ARHGAP24 p.Asn347=
c.1041T>C · rs10003909 · VCV1268964
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Common
common (popmax 45.3%, afr) — too common for a highly-penetrant pathogenic allele
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 -4.4 | GERP -3.5 |
| Overall | ||
| CADD | 0.091 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
45.3%
African / African-American · 33,950/74,866 alleles
Filtering AF
44.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 44.8%
Overall
24.8%
400,508/1,613,714 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 45.3% | 2 |
| South Asian | 38.6% | 3 |
| Admixed American | 33.6% | 3 |
| East Asian | 28.1% | 4 |
| Remaining individualsnot grpmax-eligible | 25.3% | 4 |
| Middle Eastern | 24% | 4 |
| Finnishnot grpmax-eligible | 23.4% | 4 |
| European (non-Finnish) | 22.1% | 5 |
| Ashkenazi Jewishnot grpmax-eligible | 20.6% | 5 |
| Amishnot grpmax-eligible | 14.5% | 7 |
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
- ARHGAP24
- Protein
- p.Asn347=
- Coding
- c.1041T>C
- MANE Select
- NM_001025616
- dbSNP
- rs10003909
- Type
- single nucleotide variant
- Location
- chr4:85994695 (GRCh38)
- Gene constraint
- LOEUF 0.797 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.68
Similar variants
- ARHGAP24 p.Asn347Asp Uncertain significance ★ ⚠ same residue
- ARHGAP24 p.Arg39His Uncertain significance ★★ ⚠ same type
- ARHGAP24 p.Arg483Cys Uncertain significance ★★ ⚠ same type
- ARHGAP24 p.Arg93Ter Uncertain significance ★★ same type
- ARHGAP24 p.Arg95Gln Uncertain significance ★★ ⚠ same type
- ARHGAP24 p.Asn454Ser Uncertain significance ★★ ⚠ same type
- ARHGAP24 p.Asn587Ile Uncertain significance ★★ ⚠ same type
- ARHGAP24 p.Asp55Val 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/arhgap24-p-asn347 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown