CA12 p.Ala297=
c.891G>A · VCV4925402
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0653%, 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 3.9 | GERP -1.5, phastCons 0.78 |
| Overall | ||
| CADD | 7.211 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0653%
African / African-American · 49/75,010 alleles
Filtering AF
0.0507%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0455%
Overall
0.00446%
72/1,614,018 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0653% | 1,531 |
| Remaining individualsnot grpmax-eligible | 0.0128% | 7,814 |
| Admixed American | 0.00333% | 30,007 |
| Finnishnot grpmax-eligible | 0.00312% | 32,006 |
| East Asian | 0.00223% | 44,874 |
| European (non-Finnish) | 0.000847% | 117,996 |
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
- CA12
- Protein
- p.Ala297=
- Coding
- c.891G>A
- MANE Select
- NM_001218
- Type
- single nucleotide variant
- Location
- chr15:63328114 (GRCh38)
- Gene constraint
- LOEUF 0.968 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 88.50 · 40 PDB
Similar variants
- CA12 p.Ala297Val Uncertain significance ★ ⚠ same residue
- CA12 c.107-108T>C Benign ★★ same type
- CA12 c.107-113G>A Benign ★★ same type
- CA12 c.286+92G>A Benign ★★ same type
- CA12 c.429+148G>A Benign ★★ same type
- CA12 c.429+186C>G Benign ★★ same type
- CA12 c.85+94C>G Benign ★★ same type
- CA12 c.*234C>T Benign ★★ 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/ca12-p-ala297 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown