CDKN2B p.Thr136=
c.408G>C · rs750528782 · VCV2659130
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.005%, amr)
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 -7.7 | GERP -4.1 |
| Overall | ||
| CADD | 0.156 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.005%
Admixed American · 3/59,970 alleles
Filtering AF
0.00133%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000668%
Overall
0.000374%
6/1,602,440 alleles · very rare
exomes 6/1,450,086 · genomes 0/152,354 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.005% | 19,990 |
| European (non-Finnish) | 0.000254% | 393,244 |
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.Thr136=
- Coding
- c.408G>C
- MANE Select
- NM_004936
- dbSNP
- rs750528782
- Type
- single nucleotide variant
- Location
- chr9:22005996 (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.Ala120= 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
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-thr136 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown