ENST00000430760.5:c.-94+2570A>G

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000430760.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK14	ENST00000430760.5	TSL:1	c.-94+2570A>G		intron	N/A	ENSP00000394570.1
	CDK14	ENST00000449528.5	TSL:1	c.-48+2570A>G		intron	N/A	ENSP00000393616.1
	CDK14	ENST00000456689.5	TSL:1	c.-149+2570A>G		intron	N/A	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

African (AFR) AF: 0.0768 AC: 3186 AN: 41502

American (AMR) AF: 0.189 AC: 2883 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.0709 AC: 246 AN: 3470

East Asian (EAS) AF: 0.512 AC: 2641 AN: 5158

South Asian (SAS) AF: 0.172 AC: 829 AN: 4818

European-Finnish (FIN) AF: 0.0549 AC: 581 AN: 10588

Middle Eastern (MID) AF: 0.0442 AC: 13 AN: 294

European-Non Finnish (NFE) AF: 0.0711 AC: 4832 AN: 67990

Other (OTH) AF: 0.122 AC: 257 AN: 2110

Alfa AF: 0.102 Hom.: 220

Bravo AF: 0.114

Asia WGS AF: 0.328 AC: 1137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.63
DANN	Benign	0.67
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs17869240; hg19: chr7-90195747;