rs17869240

Variant names:

• chr7-90566433-A-G
• rs17869240
• ENST00000430760.5:c.-94+2570A>G

Variant summary

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

The ENST00000430760.5(CDK14):​c.-94+2570A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 152,104 control chromosomes in the GnomAD database, including 1,460 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 0.10 (1460 hom., cov: 32)
• Consequence: CDK14 ENST00000430760.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.846

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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.496 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000430760.5	c.-94+2570A>G		intron_variant	Intron 1 of 5	1		ENSP00000394570.1
CDK14	ENST00000449528.5	c.-48+2570A>G		intron_variant	Intron 4 of 7	1		ENSP00000393616.1
CDK14	ENST00000456689.5	c.-149+2570A>G		intron_variant	Intron 1 of 6	1		ENSP00000406848.1

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15520 AN: 151984 Hom.: 1460 Cov.: 32

Gnomad AFR AF: 0.0766

Gnomad AMI AF: 0.0758

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.513

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.0549

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0710

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.102 AC: 15537 AN: 152104 Hom.: 1460 Cov.: 32 AF XY: 0.107 AC XY: 7968 AN XY: 74366

Gnomad4 AFR AF: 0.0768

Gnomad4 AMR AF: 0.189

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.512

Gnomad4 SAS AF: 0.172

Gnomad4 FIN AF: 0.0549

Gnomad4 NFE AF: 0.0711

Gnomad4 OTH AF: 0.122

Alfa AF: 0.103 Hom.: 219

Bravo AF: 0.114

Asia WGS AF: 0.328 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.67

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs17869240; hg19: chr7-90195747;