Variant X-47223273-C-T 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_006201.5(CDK16):c.-6-279C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0138 in 1,155,016 control chromosomes in the GnomAD database, including 987 homozygotes. There are 5,009 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.019 ( 127 hom., 692 hem., cov: 22)

Exomes 𝑓: 0.013 ( 860 hom. 4317 hem. )

Consequence

CDK16
NM_006201.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 3.53

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:

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 (MetaRNN=0.0010429323).

BP6

Variant X-47223273-C-T is Benign according to our data. Variant chrX-47223273-C-T is described in ClinVar as [Benign]. Clinvar id is 193185.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chrX-47223273-C-T is described in Lovd as [Benign].

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.197 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.-6-279C>T		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.-6-279C>T		intron_variant		1	NM_006201.5	ENSP00000349762	P1	Q00536-1

Frequencies

GnomAD3 genomes

AF:

0.0191

AC:

2139

AN:

111978

Hom.:

128

Cov.:

AF XY:

0.0202

AC XY:

689

AN XY:

34170

show subpopulations

Gnomad AFR

AF:

0.00568

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0968

Gnomad ASJ

AF:

0.00151

Gnomad EAS

AF:

0.210

Gnomad SAS

AF:

0.00697

Gnomad FIN

AF:

0.00687

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00183

Gnomad OTH

AF:

0.0271

GnomAD3 exomes

AF:

0.0496

AC:

5069

AN:

102145

Hom.:

326

AF XY:

0.0394

AC XY:

1471

AN XY:

37351

show subpopulations

Gnomad AFR exome

AF:

0.00293

Gnomad AMR exome

AF:

0.154

Gnomad ASJ exome

AF:

0.00389

Gnomad EAS exome

AF:

0.226

Gnomad SAS exome

AF:

0.00282

Gnomad FIN exome

AF:

0.00391

Gnomad NFE exome

AF:

0.00175

Gnomad OTH exome

AF:

0.0326

GnomAD4 exome

AF:

0.0133

AC:

13823

AN:

1042986

Hom.:

860

Cov.:

AF XY:

0.0126

AC XY:

4317

AN XY:

341456

show subpopulations

Gnomad4 AFR exome

AF:

0.00245

Gnomad4 AMR exome

AF:

0.151

Gnomad4 ASJ exome

AF:

0.00333

Gnomad4 EAS exome

AF:

0.240

Gnomad4 SAS exome

AF:

0.00347

Gnomad4 FIN exome

AF:

0.00505

Gnomad4 NFE exome

AF:

0.00206

Gnomad4 OTH exome

AF:

0.0222

GnomAD4 genome

AF:

0.0192

AC:

2146

AN:

112030

Hom.:

127

Cov.:

AF XY:

0.0202

AC XY:

692

AN XY:

34232

show subpopulations

Gnomad4 AFR

AF:

0.00567

Gnomad4 AMR

AF:

0.0973

Gnomad4 ASJ

AF:

0.00151

Gnomad4 EAS

AF:

0.209

Gnomad4 SAS

AF:

0.00625

Gnomad4 FIN

AF:

0.00687

Gnomad4 NFE

AF:

0.00183

Gnomad4 OTH

AF:

0.0300

Alfa

AF:

0.0154

Hom.:

901

Bravo

AF:

0.0292

TwinsUK

AF:

0.00351

AC:

ALSPAC

AF:

0.00277

AC:

ESP6500AA

AF:

0.00165

AC:

ESP6500EA

AF:

0.00167

AC:

ExAC

AF:

0.00861

AC:

205

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not specified

Benign:1

Benign, criteria provided, single submitter

clinical testing

Eurofins Ntd Llc (ga)

Dec 01, 2014

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.58

BayesDel_noAF

Benign

-0.46

CADD

Benign

DANN

Uncertain

1.0

FATHMM_MKL

Uncertain

0.92

LIST_S2

Benign

0.46

MetaRNN

Benign

0.0010

MetaSVM

Benign

-0.96

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.32

PROVEAN

Benign

-0.25

REVEL

Benign

0.26

Sift

Pathogenic

0.0

Sift4G

Benign

0.27

Vest4

0.12

MPC

1.3

ClinPred

0.051

GERP RS

4.2

gMVP

0.28

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