CRIPT c.16+220C>G
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Common
common (popmax 18.7%, eas) — 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 +220 | deep intronic (+220 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -1.7 | GERP -3.3 |
| Non-coding constraint | Z -1.72 | 1 kb window · o/e 1.15 · regional · uncalibrated |
| Overall | ||
| CADD | 0.643 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
18.7%
East Asian · 964/5,158 alleles
Filtering AF
17.7%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 17.3%
Overall
4.34%
6,611/152,214 alleles · common
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 18.7% | 5 |
| Finnishnot grpmax-eligible | 9.3% | 11 |
| Middle Eastern | 7.14% | 14 |
| Amishnot grpmax-eligible | 6.91% | 14 |
| South Asian | 6.63% | 15 |
| Ashkenazi Jewishnot grpmax-eligible | 6.37% | 16 |
| European (non-Finnish) | 4.5% | 22 |
| Remaining individualsnot grpmax-eligible | 4.21% | 24 |
| Admixed American | 3.35% | 30 |
| African / African-American | 0.903% | 111 |
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.16+220C>G
- MANE Select
- NM_014171
- dbSNP
- rs3754551
- Type
- single nucleotide variant
- Location
- chr2:46617518 (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-16-plus-220c-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown