SMARCA4 p.Val617=
c.1851G>A · rs1057252091 · VCV1102944
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 8.47e-05%, nfe)
Conditions
2
hereditary neoplastic syndrome
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 0.85 | GERP -0.56, phastCons 1 |
| Overall | ||
| CADD | 9.849 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.47e-05%
European (non-Finnish) · 1/1,180,024 alleles
Overall
6.2e-05%
1/1,614,184 alleles · very rare
exomes 1/1,461,852 · genomes 0/152,332 · joint denominator
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
- SMARCA4
- Protein
- p.Val617=
- Coding
- c.1851G>A
- MANE Select
- NM_003072
- dbSNP
- rs1057252091
- Type
- single nucleotide variant
- Location
- chr19:11003067 (GRCh38)
- Gene constraint
- LOEUF 0.226 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 65.38 · 31 PDB
- Residue 617
- the 'rna-binding region which is sufficient for binding to lncrna evf2' region
Similar variants
- SMARCA4 c.1943+1G>A Likely pathogenic ★★ same condition
- SMARCA4 c.2274+1G>T Likely pathogenic ★★ same condition
- SMARCA4 c.2438+1G>A Pathogenic/Likely pathogenic ★★ same condition
- SMARCA4 c.3216-1G>C Likely pathogenic ★★ same condition
- SMARCA4 c.3216-2A>G Likely pathogenic ★★ same condition
- SMARCA4 c.3546+1G>A Likely pathogenic ★★ same condition
- SMARCA4 c.3774+2T>A Likely pathogenic ★★ same condition
- SMARCA4 c.3951+2T>C Likely pathogenic ★★ 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/smarca4-p-val617 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown