SMARCD2 p.Arg133=
c.399G>A · rs2040279850 · VCV2810043
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000519%, 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 -0.091 | GERP -3.8, phastCons 0.61 |
| Overall | ||
| CADD | 11.98 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000519%
European (non-Finnish) · 6/1,157,082 alleles
Filtering AF
0.000187%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000123%
Overall
0.000382%
6/1,572,228 alleles · very rare
exomes 5/1,420,114 · genomes 1/152,114 · 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
- SMARCD2
- Protein
- p.Arg133=
- Coding
- c.399G>A
- MANE Select
- NM_001098426
- dbSNP
- rs2040279850
- Type
- single nucleotide variant
- Location
- chr17:63837443 (GRCh38)
- Gene constraint
- LOEUF 0.762 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.38
Similar variants
- SMARCD2 p.Arg133Gln 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-arg133 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown