Genetic Variant CDK14:c.703-152A>G (chr7-90917449-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001287135.2(CDK14):c.703-152A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 590,962 control chromosomes in the GnomAD database, including 90,852 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.56 ( 24500 hom., cov: 33)

Exomes 𝑓: 0.54 ( 66352 hom. )

Consequence

CDK14
NM_001287135.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0640

Publications

3 publications found

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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CDK14	NM_001287135.2 link	c.703-152A>G	intron_variant	Intron 7 of 14	ENST00000380050.8	NP_001274064.1	O94921-1
CDK14	NM_012395.3 link	c.649-152A>G	intron_variant	Intron 6 of 13		NP_036527.1	O94921-2
CDK14	NM_001287136.1 link	c.565-152A>G	intron_variant	Intron 6 of 13		NP_001274065.1	O94921-3
CDK14	NM_001287137.1 link	c.316-152A>G	intron_variant	Intron 5 of 12		NP_001274066.1	O94921E7EUK8B4DK59

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000380050.8 link	c.703-152A>G		intron_variant	Intron 7 of 14	1	NM_001287135.2	ENSP00000369390.3		O94921-1

Frequencies

GnomAD3 genomes

AF:

0.563

AC:

85545

AN:

151960

Hom.:

24485

Cov.:

show subpopulations

Gnomad AFR

AF:

0.598

Gnomad AMI

AF:

0.342

Gnomad AMR

AF:

0.533

Gnomad ASJ

AF:

0.510

Gnomad EAS

AF:

0.703

Gnomad SAS

AF:

0.561

Gnomad FIN

AF:

0.687

Gnomad MID

AF:

0.437

Gnomad NFE

AF:

0.525

Gnomad OTH

AF:

0.560

GnomAD4 exome

AF:

0.543

AC:

238465

AN:

438882

Hom.:

66352

AF XY:

0.544

AC XY:

124548

AN XY:

229068

show subpopulations

African (AFR)

AF:

0.596

AC:

7483

AN:

12564

American (AMR)

AF:

0.514

AC:

9011

AN:

17536

Ashkenazi Jewish (ASJ)

AF:

0.511

AC:

5951

AN:

11648

East Asian (EAS)

AF:

0.691

AC:

20061

AN:

29052

South Asian (SAS)

AF:

0.532

AC:

16215

AN:

30474

European-Finnish (FIN)

AF:

0.681

AC:

19635

AN:

28828

Middle Eastern (MID)

AF:

0.510

AC:

869

AN:

1704

European-Non Finnish (NFE)

AF:

0.517

AC:

146764

AN:

283914

Other (OTH)

AF:

0.539

AC:

12476

AN:

23162

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

5081

10161

15242

20322

25403

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2112

4224

6336

8448

10560

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.563

AC:

85604

AN:

152080

Hom.:

24500

Cov.:

AF XY:

0.570

AC XY:

42340

AN XY:

74332

show subpopulations

African (AFR)

AF:

0.598

AC:

24813

AN:

41492

American (AMR)

AF:

0.533

AC:

8135

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.510

AC:

1769

AN:

3470

East Asian (EAS)

AF:

0.703

AC:

3639

AN:

5176

South Asian (SAS)

AF:

0.560

AC:

2699

AN:

4818

European-Finnish (FIN)

AF:

0.687

AC:

7256

AN:

10556

Middle Eastern (MID)

AF:

0.429

AC:

126

AN:

294

European-Non Finnish (NFE)

AF:

0.525

AC:

35668

AN:

67976

Other (OTH)

AF:

0.562

AC:

1188

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1936

3872

5807

7743

9679

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

740

1480

2220

2960

3700

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.529

Hom.:

31982

Bravo

AF:

0.552

Asia WGS

AF:

0.635

AC:

2207

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

6.7

(source)

DANN

Benign

0.71

PhyloP100

-0.064

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over