Genetic Variant CDK14:c.703-152A>T (chr7-90917449-A-T) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_001287135.2(CDK14):c.703-152A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

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: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank	MANE	Protein	UniProt
CDK14	NM_001287135.2 link	c.703-152A>T	intron_variant	Intron 7 of 14	ENST00000380050.8	NP_001274064.1	O94921-1
CDK14	NM_012395.3 link	c.649-152A>T	intron_variant	Intron 6 of 13		NP_036527.1	O94921-2
CDK14	NM_001287136.1 link	c.565-152A>T	intron_variant	Intron 6 of 13		NP_001274065.1	O94921-3
CDK14	NM_001287137.1 link	c.316-152A>T	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>T		intron_variant	Intron 7 of 14	1	NM_001287135.2	ENSP00000369390.3		O94921-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

440612

Hom.:

AF XY:

0.00

AC XY:

AN XY:

229950

African (AFR)

AF:

0.00

AC:

AN:

12600

American (AMR)

AF:

0.00

AC:

AN:

17596

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

11684

East Asian (EAS)

AF:

0.00

AC:

AN:

29126

South Asian (SAS)

AF:

0.00

AC:

AN:

30590

European-Finnish (FIN)

AF:

0.00

AC:

AN:

28932

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1716

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

285116

Other (OTH)

AF:

0.00

AC:

AN:

23252

GnomAD4 genome

Cov.:

Alfa

AF:

0.00

Hom.:

31982

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

6.3

(source)

DANN

Benign

0.76

PhyloP100

-0.064

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over