CDKN2B p.Ala120=
c.360C>T · rs62637622 · VCV790615
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
low-frequency (popmax 1.74%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.3 | GERP -3.2 |
| Overall | ||
| CADD | 7.738 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
1.74%
African / African-American · 1,304/75,036 alleles
Filtering AF
1.66%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.63%
Overall
0.09%
1,445/1,604,918 alleles · low-frequency
exomes 692/1,452,572 · genomes 753/152,346 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 1.74% | 58 |
| Admixed American | 0.112% | 895 |
| Remaining individualsnot grpmax-eligible | 0.0978% | 1,022 |
| Middle Eastern | 0.0169% | 5,920 |
| European (non-Finnish) | 0.00102% | 98,293 |
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
- CDKN2B
- Protein
- p.Ala120=
- Coding
- c.360C>T
- MANE Select
- NM_004936
- dbSNP
- rs62637622
- Type
- single nucleotide variant
- Location
- chr9:22006044 (GRCh38)
- Gene constraint
- LOEUF 1.836 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 90.12
Similar variants
- CDKN2B c.157-102G>A Benign ★★ same type
- CDKN2B c.157-27C>A Benign ★★ same type
- CDKN2B p.Leu115= Likely benign ★★ same type
- CDKN2B p.Ala129Gly Uncertain significance ★ ⚠ same type
- CDKN2B p.Ala129Val Uncertain significance ★ ⚠ same type
- CDKN2B p.Ala23Val Uncertain significance ★ ⚠ same type
- CDKN2B p.Ala50Val Uncertain significance ★ ⚠ same type
- CDKN2B p.Ala59Val 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/cdkn2b-p-ala120 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown