rs10507365

chr13-26375439-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001260.3(CDK8):c.457-7375A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0569 in 152,254 control chromosomes in the GnomAD database, including 410 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 0.057 (410 hom., cov: 33)
• Consequence: CDK8 NM_001260.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347

Genes affected

CDK8 (HGNC:1779): (cyclin dependent kinase 8) This gene encodes a member of the cyclin-dependent protein kinase (CDK) family. CDK family members are known to be important regulators of cell cycle progression. This kinase and its regulatory subunit, cyclin C, are components of the Mediator transcriptional regulatory complex, involved in both transcriptional activation and repression by phosphorylation of the carboxy-terminal domain of the largest subunit of RNA polymerase II. This kinase regulates transcription by targeting the cyclin-dependent kinase 7 subunits of the general transcription initiation factor IIH, thus providing a link between the Mediator complex and the basal transcription machinery. Multiple pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2016]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.113 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDK8	NM_001260.3	c.457-7375A>T		intron_variant		ENST00000381527.8
CDK8	NM_001318368.2	c.457-7375A>T		intron_variant
CDK8	NM_001346501.2	c.-5-9772A>T		intron_variant
CDK8	XM_047430033.1	c.277-7375A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK8	ENST00000381527.8	c.457-7375A>T		intron_variant		1	NM_001260.3	P1

Frequencies

GnomAD3 genomes AF: 0.0568 AC: 8643 AN: 152136 Hom.: 409 Cov.: 33

Gnomad AFR AF: 0.116

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0811

Gnomad ASJ AF: 0.0654

Gnomad EAS AF: 0.0628

Gnomad SAS AF: 0.0930

Gnomad FIN AF: 0.00952

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0590

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0569 AC: 8657 AN: 152254 Hom.: 410 Cov.: 33 AF XY: 0.0589 AC XY: 4383 AN XY: 74444

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.0809

Gnomad4 ASJ AF: 0.0654

Gnomad4 EAS AF: 0.0628

Gnomad4 SAS AF: 0.0931

Gnomad4 FIN AF: 0.00952

Gnomad4 NFE AF: 0.0202

Gnomad4 OTH AF: 0.0621

Alfa AF: 0.0390 Hom.: 31

Bravo AF: 0.0625

Asia WGS AF: 0.109 AC: 379 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	2.9
Dann	Benign	0.30

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10507365; hg19: chr13-26949576;