ARHGAP24 c.2003+232G>A
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.35%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +232 | deep intronic (+232 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 0.63 | GERP 3.4 |
| Overall | ||
| CADD | 8.778 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.35%
African / African-American · 1,392/41,552 alleles
Filtering AF
3.2%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.14%
Overall
0.967%
1,473/152,256 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.35% | 30 |
| Remaining individualsnot grpmax-eligible | 0.804% | 124 |
| Admixed American | 0.373% | 268 |
| European (non-Finnish) | 0.0103% | 9,718 |
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
- Coding
- c.2003+232G>A
- MANE Select
- NM_001025616
- dbSNP
- rs77807692
- Type
- single nucleotide variant
- Location
- chr4:85995889 (GRCh38)
- Gene constraint
- LOEUF 0.797 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.68
Similar variants
- 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
- ARHGAP24 p.Gln158Arg 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-c-2003-plus-232g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown