10-60783609-C-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001786.5(CDK1):c.38-1096C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.739 in 151,998 control chromosomes in the GnomAD database, including 41,756 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.74 ( 41751 hom., cov: 30)
Exomes 𝑓: 0.73 ( 5 hom. )
Consequence
CDK1
NM_001786.5 intron
NM_001786.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.529
Genes affected
CDK1 (HGNC:1722): (cyclin dependent kinase 1) The protein encoded by this gene is a member of the Ser/Thr protein kinase family. This protein is a catalytic subunit of the highly conserved protein kinase complex known as M-phase promoting factor (MPF), which is essential for G2/M phase transitions of eukaryotic cell cycle. Mitotic cyclins stably associate with this protein and function as regulatory subunits. The kinase activity of this protein is controlled by cyclin accumulation and destruction through the cell cycle. The phosphorylation and dephosphorylation of this protein also play important regulatory roles in cell cycle control. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2023]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.91).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.817 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDK1 | NM_001786.5 | c.38-1096C>T | intron_variant | ENST00000395284.8 | NP_001777.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDK1 | ENST00000395284.8 | c.38-1096C>T | intron_variant | 1 | NM_001786.5 | ENSP00000378699.3 |
Frequencies
GnomAD3 genomes AF: 0.739 AC: 112248AN: 151858Hom.: 41724 Cov.: 30
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GnomAD4 exome AF: 0.727 AC: 16AN: 22Hom.: 5 Cov.: 0 AF XY: 0.714 AC XY: 10AN XY: 14
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GnomAD4 genome AF: 0.739 AC: 112332AN: 151976Hom.: 41751 Cov.: 30 AF XY: 0.746 AC XY: 55415AN XY: 74304
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ClinVar
Not reported inComputational scores
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Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at