Variant 9-87967309-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001039803.3(CDK20):c.*153C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.027 in 788,320 control chromosomes in the GnomAD database, including 1,948 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.021 ( 264 hom., cov: 33)

Exomes 𝑓: 0.028 ( 1684 hom. )

Consequence

CDK20
NM_001039803.3 3_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -0.165

Variant links:

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]

CDK20 links:

CDK20 (HGNC:):

CDK20 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

Variant 9-87967309-G-A is Benign according to our data. Variant chr9-87967309-G-A is described in ClinVar as [Benign]. Clinvar id is 1180189.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.221 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDK20	NM_001039803.3 linkuse as main transcript	c.*153C>T		3_prime_UTR_variant	8/8	ENST00000325303.9	NP_001034892.1	Q8IZL9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDK20	ENST00000325303 linkuse as main transcript	c.*153C>T		3_prime_UTR_variant	8/8	1	NM_001039803.3	ENSP00000322343.8		Q8IZL9-1

Frequencies

GnomAD3 genomes

AF:

0.0211

AC:

3204

AN:

152126

Hom.:

264

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00398

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0913

Gnomad ASJ

AF:

0.0107

Gnomad EAS

AF:

0.233

Gnomad SAS

AF:

0.0547

Gnomad FIN

AF:

0.00273

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000941

Gnomad OTH

AF:

0.0234

GnomAD3 exomes

AF:

0.0591

AC:

8838

AN:

149478

Hom.:

898

AF XY:

0.0522

AC XY:

4153

AN XY:

79536

show subpopulations

Gnomad AFR exome

AF:

0.00626

Gnomad AMR exome

AF:

0.194

Gnomad ASJ exome

AF:

0.0102

Gnomad EAS exome

AF:

0.235

Gnomad SAS exome

AF:

0.0458

Gnomad FIN exome

AF:

0.00353

Gnomad NFE exome

AF:

0.000839

Gnomad OTH exome

AF:

0.0342

GnomAD4 exome

AF:

0.0284

AC:

18061

AN:

636076

Hom.:

1684

Cov.:

AF XY:

0.0274

AC XY:

9303

AN XY:

339082

show subpopulations

Gnomad4 AFR exome

AF:

0.00539

Gnomad4 AMR exome

AF:

0.183

Gnomad4 ASJ exome

AF:

0.0106

Gnomad4 EAS exome

AF:

0.224

Gnomad4 SAS exome

AF:

0.0456

Gnomad4 FIN exome

AF:

0.00277

Gnomad4 NFE exome

AF:

0.000818

Gnomad4 OTH exome

AF:

0.0244

GnomAD4 genome

AF:

0.0210

AC:

3202

AN:

152244

Hom.:

264

Cov.:

AF XY:

0.0238

AC XY:

1774

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.00397

Gnomad4 AMR

AF:

0.0914

Gnomad4 ASJ

AF:

0.0107

Gnomad4 EAS

AF:

0.232

Gnomad4 SAS

AF:

0.0541

Gnomad4 FIN

AF:

0.00273

Gnomad4 NFE

AF:

0.000941

Gnomad4 OTH

AF:

0.0241

Alfa

AF:

0.00994

Hom.:

130

Bravo

AF:

0.0304

Asia WGS

AF:

0.119

AC:

411

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

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 11, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.87

CADD

Benign

3.9

DANN

Benign

0.44

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over