Variant X-47223121-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_006201.5(CDK16):c.-6-431A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0158 in 1,154,149 control chromosomes in the GnomAD database, including 1,756 homozygotes. There are 4,975 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: 𝑓 0.082 ( 933 hom., 2486 hem., cov: 22)

Exomes 𝑓: 0.0087 ( 823 hom. 2489 hem. )

Consequence

CDK16
NM_006201.5 intron

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 1.40

Variant links:

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]

CDK16 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -13 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0054192543).

BP6

Variant X-47223121-A-G is Benign according to our data. Variant chrX-47223121-A-G is described in ClinVar as [Benign]. Clinvar id is 3059282.Status of the report is no_assertion_criteria_provided, 0 stars. Variant chrX-47223121-A-G is described in Lovd as [Likely_benign].

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDK16	NM_006201.5 linkuse as main transcript	c.-6-431A>G		intron_variant		ENST00000357227.9	NP_006192.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDK16	ENST00000357227.9 linkuse as main transcript	c.-6-431A>G		intron_variant		1	NM_006201.5	ENSP00000349762	P1	Q00536-1

Frequencies

GnomAD3 genomes

AF:

0.0821

AC:

9116

AN:

110996

Hom.:

927

Cov.:

AF XY:

0.0740

AC XY:

2463

AN XY:

33296

show subpopulations

Gnomad AFR

AF:

0.284

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0328

Gnomad ASJ

AF:

0.00304

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000750

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.0211

Gnomad NFE

AF:

0.000984

Gnomad OTH

AF:

0.0643

GnomAD3 exomes

AF:

0.0203

AC:

2069

AN:

102034

Hom.:

194

AF XY:

0.0146

AC XY:

544

AN XY:

37332

show subpopulations

Gnomad AFR exome

AF:

0.280

Gnomad AMR exome

AF:

0.0136

Gnomad ASJ exome

AF:

0.00211

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000986

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000805

Gnomad OTH exome

AF:

0.0106

GnomAD4 exome

AF:

0.00873

AC:

9111

AN:

1043099

Hom.:

823

Cov.:

AF XY:

0.00729

AC XY:

2489

AN XY:

341567

show subpopulations

Gnomad4 AFR exome

AF:

0.289

Gnomad4 AMR exome

AF:

0.0166

Gnomad4 ASJ exome

AF:

0.00182

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00122

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.000334

Gnomad4 OTH exome

AF:

0.0227

GnomAD4 genome

AF:

0.0825

AC:

9157

AN:

111050

Hom.:

933

Cov.:

AF XY:

0.0745

AC XY:

2486

AN XY:

33360

show subpopulations

Gnomad4 AFR

AF:

0.285

Gnomad4 AMR

AF:

0.0328

Gnomad4 ASJ

AF:

0.00304

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000753

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000985

Gnomad4 OTH

AF:

0.0634

Alfa

AF:

0.0106

Hom.:

524

Bravo

AF:

0.0944

TwinsUK

AF:

0.000270

AC:

ALSPAC

AF:

0.00

AC:

ESP6500AA

AF:

0.282

AC:

341

ESP6500EA

AF:

0.00167

AC:

ExAC

AF:

0.0281

AC:

596

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

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.84

BayesDel_noAF

Benign

-0.84

CADD

Benign

8.5

DANN

Benign

0.086

FATHMM_MKL

Benign

0.023

LIST_S2

Benign

0.25

MetaRNN

Benign

0.0054

MetaSVM

Benign

-1.1

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.48

PROVEAN

Benign

0.050

REVEL

Benign

0.058

Sift

Benign

1.0

Sift4G

Pathogenic

0.0

Vest4

0.062

MPC

0.55

ClinPred

0.0020

GERP RS

2.2

gMVP

0.27

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