CRIPTO c.339-8A>G
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
rare (popmax 0.509%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | acceptor -8 | acceptor splice region (-8, within the last 20 intronic nt) · inside the BP7-excluded zone |
|---|---|---|
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -8.5 | GERP -2.3 |
| Non-coding constraint | Z 2.11 | 1 kb window · o/e 0.86 · regional · uncalibrated |
| Overall | ||
| CADD | 0.014 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.509%
African / African-American · 382/75,068 alleles
Filtering AF
0.467%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.45%
Overall
0.0357%
577/1,614,180 alleles · rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.509% | 197 |
| Middle Eastern | 0.0832% | 1,202 |
| Admixed American | 0.0766% | 1,305 |
| Remaining individualsnot grpmax-eligible | 0.048% | 2,083 |
| European (non-Finnish) | 0.00966% | 10,351 |
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
- CRIPTO
- Coding
- c.339-8A>G
- MANE Select
- NM_003212
- dbSNP
- rs150809256
- Type
- single nucleotide variant
- Location
- chr3:46579943 (GRCh38)
- Structure
- AlphaFold pLDDT 67.47
Similar variants
- CRIPTO p.Arg111Gly Benign ★★ same type
- CRIPTO p.Gly151= Benign/Likely benign ★★ same type
- CRIPTO p.Arg111His Uncertain significance ★ ⚠ same type
- CRIPTO p.Arg171His Uncertain significance ★ ⚠ same type
- CRIPTO p.Arg38Cys Uncertain significance ★ ⚠ same type
- CRIPTO p.Arg38His Uncertain significance ★ ⚠ same type
- CRIPTO p.Arg60Gln Uncertain significance ★ ⚠ same type
- CRIPTO p.Arg62Pro 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/cripto-c-339-minus-8a-g (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown