ARHGAP33 p.Asp116=
c.348C>T · rs142645416 · VCV720599
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
rare (popmax 0.324%, afr)
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 1.1, phastCons 1 |
| Overall | ||
| CADD | 11.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.324%
African / African-American · 243/75,060 alleles
Filtering AF
0.29%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.277%
Overall
0.0169%
272/1,614,196 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.324% | 309 |
| Middle Eastern | 0.165% | 606 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,946 |
| Admixed American | 0.0117% | 8,575 |
| European (non-Finnish) | 0.000254% | 393,340 |
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
- ARHGAP33
- Protein
- p.Asp116=
- Coding
- c.348C>T
- MANE Select
- NM_001366178
- dbSNP
- rs142645416
- Type
- single nucleotide variant
- Location
- chr19:35778541 (GRCh38)
- Gene constraint
- LOEUF 0.59 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 54.54
- Residue 116
- the px; atypical domain
Similar variants
- ARHGAP33 p.Leu422= Benign ★★ same type
- ARHGAP33 p.Thr544= Benign ★★ same type
- ARHGAP33 p.Ala1159Val Uncertain significance ★ same type
- ARHGAP33 p.Ala1212Val Uncertain significance ★ same type
- ARHGAP33 p.Ala461Thr Uncertain significance ★ same type
- ARHGAP33 p.Ala486Val Uncertain significance ★ same type
- ARHGAP33 p.Ala617Gly Uncertain significance ★ same type
- ARHGAP33 p.Ala647Thr 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/arhgap33-p-asp116 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown