rs2188240

Positions:

• chr7-90784986-G-A
• chr7-90784986-G-T

Variant summary

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

The NM_001287135.2(CDK14):​c.465-5587G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,848 control chromosomes in the GnomAD database, including 15,176 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 0.44 (15176 hom., cov: 32)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDK14	NM_001287135.2	c.465-5587G>A		intron_variant		ENST00000380050.8
CDK14	NM_001287136.1	c.327-5587G>A		intron_variant
CDK14	NM_001287137.1	c.78-5587G>A		intron_variant
CDK14	NM_012395.3	c.411-5587G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK14	ENST00000380050.8	c.465-5587G>A		intron_variant		1	NM_001287135.2	P4

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66068 AN: 151730 Hom.: 15175 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.350

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.428

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

GnomAD4 genome AF: 0.435 AC: 66092 AN: 151848 Hom.: 15176 Cov.: 32 AF XY: 0.442 AC XY: 32809 AN XY: 74184

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.399

Gnomad4 EAS AF: 0.817

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.424

Alfa AF: 0.371 Hom.: 4774

Bravo AF: 0.442

Asia WGS AF: 0.586 AC: 2030 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	2.1
DANN	Benign	0.51

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: rs2188240; hg19: chr7-90414301;