X-47224638-A-G
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1
The NM_006201.5(CDK16):āc.357A>Gā(p.Ser119Ser) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0137 in 1,209,531 control chromosomes in the GnomAD database, including 1,397 homozygotes. There are 4,473 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).
Frequency
Genomes: š 0.072 ( 724 hom., 2132 hem., cov: 22)
Exomes š: 0.0078 ( 673 hom. 2341 hem. )
Consequence
CDK16
NM_006201.5 synonymous
NM_006201.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -3.28
Genes affected
CDK16 (HGNC:8749): (cyclin dependent kinase 16) The protein encoded by this gene belongs to the cdc2/cdkx subfamily of the ser/thr family of protein kinases. It may play a role in signal transduction cascades in terminally differentiated cells; in exocytosis; and in transport of secretory cargo from the endoplasmic reticulum. This gene is thought to escape X inactivation. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Dec 2009]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.86).
BP6
Variant X-47224638-A-G is Benign according to our data. Variant chrX-47224638-A-G is described in ClinVar as [Benign]. Clinvar id is 3059606.Status of the report is no_assertion_criteria_provided, 0 stars.
BP7
Synonymous conserved (PhyloP=-3.28 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.243 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDK16 | NM_006201.5 | c.357A>G | p.Ser119Ser | synonymous_variant | 4/16 | ENST00000357227.9 | NP_006192.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDK16 | ENST00000357227.9 | c.357A>G | p.Ser119Ser | synonymous_variant | 4/16 | 1 | NM_006201.5 | ENSP00000349762.4 |
Frequencies
GnomAD3 genomes AF: 0.0716 AC: 7969AN: 111351Hom.: 718 Cov.: 22 AF XY: 0.0631 AC XY: 2116AN XY: 33549
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GnomAD3 exomes AF: 0.0206 AC: 3748AN: 181925Hom.: 363 AF XY: 0.0134 AC XY: 900AN XY: 66955
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GnomAD4 exome AF: 0.00777 AC: 8528AN: 1098128Hom.: 673 Cov.: 32 AF XY: 0.00644 AC XY: 2341AN XY: 363504
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GnomAD4 genome AF: 0.0718 AC: 8001AN: 111403Hom.: 724 Cov.: 22 AF XY: 0.0634 AC XY: 2132AN XY: 33611
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
CDK16-related disorder Benign:1
Benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Jun 11, 2019 | This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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