9-87969563-C-T

Position:

• chr9-87969563-C-T

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_Strong BP6_Very_Strong BA1

The NM_001039803.3(CDK20):​c.688-214G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0731 in 764,676 control chromosomes in the GnomAD database, including 2,888 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

• Frequency:
  • Genomes: 𝑓 0.073 (541 hom., cov: 32)
  • Exomes 𝑓: 0.073 (2347 hom.)
• Consequence: CDK20 NM_001039803.3 intron
• Clinical Significance: Benign criteria provided, multiple submitters, no conflicts B:2
• Conservation: PhyloP100: 0.634

Genes affected

CDK20 (HGNC:21420): (cyclin dependent kinase 20) The protein encoded by this gene contains a kinase domain most closely related to the cyclin-dependent protein kinases. The encoded kinase may activate cyclin-dependent kinase 2 and is involved in cell growth. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Dec 2009]

ACMG classification

Verdict is Benign. Variant got -20 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BP6: Variant 9-87969563-C-T is Benign according to our data. Variant chr9-87969563-C-T is described in ClinVar as [Benign]. Clinvar id is 1235349.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.192 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDK20	NM_001039803.3	c.688-214G>A		intron_variant		ENST00000325303.9	NP_001034892.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDK20	ENST00000325303.9	c.688-214G>A		intron_variant		1	NM_001039803.3	ENSP00000322343	P1

Frequencies

GnomAD3 genomes AF: 0.0726 AC: 11034 AN: 152068 Hom.: 541 Cov.: 32

Gnomad AFR AF: 0.0835

Gnomad AMI AF: 0.0231

Gnomad AMR AF: 0.0743

Gnomad ASJ AF: 0.0190

Gnomad EAS AF: 0.203

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.0338

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.0556

Gnomad OTH AF: 0.0737

GnomAD4 exome AF: 0.0732 AC: 44863 AN: 612490 Hom.: 2347 Cov.: 8 AF XY: 0.0779 AC XY: 24660 AN XY: 316632

Gnomad4 AFR exome AF: 0.0812

Gnomad4 AMR exome AF: 0.0740

Gnomad4 ASJ exome AF: 0.0236

Gnomad4 EAS exome AF: 0.151

Gnomad4 SAS exome AF: 0.179

Gnomad4 FIN exome AF: 0.0377

Gnomad4 NFE exome AF: 0.0577

Gnomad4 OTH exome AF: 0.0809

GnomAD4 genome AF: 0.0725 AC: 11034 AN: 152186 Hom.: 541 Cov.: 32 AF XY: 0.0743 AC XY: 5531 AN XY: 74400

Gnomad4 AFR AF: 0.0834

Gnomad4 AMR AF: 0.0742

Gnomad4 ASJ AF: 0.0190

Gnomad4 EAS AF: 0.203

Gnomad4 SAS AF: 0.202

Gnomad4 FIN AF: 0.0338

Gnomad4 NFE AF: 0.0556

Gnomad4 OTH AF: 0.0791

Alfa AF: 0.0621 Hom.: 507

Bravo AF: 0.0743

Asia WGS AF: 0.222 AC: 769 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

not provided Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	May 10, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.7
DANN	Benign	0.37

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs2271992; hg19: chr9-90584478; COSMIC: COSV57482126; COSMIC: COSV57482126;