Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 3.43%, afr)
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 -0.33 | GERP 3 |
| Overall | ||
| CADD | 4.918 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.43%
African / African-American · 2,573/74,984 alleles
Filtering AF
3.32%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.28%
Overall
0.177%
2,850/1,612,840 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.43% | 29 |
| Remaining individualsnot grpmax-eligible | 0.218% | 459 |
| Admixed American | 0.19% | 526 |
| Middle Eastern | 0.118% | 847 |
| European (non-Finnish) | 0.00178% | 56,187 |
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
- CASP2
- Protein
- p.Tyr151=
- Coding
- c.453C>T
- MANE Select
- NM_032982
- dbSNP
- rs4647293
- Type
- single nucleotide variant
- Location
- chr7:143292676 (GRCh38)
- Gene constraint
- LOEUF 0.936 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 78.95 · 17 PDB
- Residue 151
- a UniProt-annotated variant site (in mrt80; likely pathogenic)
Similar variants
- CASP2 p.Gln331Glu Uncertain significance ★★ ⚠ same type
- CASP2 p.Ala412= Likely benign ★★ same type
- CASP2 p.Gly7= Likely benign ★★ same type
- CASP2 p.Ile387= Benign/Likely benign ★★ same type
- CASP2 p.Lys254= Benign/Likely benign ★★ same type
- CASP2 p.Thr267= Benign/Likely benign ★★ same type
- CASP2 p.Val29= Benign ★★ same type
- CASP2 c.876+1G>T 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/casp2-p-tyr151 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown