ARFGAP2 c.-9G>A
Likely benign
No assertion criteria
Classification
Likely benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0134%, amr)
Conditions
1
ARFGAP2-related disorder
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 7.6 | GERP 2.2, phastCons 1 |
| Non-coding constraint | Z -0.68 | 1 kb window · o/e 1.04 · regional · uncalibrated |
| Overall | ||
| CADD | 22.3 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0134%
Admixed American · 8/59,874 alleles
Filtering AF
0.00663%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00483%
Overall
0.00062%
10/1,612,562 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0134% | 7,484 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,193 |
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
- ARFGAP2
- Coding
- c.-9G>A
- MANE Select
- NM_032389
- dbSNP
- rs751176662
- Type
- single nucleotide variant
- Location
- chr11:47176862 (GRCh38)
- Gene constraint
- LOEUF 0.8 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 66.19 · 1 PDB
Disease context
ARFGAP2-related disorder
Similar variants
- ARFGAP2 c.191+6C>T Likely benign same condition
- ARFGAP2 c.265-10T>C Likely benign same condition
- ARFGAP2 c.396+7G>A Likely benign same condition
- ARFGAP2 c.809+6T>C Benign same condition
- ARFGAP2 c.*4G>A Benign same condition
- ARFGAP2 p.Ala266= Benign same condition
- ARFGAP2 p.Arg255Cys Benign ⚠ same condition
- ARFGAP2 p.Arg339His Benign same condition
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/arfgap2-c-minus-9g-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown