Starting
Initialising…
0%
CDKN2A
Final classification
VUS
CDKN2A c.151G>T · p.Val51Phe
CDKN2A

NM_000077.4:c.151G>T (p.Val51Phe) is a missense variant in exon 2 of CDKN2A, located in the first ankyrin repeat domain critical for CDK4/6 binding and cyclin-dependent kinase inhibition.

Gene
CDKN2A
Transcript
NM_000077.4
HGVS · transcript:coding
NM_000077.4:c.151G>T
Consequence
N/A
GRCh38
chr9:21971208 C>A
GRCh37
chr9:21971207 C>A
Basis gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 supporting, PM2 supporting; combination = 2 supporting, which maps to VUS.
gene-specific framework lacked a usable explicit final combination framework, so generic ACMG/AMP 2015 final-combination rules were applied as fallback; applied criteria: PM1 supporting, PM2 supporting; combination = 2 supporting, which maps to VUS.
Classification rationale
PM1PM2 VUS
CDKN2A c.151G>T

NM_000077.4:c.151G>T (p.Val51Phe) is a missense variant in exon 2 of CDKN2A, located in the first ankyrin repeat domain critical for CDK4/6 binding and cyclin-dependent kinase inhibition. PM1 (supporting): The variant lies at codon 51 within ankyrin repeat 1, a well-established mutational hotspot and critical functional domain where many pathogenic missense variants cluster in familial melanoma.1 PM2 (supporting): The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada population databases (allele count 0), consistent with a rare variant.2 PVS1 is not applicable as this is a missense variant that does not fall into any null-variant bucket per the ClinGen SVI PVS1 decision tree (PMC6185798).3 In silico predictions are conflicting: REVEL score 0.561 suggests a damaging effect, while BayesDel 0.137 (benign range) and SpliceAI max delta 0.02 (no splice impact) do not support pathogenicity. Neither PP3 nor BP4 can be applied due to discordant computational evidence.4 No functional studies directly testing p.V51F, no cosegregation data, no de novo reports, and no case-control data were identified in the reviewed literature. ClinVar submissions from two clinical laboratories classify this variant as Uncertain significance.5 Based on generic ACMG/AMP 2015 combination rules (PMID:25741868), two supporting pathogenic criteria (PM1_Supporting + PM2_Supporting) in the absence of any benign criteria is insufficient to reach Likely Pathogenic. The variant is classified as a Variant of Uncertain Significance (VUS).6

PM1 + PM2 VUS
3 pvs1_variant_assessmentpvs1_generic_framework ↗
4 revelbayesdelspliceai ↗
6 generic_acmg_combination_rules
Gene diagram · NM_000077.4 · variants mapped to exon structure
CDKN2A NM_000077.4
Fetching transcript structure from UCSC…
Applied criteria · 2 met · select any tile
Met
Not met
Not assessed
N/A
Strength very strong supporting
Pathogenic evidence
PVS
PS
PM
PP
Benign evidence
BA
BS
BP
Rationale
Select a criterion.
Sources
Evidence used
    Gaps remaining
      Rule
      Research & evidence
      Population frequency
      gnomAD v4.1 screenshot
      gnomAD v4.1
      gnomAD v2.1 screenshot
      gnomAD v2.1
      v4.1
      Absent from gnomAD v4.1.
      v2.1
      Absent from gnomAD v2.1.
      🇨🇦 CA
      Absent from gnomAD-Canada v1.0.
      Allele frequency by ancestry
      three datasets · side by side
      gnomAD v4.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD v2.1
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      gnomAD Canada 🇨🇦
      Absent · 0 / ?
      0 hom
      Not observed in any ancestry group.
      ClinVar screenshot
      ClinVar
      This variant has been reported in ClinVar as Uncertain significance (2 clinical laboratories). (ClinVarID = 2735266)
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.02). REVEL score = 0.561. BayesDel score = 0.136755.
      Functional / OncoKB screenshot
      Functional Unknown Oncogenic Effect
      OncoKB did not identify variant-specific reviewed functional evidence for this variant; gene-level curated context is available for reviewer follow-up. CDKN2A, which encodes both a cyclin-dependent kinase inhibitor and an MDM2 inhibitor, is altered by mutation and deletion in various cancers.
      OncoKB ↗
      COSMIC screenshot
      COSMIC
      Cancer hotspots screenshot
      Cancer hotspots
      Somatic evidence Not in COSMIC / hotspots
      COSMIC
      This variant does not lie in a statistically significant hotspot. This variant has previously been reported in somatic cancers (COSMIC; COSV105891454, n = 1 times).
      Hotspots
      This variant does not lie in a statistically significant hotspot.
      Sources & reference links
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots
      Triaged references · 9 PMIDs not cited in assessment
      17047042 ↗ High-risk melanoma susceptibility genes and pancreatic cancer, neural system tumors, and uveal melanoma across GenoMEL. CLINVAR
      25741868 ↗ Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology. CLINVAR
      31672839 ↗ Management of patients with increased risk for familial pancreatic cancer: updated recommendations from the International Cancer of the Pancreas Screening (CAPS) Consortium. CLINVAR
      7987388 ↗ Analysis of the p16 gene (CDKN2) as a candidate for the chromosome 9p melanoma susceptibility locus. CLINVAR
      25394175 ↗ A practice guideline from the American College of Medical Genetics and Genomics and the National Society of Genetic Counselors: referral indications for cancer predisposition assessment. CLINVAR
      26389258 ↗ Cancer Genetics Risk Assessment and Counseling (PDQ®): Health Professional Version. CLINVAR
      26389333 ↗ Genetics of Skin Cancer (PDQ®): Health Professional Version. CLINVAR
      40674536 ↗ CDKN2A Cancer Predisposition. CLINVAR
      28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR