CDKN2A c.193+13del
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Not reported
no allele count reported in gnomAD v4.1 (AN 1,599,560)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +13 | near-intronic (+13 nt from the splice site) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP 1.4 | GERP 0.21, phastCons 0.023 |
Population frequency
gnomAD v4.1 · exomes + genomes
No allele count reported in gnomAD v4.1 (AN 1,599,560). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.
Variant & gene context
- Gene
- CDKN2A
- Coding
- c.193+13del
- MANE Select
- NM_000077 · reported on NM_058195
- dbSNP
- rs2489326510
- Type
- Deletion
- Location
- chr9:21994126 (GRCh38)
- Gene constraint
- LOEUF 0.791 · pLI 0.62 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 77.02 · 5 PDB
Similar variants
- CDKN2A c.193+1del Likely pathogenic ★★ same type
- CDKN2A c.457+1_457+10del Pathogenic/Likely pathogenic ★★ same type
- CDKN2A p.Ala36fs Pathogenic ★★ same type
- CDKN2A p.Ala76fs Pathogenic/Likely pathogenic ★★ same type
- CDKN2A p.Asn71fs Pathogenic/Likely pathogenic ★★ same type
- CDKN2A p.Glu120fs Pathogenic ★★ same type
- CDKN2A p.His123fs Pathogenic ★★ same type
- CDKN2A p.Leu32_Leu37del 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/cdkn2a-c-193-plus-13del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown