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CDK6
Final classification
VUS
CDK6 c.197G>A · p.Arg66Lys
CDK6

NM_001259.8:c.197G>A (p.Arg66Lys) is a missense variant in CDK6, a cyclin-dependent kinase with established oncogenic roles in cancer.

Gene
CDK6
Transcript
NM_001259.8
HGVS · transcript:coding
NM_001259.8:c.197G>A
Consequence
N/A
GRCh38
chr7:92833127 C>T
GRCh37
chr7:92462441 C>T
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, BP4 supporting benign; combination = 1 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, BP4 supporting benign; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
CDK6 c.197G>A

NM_001259.8:c.197G>A (p.Arg66Lys) is a missense variant in CDK6, a cyclin-dependent kinase with established oncogenic roles in cancer.1 This variant is extremely rare, observed in only 1 of 1,606,862 alleles (AF=6.22×10⁻⁷) in gnomAD v4.1, and absent from gnomAD v2.1 and gnomAD-Canada v1.0, meeting PM2 at supporting level.2 Multiple in silico predictors do not support a deleterious effect: REVEL score is 0.192 (benign-leaning), BayesDel score is −0.083 (benign), and SpliceAI predicts no splicing impact (max delta=0.00), meeting BP4 at supporting benign level.3 This variant is absent from ClinVar and has not been reported in the literature. No functional data, segregation data, de novo reports, or case-control studies are available.4 The variant does not lie in a statistically significant mutational hotspot per cancerhotspots.org, and no pathogenic missense variant at the same residue (Arg66) has been identified.5 PVS1 is not applicable as this is a missense variant, not a null variant; BP1 is not applicable as CDK6 is an oncogene whose primary disease mechanism is gain-of-function rather than truncating loss-of-function.6 Overall, one supporting pathogenic criterion (PM2) and one supporting benign criterion (BP4) are met. These criteria are in equipoise, resulting in a classification of Variant of Uncertain Significance (VUS) per ACMG/AMP 2015 generic combination rules.7

PM2 + BP4 VUS
3 revelbayesdelspliceai ↗
5 pm5_candidates
6 pvs1_generic_framework ↗pvs1_variant_assessment
7 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 · 2 applied · 20 assessed
Applied · 2
Strength Supporting Moderate Strong Very strong
PM2 supporting Pathogenic
This variant is extremely rare in population databases. It is absent from gnomAD v2.1 and present in gnomAD v4.1 at an allele frequency of 6.22×10⁻⁷ (1/1,606,862 alleles, no homozygotes), well below the PM2 threshold of <0.1%. It is also absent from gnomAD-Canada v1.0.
gnomAD v2.1: absentgnomAD v4.1: total AF=6.22e-7 (1/1606
BP4 supporting Benign
Multiple in silico predictors support a benign impact. REVEL score is 0.192 (below deleterious threshold), BayesDel score is −0.083 (negative, predicting benign), and SpliceAI predicts no splicing alteration (max delta = 0.00). All three independent in silico tools concur on a non-deleterious prediction.
REVEL=0.192 (threshold >0.5 for pathogenic)BayesDel=−0.083 (negative score favors benign)SpliceAI max delta=0.00 (no splice effect).
Assessed · not applied
Pathogenic
PS1 No alternative nucleotide change at position c.197 producing the same amino acid change (p.Arg66Lys) has been reported as pathogenic.
PS2 No de novo data are available for this variant.
PS3 No functional studies have been identified for this variant or for a systematically characterized range that includes codon 66 of CDK6.
PS4 No case-control or prevalence data are available for this variant.
PM1 Residue 66 does not lie within a statistically significant mutational hotspot as determined by cancerhotspots.org, and no domain-level functional characterization specific to this region of CDK6 was identified in the literature.
PM5 No pathogenic missense variant at the same amino acid residue (Arg66) has been identified.
PM6 No de novo data are available for this variant.
PP1 No segregation data are available for this variant.
PP2 Gene-specific constraint data are not available; the HCI prior does not support CDK6.
PP3 Multiple in silico predictors do not support a deleterious effect.
PP4 No patient-specific phenotype or clinical data are available for assessment.
PP5 This variant has not been reported as pathogenic by a reputable source in the recent literature or clinical databases.
Benign
BA1 The allele frequency is 6.22×10⁻⁷ (0.000062%) in gnomAD v4.1, far below the BA1 threshold of >1%.
BS1 The allele frequency is 6.22×10⁻⁷ (0.000062%) in gnomAD v4.1, far below the BS1 threshold of >0.3%.
BS2 No homozygous observations have been reported in population databases; the variant is present in heterozygous state in only 1/1,606,862 alleles in gnomAD v4.1.
BS3 No in vitro or in vivo functional studies demonstrating a benign effect are available for this variant.
BS4 No family segregation data are available to assess lack of segregation with disease.
BP2 No data are available regarding observation of this variant in trans with a known pathogenic variant.
BP5 No data are available regarding an alternative molecular basis for disease in a case harboring this variant.
BP6 This variant has not been reported as benign by any reputable source.
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= 6.22331e-07; MAF= 0.00006%, 1/1606862 alleles, homozygotes = 0) and has highest observed frequency in the African/African American population (AF= 1.33447e-05; MAF= 0.00133%, 1/74936 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 / 1,606,862
0 hom
African/African American
1 / 74,936
0.0013%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, 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 = 0.00). REVEL score = 0.192. BayesDel score = -0.0828048.
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