Variant classification summary

NM_000075.4:c.355-1G>A

CDK4 · NP_000066.1:p.? · NM_000075.4

GRCh37: chr12:58144874 C>T · GRCh38: chr12:57751091 C>T

Gene: CDK4 Transcript: NM_000075.4

Final call

VUS

PVS1 very strong PM2 supporting

Variant details

Gene

CDK4

Transcript

NM_000075.4

Protein

NP_000066.1:p.?

gnomAD AF

ClinVar

OncoKB

Classification rationale

Interpretation summary

Generated evidence synthesis

1

NM_000075.4:c.355-1G>A is a canonical splice acceptor variant in intron 3 of CDK4, a gene in which germline loss-of-function variants cause familial melanoma predisposition. PVS1 is applied at very strong strength per ClinGen SVI PVS1 recommendations (PMC6185798) for canonical ±1,2 splice consensus variants in genes with established LoF disease mechanism.

2

The variant is absent from gnomAD v2.1 and v4.1 population databases, meeting PM2 at supporting strength.

3

SpliceAI predicts strong acceptor loss (max delta 0.99), consistent with the canonical splice disruption captured by PVS1; PP3 is not applied separately per PMC6185798 guidance against double-counting splice prediction evidence.

4

Under generic ACMG/AMP 2015 combination rules, PVS1 (very strong) plus PM2 (supporting) yields a point score of 10, reaching the threshold for a pathogenic classification.

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	Met	Canonical splice acceptor variant (c.355-1G>A) in intron 3 of CDK4 (MANE select transcript NM_000075.4). CDK4 loss of function is an established disease mechanism for familial melanoma predisposition. Under PMC6185798 (ClinGen SVI PVS1 recommendations), canonical ±1,2 splice consensus variants qualify for full-strength PVS1 when germline LoF is established for the gene. No downgrade factors identified: transcript is MANE select, no evidence of population LoF enrichment in the affected exon, and no evidence the affected exon is biologically irrelevant.	pvs1_generic_framework
PS1	N/A	PS1 applies when the same amino acid change is produced by a different nucleotide substitution previously established as pathogenic. This is a canonical splice site variant producing an unknown protein consequence (p.?); no applicable amino acid-level comparison.
PS2	Not assessed	No de novo testing data available for this variant.
PS3	Not met	No functional studies have been identified for NM_000075.4:c.355-1G>A. The literature search yielded no publications with variant-specific functional data, and no systematically characterized range including this splice position was found in any study.
PS4	Not assessed	No case-control or prevalence data available. The variant is absent from ClinVar and no published case observations were identified in the literature search.
PS5	Not assessed	No data on independently verified pathogenic nucleotide variants at the c.355-1 position in CDK4. The variant is a splice site change; no comparator nucleotide substitutions at this exact intronic position were identified in ClinVar.
PM1	N/A	PM1 applies to missense variants located in a critical functional domain or mutational hotspot. This is a canonical splice site variant; it does not alter a specific amino acid residue within a domain. Domain-level impact of the splice defect is captured by PVS1.
PM2	Met	This variant is absent from gnomAD v2.1 and v4.1 population databases, consistent with a rare pathogenic variant. Under generic ACMG/AMP, absence from population controls with allele frequency below 0.1% supports PM2 at supporting strength.	gnomad_v2 gnomad_v4
PM5	N/A	PM5 requires a same-residue missense change already classified as pathogenic. This is a canonical splice site variant producing an unknown protein consequence (p.?); no residue-level comparison is possible. pm5_candidates.json confirms no eligible comparator candidates.
PM6	Not assessed	No de novo data available for this variant.
PP1	Not assessed	No family segregation data available for this variant.
PP2	N/A	PP2 applies to missense variants in genes with a low rate of benign missense variation and high missense constraint (high Z-score). This is a canonical splice site variant, not a missense change.
PP3	Not met	SpliceAI predicts strong splice disruption (max delta score 0.99, acceptor loss 0.99), but per PMC6185798 guidance, splice-effect prediction evidence should not be double-counted when PVS1 is already applied for the same canonical splice defect. BayesDel score of 0.247776 does not reach a standard pathogenic threshold for non-splice in silico evidence. No additional independent in silico pathogenic evidence is available.	spliceai bayesdel
PP4	Not assessed	No clinical phenotype data available for the individual carrying this variant. PP4 requires that the patient's phenotype or family history is highly specific for the disease associated with the gene.
PP5	Not met	This variant is absent from ClinVar. No expert panel or reputable source has classified it as pathogenic or likely pathogenic.	clinvar
BA1	Not met	Variant is absent from gnomAD v2.1 and v4.1 population databases. Allele frequency does not exceed the 1% BA1 threshold for a benign stand-alone criterion.	gnomad_v2 gnomad_v4
BS1	Not met	Variant is absent from gnomAD population databases. Allele frequency does not exceed the 0.3% BS1 threshold for a strong benign criterion.	gnomad_v2 gnomad_v4
BS2	Not assessed	No data available on observation of this variant in healthy adult controls where the associated disease is expected to be fully penetrant at an early age. Absence from gnomAD alone does not satisfy BS2.
BS3	Not met	No functional studies demonstrating no deleterious effect have been identified for NM_000075.4:c.355-1G>A. The literature search yielded no publications with variant-specific functional data.
BS4	Not assessed	No family segregation data available to evaluate lack of segregation with disease.
BP1	N/A	BP1 applies to missense variants in genes where only truncating variants cause disease. This is a canonical splice site variant expected to produce a truncating effect via aberrant splicing or NMD, not a missense change.
BP2	Not assessed	No data available on observation of this variant in trans with a known pathogenic variant in CDK4.
BP4	Not met	Multiple lines of computational evidence suggest a deleterious effect. SpliceAI predicts strong splice disruption (max delta score 0.99, acceptor loss 0.99). BayesDel score of 0.247776 does not support a benign classification. BP4 requires multiple lines of computational evidence suggesting no impact.	spliceai bayesdel
BP5	Not assessed	No data available on observation of this variant in a case with an alternate molecular basis for disease.
BP6	Not met	This variant is absent from ClinVar. No reputable source has classified it as benign or likely benign.	clinvar
BP7	N/A	BP7 applies to silent/synonymous variants with no predicted splice impact. This is a canonical splice site variant with a SpliceAI max delta score of 0.99, predicting strong splice disruption. Not applicable.

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