Genetic Variant CDK14:c.-93-12184G>A (chr7-90592034-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000430760.5(CDK14):c.-93-12184G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.449 in 151,934 control chromosomes in the GnomAD database, including 15,929 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 0.45 ( 15929 hom., cov: 32)

Exomes 𝑓: 0.38 ( 0 hom. )

Consequence

CDK14
ENST00000430760.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.376

Publications

4 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:

ENSG00000223969 (HGNC:):

ENSG00000223969 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=-0.84).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.515 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430760.5. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
CDK14	ENST00000430760.5	TSL:1	c.-93-12184G>A	intron	N/A	ENSP00000394570.1	C9IYJ9
CDK14	ENST00000449528.5	TSL:1	c.-47-12184G>A	intron	N/A	ENSP00000393616.1	C9IYJ9
CDK14	ENST00000456689.5	TSL:1	c.-148-12184G>A	intron	N/A	ENSP00000406848.1	C9IYJ9

Frequencies

GnomAD3 genomes

AF:

0.449

AC:

68149

AN:

151808

Hom.:

15926

Cov.:

show subpopulations

Gnomad AFR

AF:

0.345

Gnomad AMI

AF:

0.403

Gnomad AMR

AF:

0.380

Gnomad ASJ

AF:

0.473

Gnomad EAS

AF:

0.339

Gnomad SAS

AF:

0.469

Gnomad FIN

AF:

0.551

Gnomad MID

AF:

0.387

Gnomad NFE

AF:

0.519

Gnomad OTH

AF:

0.436

GnomAD4 exome

AF:

0.375

AC:

AN:

Hom.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<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:

0.449

AC:

68169

AN:

151926

Hom.:

15929

Cov.:

AF XY:

0.447

AC XY:

33206

AN XY:

74264

show subpopulations

African (AFR)

AF:

0.344

AC:

14262

AN:

41436

American (AMR)

AF:

0.379

AC:

5789

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.473

AC:

1641

AN:

3472

East Asian (EAS)

AF:

0.339

AC:

1750

AN:

5166

South Asian (SAS)

AF:

0.469

AC:

2257

AN:

4812

European-Finnish (FIN)

AF:

0.551

AC:

5804

AN:

10540

Middle Eastern (MID)

AF:

0.382

AC:

110

AN:

288

European-Non Finnish (NFE)

AF:

0.519

AC:

35265

AN:

67940

Other (OTH)

AF:

0.440

AC:

924

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1830

3660

5489

7319

9149

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

630

1260

1890

2520

3150

<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:

0.502

Hom.:

9548

Bravo

AF:

0.430

Asia WGS

AF:

0.416

AC:

1446

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.66

(source)

DANN

Benign

0.56

PhyloP100

-0.38

Splicing

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over