CRIPT c.138-5del
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.38%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | acceptor -5 | acceptor splice region (-5, within the last 20 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP -3.5, phastCons 0.022 |
| Non-coding constraint | Z -1.71 | 1 kb window · o/e 1.12 · regional · uncalibrated |
| Overall | ||
| CADD | 0.031 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.38%
African / African-American · 1,008/73,048 alleles
Filtering AF
1.31%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.28%
Overall
0.0711%
1,106/1,556,584 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.38% | 72 |
| Remaining individualsnot grpmax-eligible | 0.078% | 1,282 |
| Admixed American | 0.0759% | 1,317 |
| South Asian | 0.00229% | 43,661 |
| European (non-Finnish) | 0.000528% | 189,353 |
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.138-5del
- MANE Select
- NM_014171
- dbSNP
- rs60552651
- Type
- Deletion
- Location
- chr2:46623757 (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.-422_17-582del Pathogenic ★ same type
- CRIPT c.138-11_138-8del Likely benign ★ same type
- CRIPT c.242-15_242-14del Likely benign ★ same type
- CRIPT c.83-10_83-5del Likely benign ★ same type
- CRIPT p.Phe47fs Pathogenic 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-5del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown