T · rs367639859 · VCV2998221
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00873%, nfe)
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 3 | GERP 0.77, phastCons 1 |
| Overall | ||
| CADD | 8.272 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00873%
European (non-Finnish) · 103/1,179,968 alleles
Filtering AF
0.00733%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00684%
Overall
0.00651%
105/1,613,910 alleles · very rare
exomes 102/1,461,782 · genomes 3/152,128 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00873% | 11,456 |
| African / African-American | 0.00267% | 37,447 |
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.Val850=
- Coding
- c.2550G>T
- MANE Select
- NM_003070
- dbSNP
- rs367639859
- Type
- single nucleotide variant
- Location
- chr9:2086852 (GRCh38)
- Gene constraint
- LOEUF 0.317 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 66.06 · 32 PDB
- Residue 850
- a β-strand; the helicase atp-binding domain
Similar variants
- 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
- SMARCA2 p.Arg1159Gln 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-val850 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown