CRIPT c.138-12A>C
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00177%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | acceptor -12 | acceptor splice region (-12, within the last 20 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | <0.2 | all four deltas below 0.2 · A>G here scores Δ0.96 · evaluated, not missing |
| Constraint at this position | ||
| Conservation | phyloP 0.42 | GERP -0.84, phastCons 0.002 |
| Non-coding constraint | Z -1.71 | 1 kb window · o/e 1.12 · regional · uncalibrated |
| Overall | ||
| CADD | 5.403 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00177%
Admixed American · 1/56,638 alleles
Overall
7.21e-05%
1/1,386,302 alleles · very rare
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
- CRIPT
- Coding
- c.138-12A>C
- MANE Select
- NM_014171
- dbSNP
- rs2466594844
- Type
- single nucleotide variant
- Location
- chr2:46623752 (GRCh38)
- Gene constraint
- LOEUF 1.852 · pLI 0.19 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 78.77 · 1 PDB
Similar variants
- CRIPT c.83-1G>A Likely pathogenic ★★ same type
- CRIPT p.Ala45Pro Uncertain significance ★★ ⚠ same type
- CRIPT p.Ala84Val Uncertain significance ★★ ⚠ same type
- CRIPT p.Cys86Phe Uncertain significance ★★ ⚠ same type
- CRIPT p.Gln74Arg Uncertain significance ★★ ⚠ same type
- CRIPT p.Gly81Val Uncertain significance ★★ ⚠ same type
- CRIPT p.Lys88Arg Uncertain significance ★★ ⚠ same type
- CRIPT p.Ser64Phe 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/cript-c-138-minus-12a-c (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown