Variant 7-91112566-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BS1BS2

The NM_001287135.2(CDK14):c.1179G>A(p.Glu393=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00164 in 1,613,642 control chromosomes in the GnomAD database, including 30 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0076 ( 9 hom., cov: 32)

Exomes 𝑓: 0.0010 ( 21 hom. )

Consequence

CDK14
NM_001287135.2 synonymous

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.242

Variant links:

Genes affected

CDK14 (HGNC:8883): (cyclin dependent kinase 14) Enables cyclin binding activity and cyclin-dependent protein serine/threonine kinase activity. Involved in G2/M transition of mitotic cell cycle and regulation of canonical Wnt signaling pathway. Located in cytosol; nucleoplasm; and plasma membrane. Part of cytoplasmic cyclin-dependent protein kinase holoenzyme complex. [provided by Alliance of Genome Resources, Apr 2022]

CDK14 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.51).

BP6

Variant 7-91112566-G-A is Benign according to our data. Variant chr7-91112566-G-A is described in ClinVar as [Benign]. Clinvar id is 720372.Status of the report is criteria_provided_single_submitter, 1 stars.

BP7

Synonymous conserved (PhyloP=0.242 with no splicing effect.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00756 (1150/152118) while in subpopulation AFR AF= 0.0246 (1021/41462). AF 95% confidence interval is 0.0234. There are 9 homozygotes in gnomad4. There are 521 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High AC in GnomAd4 at 1150 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE
CDK14	NM_001287135.2 linkuse as main transcript	c.1179G>A	p.Glu393=	synonymous_variant	13/15	ENST00000380050.8
CDK14	NM_012395.3 linkuse as main transcript	c.1125G>A	p.Glu375=	synonymous_variant	12/14
CDK14	NM_001287136.1 linkuse as main transcript	c.1041G>A	p.Glu347=	synonymous_variant	12/14
CDK14	NM_001287137.1 linkuse as main transcript	c.792G>A	p.Glu264=	synonymous_variant	11/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK14	ENST00000380050.8 linkuse as main transcript	c.1179G>A	p.Glu393=	synonymous_variant	13/15	1	NM_001287135.2	P4	O94921-1
CDK14	ENST00000265741.7 linkuse as main transcript	c.1125G>A	p.Glu375=	synonymous_variant	12/14	1			O94921-2
CDK14	ENST00000406263.5 linkuse as main transcript	c.1041G>A	p.Glu347=	synonymous_variant	12/14	1		A1	O94921-3
CDK14	ENST00000436577.3 linkuse as main transcript	c.792G>A	p.Glu264=	synonymous_variant	11/13	2

Frequencies

GnomAD3 genomes

AF:

0.00757

AC:

1151

AN:

152000

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0247

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00551

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000207

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000485

Gnomad OTH

AF:

0.00575

GnomAD3 exomes

AF:

0.00234

AC:

588

AN:

250952

Hom.:

AF XY:

0.00170

AC XY:

231

AN XY:

135614

show subpopulations

Gnomad AFR exome

AF:

0.0266

Gnomad AMR exome

AF:

0.00260

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0000327

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000406

Gnomad OTH exome

AF:

0.00294

GnomAD4 exome

AF:

0.00103

AC:

1502

AN:

1461524

Hom.:

Cov.:

AF XY:

0.000849

AC XY:

617

AN XY:

727070

show subpopulations

Gnomad4 AFR exome

AF:

0.0259

Gnomad4 AMR exome

AF:

0.00322

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000232

Gnomad4 FIN exome

AF:

0.0000187

Gnomad4 NFE exome

AF:

0.000276

Gnomad4 OTH exome

AF:

0.00268

GnomAD4 genome

AF:

0.00756

AC:

1150

AN:

152118

Hom.:

Cov.:

AF XY:

0.00701

AC XY:

521

AN XY:

74370

show subpopulations

Gnomad4 AFR

AF:

0.0246

Gnomad4 AMR

AF:

0.00550

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000485

Gnomad4 OTH

AF:

0.00569

Alfa

AF:

0.00363

Hom.:

Bravo

AF:

0.00941

Asia WGS

AF:

0.00144

AC:

AN:

3478

EpiCase

AF:

0.000546

EpiControl

AF:

0.000475

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jan 30, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.51

CADD

Benign

3.1

DANN

Benign

0.79

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