Variant classification summary

NM_000077.4:c.151G>T

CDKN2A · NP_000068.1:p.(Val51Phe) · NM_000077.4

GRCh37: chr9:21971207 C>A · GRCh38: chr9:21971208 C>A

Gene: CDKN2A Transcript: NM_000077.4

Final call

VUS

PM1 supporting PM2 supporting

Variant details

Gene

CDKN2A

Transcript

NM_000077.4

Protein

NP_000068.1:p.(Val51Phe)

gnomAD AF

ClinVar

Uncertain significance

OncoKB

Unknown Oncogenic Effect

Classification rationale

Interpretation summary

Generated evidence synthesis

1

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.

2

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.

3

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.

4

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).

5

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.

6

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.

7

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).

Final determination: Generic ACMG/AMP 2015 fallback rules do not meet benign, likely benign, likely pathogenic, or pathogenic combination thresholds, so the variant is classified as Variant of Uncertain Significance.

Criteria assessment

ACMG/AMP criteria review

Criteria shown when status is available

All criteria require review: For research and educational purposes only.

Criterion	Status	Rationale	Evidence used
PVS1	N/A	PVS1 applies only to null variants (nonsense, frameshift, canonical ±1,2 splice consensus). NM_000077.4:c.151G>T is a missense variant (p.Val51Phe) and does not fall into any PVS1 null-variant bucket per ClinGen SVI PVS1 recommendations (PMC6185798).	pvs1_variant_assessment pvs1_generic_framework
PS1	Not assessed	PS1 requires a different nucleotide change at the same position that is a known pathogenic variant. The PM5 candidate search found no comparator variants at codon 51 with established pathogenicity; no same-residue pathogenic comparator could be identified.	pm5_candidates
PS2	Not met	PS2 requires a de novo occurrence with confirmed maternity and paternity. No de novo observation of c.151G>T in CDKN2A has been reported in the literature, ClinVar submissions, or public databases.
PS3	Not met	PS3 requires well-established in vitro or in vivo functional studies demonstrating a damaging effect. No published functional assay directly testing p.V51F (e.g., CDK4/6 binding, cell-cycle arrest, subcellular localization) was identified. The variant lies in the first ankyrin repeat domain, which is functionally critical for CDK4/6 inhibition, but variant-specific functional data are absent.	oncokb
PS4	Not met	PS4 requires a statistically significant enrichment of the variant in affected individuals compared to controls. No case-control study has been published for p.V51F. Three ClinVar submitters classify it as Uncertain significance, but no proband counts with odds ratios are available. The variant's absence from gnomAD supports rarity (PM2) but does not independently satisfy PS4 prevalence requirements.	gnomad_v2 gnomad_v4 gnomad_canada clinvar
PS5	Not assessed	PS5 is not a valid ACMG/AMP 2015 criterion. PS5 was retired from the original nomenclature; PM5 covers same-residue alternate pathogenic changes. See PM5 assessment.	pm5_candidates
PM1	Met	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.	oncokb
PM2	Met	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.	gnomad_v2 gnomad_v4 gnomad_canada
PM5	N/A	PM5 requires a different amino acid change at the same residue that has been classified as pathogenic. The automated PM5 candidate search found zero same-residue comparator variants in ClinVar with pathogenic or likely pathogenic classification. Classic PM5 semantics cannot be applied.	pm5_candidates
PM6	Not met	PM6 requires a de novo observation with confirmed parental relationships. No de novo report of c.151G>T has been identified in the literature, databases, or ClinVar submissions.
PP1	Not met	PP1 requires cosegregation of the variant with disease in multiple affected family members. No published cosegregation data for p.V51F in melanoma-prone families was identified.
PP2	Not assessed	PP2 applies when a gene has a low rate of benign missense variation and missense variants are a common disease mechanism. CDKN2A is a tumor suppressor with missense variants as a known disease mechanism. However, without CSPEC/VCEP-defined missense constraint metrics (z-score, HCI prior) for CDKN2A, PP2 cannot be reliably applied in the generic ACMG framework.
