SMARCD2 p.Val296=
c.888C>T · rs779996760 · VCV1578214
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 4 submitters
gnomAD v4.1
Rare
rare (popmax 0.297%, mid)
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 2.5 | GERP -1.6, phastCons 1 |
| Overall | ||
| CADD | 11.48 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.297%
Middle Eastern · 18/6,052 alleles
Filtering AF
0.192%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.159%
Overall
0.00306%
49/1,603,676 alleles · rare
exomes 45/1,451,462 · genomes 4/152,214 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.297% | 336 |
| Admixed American | 0.027% | 3,704 |
| Remaining individualsnot grpmax-eligible | 0.00807% | 12,384 |
| African / African-American | 0.00134% | 74,640 |
| European (non-Finnish) | 0.000767% | 130,307 |
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
- SMARCD2
- Protein
- p.Val296=
- Coding
- c.888C>T
- MANE Select
- NM_001098426
- dbSNP
- rs779996760
- Type
- single nucleotide variant
- Location
- chr17:63834507 (GRCh38)
- Gene constraint
- LOEUF 0.762 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.38
Similar variants
- SMARCD2 p.Val296Ile Uncertain significance ★ ⚠ same residue
- SMARCD2 p.Arg192Ter Pathogenic/Likely pathogenic ★★ same type
- SMARCD2 c.922-3C>T Uncertain significance ★★ same type
- SMARCD2 p.Ala434Thr Uncertain significance ★★ ⚠ same type
- SMARCD2 p.Ala6Val Uncertain significance ★★ ⚠ same type
- SMARCD2 p.Arg118Cys Uncertain significance ★★ ⚠ same type
- SMARCD2 p.Arg148Gln Uncertain significance ★★ ⚠ same type
- SMARCD2 p.Arg150Trp Uncertain significance ★★ ⚠ 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/smarcd2-p-val296 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown