ARHGAP12 p.Arg6=
c.16A>C · rs61748334 · VCV781939
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.7%, sas)
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 3.4 | GERP -0.78, phastCons 1 |
| Overall | ||
| CADD | 9.642 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.7%
South Asian · 3,298/89,222 alleles
Filtering AF
3.59%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.55%
Overall
0.739%
11,764/1,591,894 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 3.7% | 27 |
| Middle Eastern | 2.22% | 45 |
| Ashkenazi Jewishnot grpmax-eligible | 1.29% | 78 |
| Remaining individualsnot grpmax-eligible | 0.879% | 114 |
| European (non-Finnish) | 0.596% | 168 |
| Admixed American | 0.538% | 186 |
| Amishnot grpmax-eligible | 0.11% | 912 |
| African / African-American | 0.1% | 996 |
| Finnishnot grpmax-eligible | 0.0512% | 1,953 |
| East Asian | 0.0112% | 8,955 |
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
- ARHGAP12
- Protein
- p.Arg6=
- Coding
- c.16A>C
- MANE Select
- NM_018287
- dbSNP
- rs61748334
- Type
- single nucleotide variant
- Location
- chr10:31908840 (GRCh38)
- Gene constraint
- LOEUF 0.681 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 67.68
Similar variants
- ARHGAP12 p.Arg6Gly Uncertain significance ★ ⚠ same residue
- ARHGAP12 p.Ala393Val Uncertain significance ★ ⚠ same type
- ARHGAP12 p.Ala458Ser Uncertain significance ★ ⚠ same type
- ARHGAP12 p.Ala458Val Uncertain significance ★ ⚠ same type
- ARHGAP12 p.Ala491Ser Uncertain significance ★ ⚠ same type
- ARHGAP12 p.Ala491Val Uncertain significance ★ ⚠ same type
- ARHGAP12 p.Ala698Thr Uncertain significance ★ ⚠ same type
- ARHGAP12 p.Ala753Ser 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/arhgap12-p-arg6 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown