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CDK6
Final classification
VUS
CDK6 c.763C>T · p.His255Tyr
CDK6

NM_001259.8:c.763C>T (p.His255Tyr) is a missense variant in CDK6, a gene without an established ClinGen CSPEC/VCEP framework. Assessment follows generic ACMG/AMP 2015 guidelines (PMID:25741868).

Gene
CDK6
Transcript
NM_001259.8
HGVS · transcript:coding
NM_001259.8:c.763C>T
Consequence
N/A
GRCh38
chr7:92618143 G>A
GRCh37
chr7:92247457 G>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, BP4 supporting; 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; combination = 1 supporting + 1 supporting benign, which maps to VUS.
Classification rationale
PM2 BP4 VUS
CDK6 c.763C>T

NM_001259.8:c.763C>T (p.His255Tyr) is a missense variant in CDK6, a gene without an established ClinGen CSPEC/VCEP framework. Assessment follows generic ACMG/AMP 2015 guidelines (PMID:25741868).1 This variant is extremely rare in population databases, present at an allele frequency of 6.2 × 10⁻⁷ (1/1,614,060 alleles, 0 homozygotes) in gnomAD v4.1 and absent from gnomAD v2.1 and gnomAD-Canada, meeting PM2 at supporting level (PM2_Supporting).2 Multiple in silico tools predict a benign effect: REVEL score 0.062, BayesDel score -0.465931, and SpliceAI max delta 0.00, meeting BP4 at supporting level (BP4_Supporting).3 No pathogenic criteria above supporting level are met. PVS1 is not applicable (missense variant). PS1-PS5 are not met due to absence from ClinVar and lack of functional, segregation, or de novo data. PM1 and PM5 are not met. PP1-PP5 are not met.4 No benign criteria above supporting level are met. BA1 and BS1 are not met (allele frequency far below thresholds). BS2-BS4 are not met. BP1, BP2, BP5, and BP6 are not met. BP3 and BP7 are not applicable.5 With one supporting pathogenic criterion (PM2_Supporting) and one supporting benign criterion (BP4_Supporting), the evidence is balanced with no criteria above supporting strength on either side. Under ACMG/AMP 2015 combination rules, this results in a classification of Variant of Uncertain Significance (VUS).6

PM2 + BP4 VUS
1 generic_acmg_combination_rules
3 revelbayesdelspliceai ↗
4 clinvar ↗oncokb ↗pm5_candidatespvs1_variant_assessment
5 gnomad_v4 ↗pvs1_gene_context
6 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: absent from gnomAD v2.1 (exomes) and present at an allele frequency of 6.2 × 10⁻⁷ (1/1,614,060 alleles, 0 homozygotes) in gnomAD v4.1, well below the PM2 threshold of <0.1%. Also absent from gnomAD-Canada v1.0.
gnomAD v2.1: absent (0 alleles)gnomAD v4.1: 1 allele in 1614
BP4 supporting Benign
Multiple lines of computational evidence predict no deleterious effect: REVEL score 0.062 (benign, well below 0.5 pathogenicity threshold), BayesDel score -0.465931 (negative value, consistent with benign), and SpliceAI max delta 0.00 (no predicted splicing impact). Three independent in silico tools consistently support a benign interpretation.
REVEL score: 0.062 (benign)BayesDel score: -0.465931 (benign)SpliceAI max delta: 0.00 (no splicing impact)
Assessed · not applied
Pathogenic
PS1 This variant is absent from ClinVar.
PS2 No de novo occurrence data with confirmed maternity and paternity is available for this variant.
PS3 No variant-specific functional studies were identified.
PS4 No case-control or prevalence data are available to assess whether this variant is significantly enriched in affected individuals versus controls.
PM1 Residue H255 is not located in a statistically significant mutational hotspot (cancerhotspots.org: residue_significant=false, exact_variant_listed=no).
PM6 No de novo observation with confirmed maternity and paternity is available for this variant.
PP1 No co-segregation data are available for this variant in affected families.
PP2 Insufficient data to assess whether CDK6 has a low rate of benign missense variation.
PP3 In silico tools consistently predict a benign effect: REVEL score 0.062 (well below the 0.5 threshold), BayesDel score -0.465931 (negative value indicating benign), and SpliceAI shows no splicing impact (max delta 0.00).
PP4 No patient phenotype or clinical data are available for adjudication.
PP5 No reputable source has reported this variant as pathogenic.
Benign
BA1 Allele frequency of 6.2 × 10⁻⁷ (0.00006%) in gnomAD v4.1 is far below the BA1 threshold of >1%.
BS1 Allele frequency of 6.2 × 10⁻⁷ (0.00006%) in gnomAD v4.1 is far below the BS1 threshold of >0.3%.
BS2 No homozygous observations in population databases (gnomAD v4.1 homozygous count = 0; gnomAD v2.1 absent entirely).
BS3 No well-established in vitro or in vivo functional studies demonstrate no deleterious effect for this variant.
BS4 No segregation data are available to assess whether this variant fails to segregate with disease in affected family members.
BP1 CDK6 is not established as a gene where only truncating variants cause disease with missense variants being benign.
BP2 No observation of this variant in trans with a known pathogenic variant for a fully penetrant dominant disorder.
BP5 No case has been identified where this variant occurs in an individual with an alternate molecular basis for disease.
BP6 No reputable source has classified this variant as benign.
N/A · 6 PVS1 · PM3 · PM4 · PM5 · 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= 6.19556e-07; MAF= 0.00006%, 1/1614060 alleles, homozygotes = 0) and has highest observed frequency in the European (non-Finnish) population (AF= 8.47527e-07; MAF= 0.00008%, 1/1179904 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 / 1,614,060
0 hom
European (non-Finnish)
1 / 1,179,904
8.5e-05%
+ 9 not observed (Remaining individuals, Admixed American, European (Finnish), Amish, East Asian, Middle Eastern, South Asian, Ashkenazi Jewish, African/African American)
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 = 0.062. BayesDel score = -0.465931.
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