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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 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM1 supporting Pathogenic
The variant is located at codon 51 within the first ankyrin repeat domain of p16INK4A (residues ~34-76), a well-established critical functional domain required for CDK4/6 binding and cyclin-dependent kinase inhibition. This region is a known mutational hotspot in familial melanoma, and many pathogenic missense variants cluster in the ankyrin repeats.
Codon 51 lies in ankyrin repeat 1a critical CDK4/6-binding domainmultiple pathogenic missense variants map to this region in melanoma
PM2 supporting Pathogenic
The variant is absent from all large population databases including gnomAD v2.1 (0 alleles), gnomAD v4.1 (0 alleles), and gnomAD-Canada v1.0 (0 alleles), consistent with a rare variant that may be associated with disease.
Absent from gnomAD v2.1 (AC=0)gnomAD v4.1 (AC=0)gnomAD-Canada v1.0 (AC=0)
Assessed · not applied
Pathogenic
PS1 PS1 requires a different nucleotide change at the same position that is a known pathogenic variant.
PS2 PS2 requires a de novo occurrence with confirmed maternity and paternity.
PS3 PS3 requires well-established in vitro or in vivo functional studies demonstrating a damaging effect.
PS4 PS4 requires a statistically significant enrichment of the variant in affected individuals compared to controls.
PM6 PM6 requires a de novo observation with confirmed parental relationships.
PP1 PP1 requires cosegregation of the variant with disease in multiple affected family members.
PP2 PP2 applies when a gene has a low rate of benign missense variation and missense variants are a common disease mechanism.
PP3 PP3 requires multiple lines of computational evidence supporting a deleterious effect.
PP4 PP4 requires that the patient's phenotype or family history is highly specific for the disease.
PP5 PP5 requires a reputable source (e.g., clinical diagnostic laboratory with expertise in the disease) to have classified the variant as pathogenic.
Benign
BA1 BA1 requires an allele frequency >1% in any population database.
BS1 BS1 requires an allele frequency >0.3% in population databases for a dominant disorder.
BS2 BS2 requires observation of the variant in a healthy adult individual, or in homozygous state without disease.
BS3 BS3 requires well-established functional studies demonstrating no damaging effect.
BS4 BS4 requires lack of segregation with disease in multiple affected family members.
BP1 BP1 applies when a missense variant is found in a gene where only truncating variants are known to cause disease.
BP2 BP2 requires observation of the variant in trans with a known pathogenic variant for a fully penetrant dominant disorder, without clinical consequences.
BP4 BP4 requires multiple lines of computational evidence suggesting no impact on gene or gene product.
BP5 BP5 requires observation of the variant in a case with an alternate molecular basis for disease.
BP6 BP6 requires a reputable source to classify the variant as Benign or Likely Benign.
N/A · 6 PVS1 · PM3 · PM4 · PM5 · BP3 · BP7
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