rs3802030

chr7-90855263-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001287135.2(CDK14):c.545-7912T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.73 in 152,118 control chromosomes in the GnomAD database, including 40,981 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 0.73 (40981 hom., cov: 32)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.44

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDK14	NM_001287135.2	c.545-7912T>G		intron_variant		ENST00000380050.8
CDK14	NM_001287136.1	c.407-7912T>G		intron_variant
CDK14	NM_001287137.1	c.158-7912T>G		intron_variant
CDK14	NM_012395.3	c.491-7912T>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK14	ENST00000380050.8	c.545-7912T>G		intron_variant		1	NM_001287135.2	P4

Frequencies

GnomAD3 genomes AF: 0.731 AC: 111071 AN: 152002 Hom.: 40969 Cov.: 32

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.786

Gnomad ASJ AF: 0.736

Gnomad EAS AF: 0.961

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.729

Gnomad OTH AF: 0.734

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

GnomAD4 genome AF: 0.730 AC: 111119 AN: 152118 Hom.: 40981 Cov.: 32 AF XY: 0.735 AC XY: 54635 AN XY: 74366

Gnomad4 AFR AF: 0.664

Gnomad4 AMR AF: 0.786

Gnomad4 ASJ AF: 0.736

Gnomad4 EAS AF: 0.961

Gnomad4 SAS AF: 0.787

Gnomad4 FIN AF: 0.781

Gnomad4 NFE AF: 0.729

Gnomad4 OTH AF: 0.729

Alfa AF: 0.738 Hom.: 22921

Bravo AF: 0.729

Asia WGS AF: 0.802 AC: 2783 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
Cadd	Benign	1.8
Dann	Benign	0.77

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

Other links and lift over

dbSNP: rs3802030; hg19: chr7-90484578;