SMARCD1 p.Ala115=
c.345G>A · VCV4916750
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0167%, 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 0.66 | GERP -2.5, phastCons 1 |
| Overall | ||
| CADD | 12.27 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0167%
Middle Eastern · 1/5,976 alleles
Filtering AF
0.00365%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00259%
Overall
0.00213%
34/1,598,464 alleles · ultra-rare
exomes 30/1,446,336 · genomes 4/152,128 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0167% | 5,976 |
| South Asian | 0.00784% | 12,761 |
| Admixed American | 0.00526% | 19,013 |
| Remaining individualsnot grpmax-eligible | 0.00324% | 30,849 |
| European (non-Finnish) | 0.00179% | 55,833 |
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
- SMARCD1
- Protein
- p.Ala115=
- Coding
- c.345G>A
- MANE Select
- NM_003076
- Type
- single nucleotide variant
- Location
- chr12:50086328 (GRCh38)
- Gene constraint
- LOEUF 0.339 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 78.37 · 12 PDB
- Residue 115
- the 'interaction with esr1, nr1h4, nr3c1, pgr and smarca4' region
Similar variants
- SMARCD1 p.Ala115Val Uncertain significance ★ ⚠ same residue
- SMARCD1 p.Ala302Gly Uncertain significance ★★ same type
- SMARCD1 p.Arg334Gln Uncertain significance ★★ ⚠ same type
- SMARCD1 p.Asp247Gly Uncertain significance ★★ ⚠ same type
- SMARCD1 p.Ile184Val Uncertain significance ★★ ⚠ same type
- SMARCD1 p.Ile323Val Uncertain significance ★★ ⚠ same type
- SMARCD1 p.Thr189Ser Uncertain significance ★★ ⚠ same type
- SMARCD1 p.Thr203Met 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/smarcd1-p-ala115 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown