CRIPT c.241+19C>T
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 5.29%, 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 | donor +19 | near-intronic (+19 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -2.4 | GERP -3.4 |
| Non-coding constraint | Z -1.71 | 1 kb window · o/e 1.12 · regional · uncalibrated |
| Overall | ||
| CADD | 0.34 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
5.29%
African / African-American · 3,807/72,002 alleles
Filtering AF
5.15%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 5.09%
Overall
0.275%
4,171/1,516,078 alleles · common
exomes 1,927/1,363,932 · genomes 2,244/152,146 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 5.29% | 19 |
| Remaining individualsnot grpmax-eligible | 0.273% | 366 |
| Admixed American | 0.243% | 411 |
| Middle Eastern | 0.0689% | 1,451 |
| South Asian | 0.0177% | 5,646 |
| European (non-Finnish) | 0.00453% | 22,077 |
| East Asian | 0.00229% | 43,700 |
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.241+19C>T
- MANE Select
- NM_014171
- dbSNP
- rs10194490
- Type
- single nucleotide variant
- Location
- chr2:46623886 (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-241-plus-19c-t (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown