CDKN2A c.150+214del
Benign
Single submitter
Classification
Benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
low-frequency (popmax 3.28%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| Splice region | donor +214 | deep intronic (+214 nt into the intron) |
|---|---|---|
| SpliceAI | — | not assessed · substitutions only |
| Constraint at this position | ||
| Conservation | phyloP -0.17 | GERP -3.9 |
| Non-coding constraint | Z 5.22 | 1 kb window · o/e 0.70 · regional · uncalibrated |
| Overall | ||
| CADD | 2.321 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
3.28%
African / African-American · 2,464/75,024 alleles
Filtering AF
3.18%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 3.13%
Overall
0.193%
3,106/1,612,006 alleles · low-frequency
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 3.28% | 30 |
| Admixed American | 0.355% | 282 |
| Middle Eastern | 0.264% | 378 |
| Remaining individualsnot grpmax-eligible | 0.258% | 388 |
| Ashkenazi Jewishnot grpmax-eligible | 0.223% | 448 |
| European (non-Finnish) | 0.0148% | 6,777 |
| South Asian | 0.00887% | 11,278 |
| Finnishnot grpmax-eligible | 0.00627% | 15,959 |
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
- CDKN2A
- Coding
- c.150+214del
- MANE Select
- NM_000077
- dbSNP
- rs200129494
- Type
- Deletion
- Location
- chr9:21974464 (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-150-plus-214del (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown