RASA2 p.Ile844=
c.2532T>C · rs776362955 · VCV1792720
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.000258%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 1.3 | GERP -0.84, phastCons 1 |
| Overall | ||
| CADD | 6.023 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.000258%
European (non-Finnish) · 3/1,163,090 alleles
Filtering AF
6.9e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.9e-05%
Overall
0.000189%
3/1,589,162 alleles · very rare
exomes 1/1,436,906 · genomes 2/152,256 · joint denominator
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
- RASA2
- Protein
- p.Ile844=
- Coding
- c.2532T>C
- MANE Select
- NM_006506
- dbSNP
- rs776362955
- Type
- single nucleotide variant
- Location
- chr3:141612295 (GRCh38)
- Gene constraint
- LOEUF 1.484 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.63
- Residue 844
- the 'disordered' region
Similar variants
- RASA2 p.Ile844Val Uncertain significance ★★ same residue
- RASA2 p.Ile844Thr Uncertain significance ★ same residue
- RASA2 c.612-3C>T Uncertain significance ★★ same type
- RASA2 p.Ala360Gly Uncertain significance ★★ same type
- RASA2 p.Ala489Thr Uncertain significance ★★ same type
- RASA2 p.Ala503Ser Uncertain significance ★★ same type
- RASA2 p.Ala742Val Uncertain significance ★★ same type
- RASA2 p.Arg117His 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/rasa2-p-ile844 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown