ARFGAP2 c.809+6T>C
Benign
No assertion criteria
Classification
Benign
ClinVar
Review
No assertion criteria ☆☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.25%, afr)
Conditions
1
ARFGAP2-related disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +6 | donor splice region (+6, within the first 6 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.8 | GERP -5, phastCons 0.42 |
| Non-coding constraint | Z 2.75 | 1 kb window · o/e 0.80 · regional · uncalibrated |
| Overall | ||
| CADD | 10.06 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.25%
African / African-American · 1,685/75,014 alleles
Filtering AF
2.16%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.12%
Overall
0.121%
1,950/1,613,720 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.25% | 45 |
| Middle Eastern | 0.247% | 404 |
| Remaining individualsnot grpmax-eligible | 0.176% | 568 |
| Admixed American | 0.123% | 811 |
| Ashkenazi Jewishnot grpmax-eligible | 0.0811% | 1,234 |
| European (non-Finnish) | 0.00331% | 30,257 |
| South Asian | 0.00329% | 30,359 |
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.809+6T>C
- MANE Select
- NM_032389
- dbSNP
- rs114371790
- Type
- single nucleotide variant
- Location
- chr11:47171658 (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.-9G>A Likely 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-809-plus-6t-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown