SMARCA1 p.Arg1007=
c.3021G>A · rs1393142880 · VCV2661389
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00221%, amr)
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 2.8 | GERP 1.4, phastCons 1 |
| Overall | ||
| CADD | 8.291 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00221%
Admixed American · 1/45,241 alleles
Filtering AF
0.000245%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000161%
Overall
0.000742%
8/1,078,538 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00221% | 45,241 |
| Remaining individualsnot grpmax-eligible | 0.00213% | 46,949 |
| European (non-Finnish) | 0.000682% | 146,709 |
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
- SMARCA1
- Protein
- p.Arg1007=
- Coding
- c.3021G>A
- MANE Select
- NM_001282874
- dbSNP
- rs1393142880
- Type
- single nucleotide variant
- Location
- chrX:129465529 (GRCh38)
- Structure
- AlphaFold pLDDT 75.48
- Residue 1007
- the sant 2 domain
Similar variants
- SMARCA1 p.Ala39Thr Uncertain significance ★★ ⚠ same type
- SMARCA1 p.Ala48Glu Uncertain significance ★★ ⚠ same type
- SMARCA1 p.Ala6Pro Uncertain significance ★★ ⚠ same type
- SMARCA1 p.Arg751Gln Uncertain significance ★★ ⚠ same type
- SMARCA1 p.Asp721Asn Uncertain significance ★★ ⚠ same type
- SMARCA1 p.Gly30Arg Uncertain significance ★★ ⚠ same type
- SMARCA1 p.Lys680Glu Uncertain significance ★★ same type
- SMARCA1 p.Met1028Ile 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/smarca1-p-arg1007 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown