rs975004

chr7-90971314-A-Gchr7-90971314-A-T

Variant summary

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

The NM_001287135.2(CDK14):c.948-12834A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0702 in 152,208 control chromosomes in the GnomAD database, including 453 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 0.070 (453 hom., cov: 30)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.763

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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.168 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDK14	NM_001287135.2	c.948-12834A>G		intron_variant		ENST00000380050.8
CDK14	NM_001287136.1	c.810-12834A>G		intron_variant
CDK14	NM_001287137.1	c.561-12834A>G		intron_variant
CDK14	NM_012395.3	c.894-12834A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK14	ENST00000380050.8	c.948-12834A>G		intron_variant		1	NM_001287135.2	P4

Frequencies

GnomAD3 genomes AF: 0.0702 AC: 10680 AN: 152090 Hom.: 453 Cov.: 30

Gnomad AFR AF: 0.0802

Gnomad AMI AF: 0.00441

Gnomad AMR AF: 0.0942

Gnomad ASJ AF: 0.0945

Gnomad EAS AF: 0.178

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.0600

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0494

Gnomad OTH AF: 0.0770

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

GnomAD4 genome AF: 0.0702 AC: 10684 AN: 152208 Hom.: 453 Cov.: 30 AF XY: 0.0721 AC XY: 5363 AN XY: 74422

Gnomad4 AFR AF: 0.0801

Gnomad4 AMR AF: 0.0941

Gnomad4 ASJ AF: 0.0945

Gnomad4 EAS AF: 0.178

Gnomad4 SAS AF: 0.103

Gnomad4 FIN AF: 0.0600

Gnomad4 NFE AF: 0.0494

Gnomad4 OTH AF: 0.0776

Alfa AF: 0.0572 Hom.: 378

Bravo AF: 0.0728

Asia WGS AF: 0.113 AC: 393 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	7.3
Dann	Benign	0.53

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: rs975004; hg19: chr7-90600629;