SMARCA2 p.Asp684=
c.2052C>T · rs149890563 · VCV2177082
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 -14 | GERP -5.4 |
| Overall | ||
| CADD | 1.256 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,858 alleles
Filtering AF
0.000739%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000277%
Overall
0.000868%
14/1,613,768 alleles · very rare
exomes 10/1,461,538 · genomes 4/152,230 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,429 |
| South Asian | 0.0022% | 45,530 |
| Admixed American | 0.00167% | 60,008 |
| African / African-American | 0.00133% | 75,012 |
| European (non-Finnish) | 0.000678% | 147,470 |
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.Asp684=
- Coding
- c.2052C>T
- MANE Select
- NM_003070
- dbSNP
- rs149890563
- Type
- single nucleotide variant
- Location
- chr9:2077644 (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 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-asp684 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown