SMARCB1 p.Val96=
c.288G>A · rs2145963990 · VCV2452596
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
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 -1.5 | GERP -1.9 |
| Overall | ||
| CADD | 5.709 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- SMARCB1
- Protein
- p.Val96=
- Coding
- c.288G>A
- MANE Select
- NM_003073
- dbSNP
- rs2145963990
- Type
- single nucleotide variant
- Location
- chr22:23793614 (GRCh38)
- Gene constraint
- LOEUF 0.221 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 80.77 · 17 PDB
- Residue 96
- the 'dna-binding' region; an α-helix
Similar variants
- SMARCB1 p.Val96Met Uncertain significance ★★ ⚠ same residue
- SMARCB1 c.795+1G>A Likely pathogenic ★★ same condition
- SMARCB1 c.93+1G>A Likely pathogenic ★★ same condition
- SMARCB1 c.986+1G>A Likely pathogenic ★★ same condition
- SMARCB1 c.*82C>T Pathogenic/Likely pathogenic ★★ same condition
- SMARCB1 p.Arg158Ter Pathogenic ★★ same condition
- SMARCB1 p.Arg201Ter Pathogenic ★★ same condition
- SMARCB1 p.Arg374Gln Pathogenic/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/smarcb1-p-val96 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown