ARHGAP31 c.100+148del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Common
common (popmax 52.6%, afr) — too common for a highly-penetrant pathogenic allele
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +148 | deep intronic (+148 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -1.9 | GERP -1.8, phastCons 0.003 |
| Overall | ||
| CADD | 0.878 | PHRED · no single calibrated threshold — expert panels disagree |
| Region caveats | ||
| Repeat context | tandem | (T)n simple repeat · ambiguous alignment · confidence, not pathogenicity |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
52.6%
African / African-American · 26,223/49,826 alleles
Filtering AF
52.1%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 51.9%
Overall
30.1%
163,070/542,454 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 52.6% | 2 |
| South Asian | 37.2% | 3 |
| Remaining individualsnot grpmax-eligible | 32.5% | 3 |
| Middle Eastern | 28.9% | 3 |
| Finnishnot grpmax-eligible | 28.5% | 4 |
| Ashkenazi Jewishnot grpmax-eligible | 28.3% | 4 |
| Admixed American | 26.4% | 4 |
| European (non-Finnish) | 26.4% | 4 |
| East Asian | 26.3% | 4 |
| Amishnot grpmax-eligible | 7.31% | 14 |
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.100+148del
- MANE Select
- NM_020754
- dbSNP
- rs10707359
- Type
- Deletion
- Location
- chr3:119295141 (GRCh38)
- Gene constraint
- LOEUF 0.38 · pLI 1.00 · ClinGen HI 0/3 (gnomAD)
- Structure
- AlphaFold pLDDT 43.32
Similar variants
- ARHGAP31 c.100+19del Benign/Likely benign ★★ same type
- ARHGAP31 p.Pro567fs Likely pathogenic ★ same type
- ARHGAP31 c.882-11_882-5del Uncertain significance ★ same type
- ARHGAP31 p.Cys1424fs Uncertain significance ★ same type
- ARHGAP31 p.Gly49fs Uncertain significance ★ same type
- ARHGAP31 p.Leu1050_His1052del Conflicting classifications of pathogenicity ★ same type
- ARHGAP31 p.Leu602del Uncertain significance ★ same type
- ARHGAP31 p.Pro739fs 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-100-plus-148del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown