Genetic Variant CDK14:c.123+26349C>T (chr7-90630598-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001287135.2(CDK14):c.123+26349C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,026 control chromosomes in the GnomAD database, including 2,608 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 0.18 ( 2608 hom., cov: 32)

Consequence

CDK14
NM_001287135.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0310

Publications

6 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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001287135.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.92).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001287135.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK14	NM_001287135.2	MANE Select	c.123+26349C>T		intron	N/A	NP_001274064.1	O94921-1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CDK14	ENST00000380050.8	TSL:1 MANE Select	c.123+26349C>T	intron	N/A	ENSP00000369390.3	O94921-1
CDK14	ENST00000430760.5	TSL:1	c.-16+22023C>T	intron	N/A	ENSP00000394570.1	C9IYJ9
CDK14	ENST00000449528.5	TSL:1	c.-16+26349C>T	intron	N/A	ENSP00000393616.1	C9IYJ9

Frequencies

GnomAD3 genomes

AF:

0.181

AC:

27444

AN:

151908

Hom.:

2599

Cov.:

show subpopulations

Gnomad AFR

AF:

0.164

Gnomad AMI

AF:

0.319

Gnomad AMR

AF:

0.145

Gnomad ASJ

AF:

0.191

Gnomad EAS

AF:

0.0337

Gnomad SAS

AF:

0.194

Gnomad FIN

AF:

0.222

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.200

Gnomad OTH

AF:

0.188

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome

AF:

0.181

AC:

27485

AN:

152026

Hom.:

2608

Cov.:

AF XY:

0.181

AC XY:

13440

AN XY:

74290

show subpopulations

African (AFR)

AF:

0.165

AC:

6835

AN:

41472

American (AMR)

AF:

0.144

AC:

2207

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.191

AC:

662

AN:

3472

East Asian (EAS)

AF:

0.0337

AC:

175

AN:

5186

South Asian (SAS)

AF:

0.193

AC:

928

AN:

4816

European-Finnish (FIN)

AF:

0.222

AC:

2336

AN:

10520

Middle Eastern (MID)

AF:

0.214

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.200

AC:

13581

AN:

67964

Other (OTH)

AF:

0.193

AC:

407

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1140

2281

3421

4562

5702

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

302

604

906

1208

1510

<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:

0.194

Hom.:

2276

Bravo

AF:

0.173

Asia WGS

AF:

0.161

AC:

560

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

2.3

(source)

DANN

Benign

0.78

PhyloP100

0.031

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over