CASP12 c.22A>G
Uncertain significance
Single submitter
Classification
Uncertain significance
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0161%, nfe)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.024 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.8 | GERP -2.7 |
| Overall | ||
| CADD | 0.026 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0161%
European (non-Finnish) · 184/1,141,020 alleles
Filtering AF
0.0142%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0135%
Overall
0.0123%
188/1,524,552 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.0161% | 6,201 |
| Remaining individualsnot grpmax-eligible | 0.00672% | 14,891 |
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
- CASP12
- Coding
- c.22A>G
- Type
- single nucleotide variant
- Location
- chr11:104897454 (GRCh38)
- Structure
- AlphaFold pLDDT 77.13
Similar variants
- CASP12 p.Arg125Ter Likely benign ★★ same type
- CASP12 c.1013T>G Uncertain significance ★ same type
- CASP12 c.107T>C Uncertain significance ★ same type
- CASP12 c.19T>A Uncertain significance ★ same type
- CASP12 c.254G>A Uncertain significance ★ same type
- CASP12 c.269G>C Uncertain significance ★ same type
- CASP12 c.274G>A Uncertain significance ★ same type
- CASP12 c.275G>A 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/casp12-c-22a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown