ARHGAP10 p.Ser487=
c.1461C>T · rs17024215 · VCV713457
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.77%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.071 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP 1.1 | GERP -2.2, phastCons 1 |
| Overall | ||
| CADD | 4.888 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.77%
African / African-American · 2,019/72,804 alleles
Filtering AF
2.67%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 2.63%
Overall
0.204%
3,191/1,567,386 alleles · low-frequency
exomes 1,891/1,415,468 · genomes 1,300/151,918 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 2.77% | 36 |
| Ashkenazi Jewishnot grpmax-eligible | 1.09% | 92 |
| Middle Eastern | 0.392% | 255 |
| Admixed American | 0.372% | 269 |
| Remaining individualsnot grpmax-eligible | 0.355% | 282 |
| European (non-Finnish) | 0.0359% | 2,789 |
| South Asian | 0.0163% | 6,121 |
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
- ARHGAP10
- Protein
- p.Ser487=
- Coding
- c.1461C>T
- MANE Select
- NM_024605
- dbSNP
- rs17024215
- Type
- single nucleotide variant
- Location
- chr4:147965034 (GRCh38)
- Gene constraint
- LOEUF 0.894 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 80.30 · 1 PDB
- Residue 487
- the rho-gap domain
Similar variants
- ARHGAP10 p.Asn222Ser Uncertain significance ★★ ⚠ same type
- ARHGAP10 p.Ala405= Benign ★★ same type
- ARHGAP10 p.Arg243= Benign ★★ same type
- ARHGAP10 p.Ile676Val Likely benign ★★ same type
- ARHGAP10 p.Tyr614= Benign ★★ same type
- ARHGAP10 p.Ala163Ser Uncertain significance ★ ⚠ same type
- ARHGAP10 p.Ala263Thr Uncertain significance ★ ⚠ same type
- ARHGAP10 p.Ala366Thr 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/arhgap10-p-ser487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown