Starting
Initialising…
0%
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 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
      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