PP3	Not met	PP3 requires multiple lines of computational evidence supporting a deleterious effect. In silico predictions are conflicting: REVEL score 0.561 supports a damaging effect, but BayesDel score 0.137 (below the ~0.27 damaging threshold) and SpliceAI max delta 0.02 (no predicted splice impact) do not support pathogenicity. The computational evidence is not consistently deleterious; REVEL alone does not constitute 'multiple lines.'	revel bayesdel spliceai
PP4	Not met	PP4 requires that the patient's phenotype or family history is highly specific for the disease. No individual-level phenotypic data for probands carrying this variant has been reported in the available literature or ClinVar submissions.
PP5	Not met	PP5 requires a reputable source (e.g., clinical diagnostic laboratory with expertise in the disease) to have classified the variant as pathogenic. All three ClinVar submissions classify c.151G>T as Uncertain significance; none report Pathogenic or Likely Pathogenic. PP5 is therefore not satisfied.	clinvar
BA1	Not met	BA1 requires an allele frequency >1% in any population database. The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (allele count 0, allele frequency 0.0). Far below the BA1 threshold.	gnomad_v2 gnomad_v4 gnomad_canada
BS1	Not met	BS1 requires an allele frequency >0.3% in population databases for a dominant disorder. The variant is absent from gnomAD v2.1, v4.1, and gnomAD-Canada (allele frequency 0.0). Far below the BS1 threshold.	gnomad_v2 gnomad_v4 gnomad_canada
BS2	Not met	BS2 requires observation of the variant in a healthy adult individual, or in homozygous state without disease. No such observation has been reported for c.151G>T.
BS3	Not met	BS3 requires well-established functional studies demonstrating no damaging effect. No functional assay directly testing p.V51F has been published. The variant lies in the functionally critical ankyrin repeat domain, where many substitutions impair CDK4/6 binding; a benign functional outcome for V51F should not be assumed without direct evidence.
BS4	Not met	BS4 requires lack of segregation with disease in multiple affected family members. No segregation data (positive or negative) has been published for this variant.
BP1	Not met	BP1 applies when a missense variant is found in a gene where only truncating variants are known to cause disease. CDKN2A-associated familial melanoma can be caused by both missense and truncating variants; missense changes in the ankyrin repeat domains are a well-established pathogenic mechanism. BP1 is not applicable.
BP2	Not met	BP2 requires observation of the variant in trans with a known pathogenic variant for a fully penetrant dominant disorder, without clinical consequences. No such observation has been reported for p.V51F.
BP4	Not met	BP4 requires multiple lines of computational evidence suggesting no impact on gene or gene product. In silico predictions are conflicting: BayesDel 0.137 (benign range) and SpliceAI 0.02 (no splice impact) suggest no effect, but REVEL 0.561 predicts a damaging effect. The discordance between tools precludes application of BP4 under standard ACMG/AMP guidance.	revel bayesdel spliceai
BP5	Not met	BP5 requires observation of the variant in a case with an alternate molecular basis for disease. No such case has been reported for c.151G>T.
BP6	Not met	BP6 requires a reputable source to classify the variant as Benign or Likely Benign. All ClinVar submissions classify c.151G>T as Uncertain significance; no submitter reports a benign classification.	clinvar
BP7	N/A	BP7 applies to synonymous (silent) variants where splicing algorithms predict no impact and the nucleotide is not highly conserved. NM_000077.4:c.151G>T is a missense variant (p.Val51Phe), not a synonymous change. BP7 is reserved for synonymous/intronic variants that do not alter the amino acid sequence.	spliceai
BP3	N/A	BP3 applies to in-frame indels in repetitive regions without a known function. Skipped per case instructions.
PM3	N/A	PM3 applies to recessive disorders. CDKN2A-associated familial melanoma is autosomal dominant. Skipped per case instructions.
PM4	N/A	PM4 applies to in-frame deletions/insertions or stop-loss variants. This is a missense substitution. Skipped per case instructions.

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