NM_052988.5:c.51T>G
Variant names:
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6BP7BS1
The NM_052988.5(CDK10):āc.51T>Gā(p.Arg17Arg) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000324 in 1,612,354 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Genomes: š 0.00049 ( 1 hom., cov: 34)
Exomes š: 0.00031 ( 1 hom. )
Consequence
CDK10
NM_052988.5 synonymous
NM_052988.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.216
Genes affected
CDK10 (HGNC:1770): (cyclin dependent kinase 10) The protein encoded by this gene belongs to the CDK subfamily of the Ser/Thr protein kinase family. The CDK subfamily members are highly similar to the gene products of S. cerevisiae cdc28, and S. pombe cdc2, and are known to be essential for cell cycle progression. This kinase has been shown to play a role in cellular proliferation and its function is limited to cell cycle G2-M phase. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
Variant 16-89686761-T-G is Benign according to our data. Variant chr16-89686761-T-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 1027754.We mark this variant Likely_benign, oryginal submissions are: {Uncertain_significance=1, Likely_benign=1}.
BP7
Synonymous conserved (PhyloP=-0.216 with no splicing effect.
BS1
Variant frequency is greater than expected in population mid. gnomad4_exome allele frequency = 0.000307 (448/1460330) while in subpopulation MID AF= 0.00954 (55/5766). AF 95% confidence interval is 0.00753. There are 1 homozygotes in gnomad4_exome. There are 223 alleles in male gnomad4_exome subpopulation. Median coverage is 31. This position pass quality control queck.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000494 AC: 75AN: 151906Hom.: 1 Cov.: 34
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GnomAD3 exomes AF: 0.000601 AC: 147AN: 244612Hom.: 0 AF XY: 0.000562 AC XY: 75AN XY: 133502
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GnomAD4 exome AF: 0.000307 AC: 448AN: 1460330Hom.: 1 Cov.: 31 AF XY: 0.000307 AC XY: 223AN XY: 726472
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GnomAD4 genome AF: 0.000493 AC: 75AN: 152024Hom.: 1 Cov.: 34 AF XY: 0.000592 AC XY: 44AN XY: 74328
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ClinVar
Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:1
Revision: criteria provided, conflicting classifications
LINK: link
Submissions by phenotype
Al Kaissi syndrome Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Baylor Genetics | Feb 07, 2020 | This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868]. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2025 | CDK10: BP4, BP7 - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at