rs758706

chr7-90865604-C-T

Variant summary

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

The NM_001287135.2(CDK14):c.639+2335C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,876 control chromosomes in the GnomAD database, including 13,623 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 0.41 (13623 hom., cov: 32)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDK14	NM_001287135.2	c.639+2335C>T		intron_variant		ENST00000380050.8
CDK14	NM_001287136.1	c.501+2335C>T		intron_variant
CDK14	NM_001287137.1	c.252+2335C>T		intron_variant
CDK14	NM_012395.3	c.585+2335C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK14	ENST00000380050.8	c.639+2335C>T		intron_variant		1	NM_001287135.2	P4

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62996 AN: 151758 Hom.: 13621 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.415 AC: 63021 AN: 151876 Hom.: 13623 Cov.: 32 AF XY: 0.422 AC XY: 31321 AN XY: 74218

Gnomad4 AFR AF: 0.352

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.407

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.407

Gnomad4 OTH AF: 0.424

Alfa AF: 0.411 Hom.: 27502

Bravo AF: 0.405

Asia WGS AF: 0.499 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.20
Dann	Benign	0.42

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: rs758706; hg19: chr7-90494919;