ARHGAP31 c.203+9A>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0331%, mid)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +9 | near-intronic (+9 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -2.6 |
| Non-coding constraint | Z 1.11 | 1 kb window · o/e 0.92 · regional · uncalibrated |
| Overall | ||
| CADD | 5.707 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0331%
Middle Eastern · 2/6,048 alleles
Filtering AF
0.0155%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0128%
Overall
0.00435%
70/1,607,744 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0331% | 3,024 |
| African / African-American | 0.024% | 4,162 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,783 |
| Admixed American | 0.00666% | 15,006 |
| European (non-Finnish) | 0.00324% | 30,908 |
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
- ARHGAP31
- Coding
- c.203+9A>C
- MANE Select
- NM_020754
- dbSNP
- rs543552697
- Type
- single nucleotide variant
- Location
- chr3:119365427 (GRCh38)
- Gene constraint
- LOEUF 0.38 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.32
Similar variants
- ARHGAP31 p.Ala18Val Uncertain significance ★★ ⚠ same type
- ARHGAP31 p.Ala634Asp Uncertain significance ★★ ⚠ same type
- ARHGAP31 p.Arg1377Ser Uncertain significance ★★ ⚠ same type
- ARHGAP31 p.Arg199Gln Uncertain significance ★★ ⚠ same type
- ARHGAP31 p.Arg256Cys Uncertain significance ★★ ⚠ same type
- ARHGAP31 p.Arg426Gly Uncertain significance ★★ ⚠ same type
- ARHGAP31 p.Arg478His Uncertain significance ★★ ⚠ same type
- ARHGAP31 p.Arg510Ser 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/arhgap31-c-203-plus-9a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown