CRIPT c.242-120T>A
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 23.3%, 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 | ||
| Splice region | acceptor -120 | deep intronic (-120 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -3.6 | GERP -2.3 |
| Non-coding constraint | Z 0.89 | 1 kb window · o/e 0.94 · regional · uncalibrated |
| Overall | ||
| CADD | 0.991 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
23.3%
African / African-American · 9,094/39,066 alleles
Filtering AF
22.9%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 22.7%
Overall
6.23%
20,551/329,754 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 23.3% | 4 |
| Admixed American | 6.69% | 15 |
| Ashkenazi Jewishnot grpmax-eligible | 5.98% | 17 |
| Amishnot grpmax-eligible | 5.4% | 19 |
| Middle Eastern | 4.73% | 21 |
| Remaining individualsnot grpmax-eligible | 4.39% | 23 |
| East Asian | 4.23% | 24 |
| Finnishnot grpmax-eligible | 4.07% | 25 |
| European (non-Finnish) | 3.64% | 28 |
| South Asian | 3.51% | 28 |
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.242-120T>A
- MANE Select
- NM_014171
- dbSNP
- rs13430706
- Type
- single nucleotide variant
- Location
- chr2:46624043 (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-242-minus-120t-a (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown