RASA2 p.Leu720=
c.2160G>A · rs295323 · VCV1576065
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 68.2%, 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 | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.1 | GERP -3.7 |
| Overall | ||
| CADD | 0.214 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
68.2%
African / African-American · 51,072/74,926 alleles
Filtering AF
67.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 67.5%
Overall
40%
646,150/1,613,434 alleles · common
exomes 575,218/1,461,342 · genomes 70,932/152,092 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 68.2% | 1 |
| Admixed American | 44.5% | 2 |
| European (non-Finnish) | 39.1% | 3 |
| Remaining individualsnot grpmax-eligible | 39.1% | 3 |
| Amishnot grpmax-eligible | 38.4% | 3 |
| Ashkenazi Jewishnot grpmax-eligible | 37% | 3 |
| Finnishnot grpmax-eligible | 36.8% | 3 |
| Middle Eastern | 36.8% | 3 |
| South Asian | 33.7% | 3 |
| East Asian | 32.7% | 3 |
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.Leu720=
- Coding
- c.2160G>A
- MANE Select
- NM_006506
- dbSNP
- rs295323
- Type
- single nucleotide variant
- Location
- chr3:141608632 (GRCh38)
- Gene constraint
- LOEUF 1.484 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 83.63
Similar variants
- 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
- RASA2 p.Arg310Gln Uncertain significance ★★ same type
- RASA2 p.Arg366Gln 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-leu720 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown