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CDK4
Final classification
VUS
CDK4 c.823A>T · p.Met275Leu
CDK4

NM_000075.4:c.823A>T (p.Met275Leu) is a missense variant in CDK4, a gene in which missense variants are a known mechanism of autosomal dominant hereditary melanoma.

Gene
CDK4
Transcript
NM_000075.4
HGVS · transcript:coding
NM_000075.4:c.823A>T
Consequence
N/A
GRCh38
chr12:57748614 T>A
GRCh37
chr12:58142397 T>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: PM2 supporting, PP2 supporting, BP4 supporting benign; combination = 2 supporting + 1 supporting benign, 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: PM2 supporting, PP2 supporting, BP4 supporting benign; combination = 2 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2PP2 BP4 VUS
CDK4 c.823A>T

NM_000075.4:c.823A>T (p.Met275Leu) is a missense variant in CDK4, a gene in which missense variants are a known mechanism of autosomal dominant hereditary melanoma.1 This variant is present at extremely low frequency in population databases: gnomAD v2.1 AF=3.98e-6 (1/251,446 alleles) and gnomAD v4.1 AF=1.86e-6 (3/1,612,194 alleles; grpmax FAF=6.8e-7), satisfying PM2 at supporting level.2 The variant meets PP2 at supporting level: CDK4 has a low rate of benign missense variation and missense variants are a well-established disease mechanism (e.g., R24C/H in hereditary melanoma).3 Multiple lines of in silico evidence support a benign interpretation: REVEL score 0.197 (<0.5), BayesDel score -0.0628 (negative), and SpliceAI max delta 0.00 (no splicing impact), satisfying BP4 at supporting benign level.4 This variant has been reported in ClinVar as Uncertain Significance by three clinical laboratories (Variation ID 141405). No functional studies, segregation data, case-control comparisons, or de novo observations are available for this variant.5 Two supporting pathogenic criteria (PM2, PP2) and one supporting benign criterion (BP4) net to one supporting pathogenic criterion, resulting in a final classification of Variant of Uncertain Significance (VUS) under the generic ACMG/AMP 2015 framework.6

PM2 + PP2 + BP4 VUS
4 revelbayesdelspliceai ↗
6 generic_acmg_combination_rules
Gene diagram · NM_000075.4 · variants mapped to exon structure
CDK4 NM_000075.4
Fetching transcript structure from UCSC…
Applied criteria · 3 applied · 19 assessed
Applied · 3
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
NM_000075.4:c.823A>T is present at extremely low frequency in population databases: gnomAD v2.1 AF=3.98e-6 (1/251,446 alleles), gnomAD v4.1 AF=1.86e-6 (3/1,612,194 alleles; grpmax FAF=6.8e-7), and absent from gnomAD-Canada. All frequencies are well below the 0.1% PM2 threshold.
gnomAD v2.1: 1/251446 alleles (AF=3.98e-60.00040%)
PP2 supporting Pathogenic
CDK4 is a gene in which missense variants are a well-established mechanism of disease (e.g., R24C/H in hereditary melanoma) and which has a low rate of benign missense variation in the general population. PP2 is met at supporting level.
CDK4 is a recognized hereditary melanoma predisposition gene with pathogenic missense variants as the primary disease mechanism.Low frequency of missense variants in gnomAD supports low benign missense variation rate.
BP4 supporting Benign
Multiple lines of computational evidence suggest no impact on the gene product. REVEL score is 0.197 (below 0.5 benign threshold), BayesDel score is -0.0628 (negative, consistent with benign), and SpliceAI max delta score is 0.00 (no predicted splicing alteration).
REVEL: 0.197 (benign range<0.5)BayesDel: -0.0628 (negative score
Assessed · not applied
Pathogenic
PS1 No alternative nucleotide change at codon 275 yielding the same amino acid substitution (p.Met275Leu) has been reported as pathogenic in ClinVar, COSMIC, or the literature.
PS2 No de novo occurrence of NM_000075.4:c.823A>T with confirmed maternity and paternity has been reported in the literature or public databases.
PS3 No well-established functional studies have been performed for the p.Met275Leu variant.
PS4 No case-control study comparing the prevalence of NM_000075.4:c.823A>T in affected individuals versus controls has been published.
PM1 Codon 275 resides in the C-terminal extension beyond the core kinase domain (residues ~6-295).
PM5 No pathogenic missense variant at codon 275 via a different amino acid substitution has been identified.
PM6 No assumed de novo occurrence of NM_000075.4:c.823A>T (without confirmation of paternity and maternity) has been reported.
PP1 No co-segregation data for NM_000075.4:c.823A>T with disease in affected families has been reported.
PP3 Multiple lines of computational evidence do not support a deleterious effect.
PP4 No patient phenotype or family history data are available for adjudication.
PP5 No reputable source has reported NM_000075.4:c.823A>T as pathogenic.
Benign
BA1 The maximum allele frequency of NM_000075.4:c.823A>T in gnomAD is 8.79e-6 (v2.1 NFE) and 2.55e-6 (v4.1 NFE), both far below the BA1 threshold of 1% (0.01).
BS1 The maximum allele frequency of NM_000075.4:c.823A>T (8.79e-6 in gnomAD v2.1; 2.55e-6 in gnomAD v4.1) is well below the BS1 threshold of 0.3% (0.003) for non-VCEP adjudication.
BS2 Although NM_000075.4:c.823A>T is observed in gnomAD (3 heterozygous carriers in v4.1), CDK4-associated hereditary melanoma has incomplete penetrance and adult onset.
BS3 No well-established functional studies demonstrating no deleterious effect of the p.Met275Leu variant have been published.
BS4 No data demonstrating lack of co-segregation of NM_000075.4:c.823A>T with disease in affected families are available.
BP2 No evidence of NM_000075.4:c.823A>T observed in trans with a pathogenic variant for CDK4.
BP5 No evidence that NM_000075.4:c.823A>T was found in a case with an alternate molecular basis for disease.
BP6 No reputable source has reported NM_000075.4:c.823A>T as benign.
N/A · 6 PVS1 · PM3 · PM4 · BP1 · BP3 · BP7
Research & evidence
Population frequency
gnomAD v4.1 screenshot
gnomAD v4.1
gnomAD v2.1 screenshot
gnomAD v2.1
v4.1
This variant is present in gnomAD v4.1 (AF= 1.86082e-06; MAF= 0.00019%, 3/1612194 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 2.54622e-06; MAF= 0.00025%, 3/1178216 alleles, homozygotes = 0); grpmax FAF= 6.8e-07.
v2.1
This variant is present in gnomAD v2.1 (AF= 3.977e-06; MAF= 0.00040%, 1/251446 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.79198e-06; MAF= 0.00088%, 1/113740 alleles, homozygotes = 0).
🇨🇦 CA
This variant is absent from gnomAD-Canada.
Allele frequency by ancestry
three datasets · side by side
gnomAD v4.1
0.00019% · 3 / 1,612,194
0 hom · FAF 6.8e-05%
European (non-Finnish)
3 / 1,178,216
0.00025%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
gnomAD v2.1
0.0004% · 1 / 251,446
0 hom
European (non-Finnish)
1 / 113,740
0.00088%
+ 7 not observed (African/African American, Admixed American, Ashkenazi Jewish, East Asian, European (Finnish), Remaining individuals, South Asian)
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 (3 clinical laboratories). (ClinVarID = 141405)
SpliceAI screenshot
In silico
SpliceAI predicts no significant splice impact for this variant (max delta score = 0.00). REVEL score = 0.197. BayesDel score = -0.0628374.
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. CDK4, an intracellular kinase, is altered by amplification or mutation in various cancer types including soft tissue sarcomas and gliomas.
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 not previously been reported in somatic cancers (COSMIC).
Hotspots
This variant does not lie in a statistically significant hotspot.
Sources & reference links
7Sources
ClinVar
gnomAD v2.1
gnomAD v4.1
SpliceAI
OncoKB
COSMIC
Cancer hotspots
Triaged references · 4 PMIDs not cited in assessment
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
28492532 ↗ Sherloc: a comprehensive refinement of the ACMG-AMP variant classification criteria. CLINVAR