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CDK6
Final classification
VUS
CDK6 c.401A>G · p.Asp134Gly
CDK6

This variant is essentially absent from population databases, with a single heterozygous observation in gnomAD v4.1 (1/1,613,826 alleles; AF = 6.2×10⁻⁷) and no observations in gnomAD v2.1 or gnomAD-Canada, satisfying PM2 at supporting strength.

Gene
CDK6
Transcript
NM_001259.8
HGVS · transcript:coding
NM_001259.8:c.401A>G
Consequence
N/A
GRCh38
chr7:92725762 T>C
GRCh37
chr7:92355076 T>C
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; combination = 1 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: PM2 supporting; combination = 1 supporting, which maps to VUS.
Classification rationale
PM2 VUS
CDK6 c.401A>G

This variant is essentially absent from population databases, with a single heterozygous observation in gnomAD v4.1 (1/1,613,826 alleles; AF = 6.2×10⁻⁷) and no observations in gnomAD v2.1 or gnomAD-Canada, satisfying PM2 at supporting strength.1 No pathogenic or benign classifications exist in ClinVar. No functional studies, segregation data, de novo observations, or variant-specific publications are available. In silico predictors are conflicting (REVEL 0.638 suggesting possible deleterious effect; BayesDel 0.209 in benign range; SpliceAI delta 0.01).2 With only one supporting pathogenic criterion (PM2_supporting) met and no benign criteria met, the variant does not reach the threshold for likely pathogenic, likely benign, or benign classification under generic ACMG/AMP 2015 combination rules. The variant is classified as a Variant of Uncertain Significance (VUS).3

PM2 VUS
3 generic_acmg_combination_rules
Gene diagram · NM_001259.8 · variants mapped to exon structure
CDK6 NM_001259.8
Fetching transcript structure from UCSC…
Applied criteria · 1 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= 6.19645e-07; MAF= 0.00006%, 1/1613826 alleles, homozygotes = 0) and has highest observed frequency in the European (Finnish) population (AF= 1.56196e-05; MAF= 0.00156%, 1/64022 alleles, homozygotes = 0).
      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
      6.2e-05% · 1 / 1,613,826
      0 hom
      European (Finnish)
      1 / 64,022
      0.0016%
      + 9 not observed (Remaining individuals, Admixed American, Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American, European (non-Finnish))
      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 is absent from ClinVar.
      SpliceAI screenshot
      In silico
      SpliceAI predicts no significant splice impact for this variant (max delta score = 0.01). REVEL score = 0.638. BayesDel score = 0.208709.
      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. CDK6, an intracellular kinase, is amplified in various cancer types.
      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
      8Sources
      ClinVar
      gnomAD v2.1
      gnomAD v4.1
      gnomAD-Canada
      SpliceAI
      OncoKB
      COSMIC
      Cancer hotspots