RAC1 p.Ala172=
c.516G>A · rs140589960 · VCV2499036
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0836%, nfe)
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 -4.6 | GERP -3.7 |
| Overall | ||
| CADD | 5.178 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0836%
European (non-Finnish) · 986/1,179,692 alleles
Filtering AF
0.0792%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0774%
Overall
0.0635%
1,024/1,611,596 alleles · ultra-rare
exomes 967/1,459,818 · genomes 57/151,778 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0836% | 1,196 |
| Remaining individualsnot grpmax-eligible | 0.0257% | 3,895 |
| South Asian | 0.011% | 9,096 |
| African / African-American | 0.00937% | 10,669 |
| Admixed American | 0.00335% | 29,893 |
| Finnishnot grpmax-eligible | 0.00313% | 31,948 |
| East Asian | 0.00223% | 44,864 |
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
- RAC1
- Protein
- p.Ala172=
- Coding
- c.516G>A
- MANE Select
- NM_006908
- dbSNP
- rs140589960
- Type
- single nucleotide variant
- Location
- chr7:6402383 (GRCh38)
- Structure
- AlphaFold pLDDT 92.87 · 12 PDB
Similar variants
- RAC1 p.Arg66Ser Likely pathogenic ★★ same type
- RAC1 p.Asn26Ser Pathogenic ★★ ⚠ same type
- RAC1 p.Asn39Ser Pathogenic/Likely pathogenic ★★ same type
- RAC1 p.Pro73Leu Pathogenic/Likely pathogenic ★★ same type
- RAC1 p.Ser71Phe Pathogenic/Likely pathogenic ★★ same type
- RAC1 p.Tyr32His Pathogenic/Likely pathogenic ★★ same type
- RAC1 p.Tyr64Asp Pathogenic/Likely pathogenic ★★ same type
- RAC1 p.Val51Met Pathogenic/Likely pathogenic ★★ 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/rac1-p-ala172 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown