7-90917449-A-G

Position:

• chr7-90917449-A-G

Variant summary

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

The NM_001287135.2(CDK14):​c.703-152A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 590,962 control chromosomes in the GnomAD database, including 90,852 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 0.56 (24500 hom., cov: 33)
  • Exomes 𝑓: 0.54 (66352 hom.)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640

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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDK14	NM_001287135.2	c.703-152A>G		intron_variant		ENST00000380050.8	NP_001274064.1
CDK14	NM_001287136.1	c.565-152A>G		intron_variant			NP_001274065.1
CDK14	NM_001287137.1	c.316-152A>G		intron_variant			NP_001274066.1
CDK14	NM_012395.3	c.649-152A>G		intron_variant			NP_036527.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000380050.8	c.703-152A>G		intron_variant		1	NM_001287135.2	ENSP00000369390	P4

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85545 AN: 151960 Hom.: 24485 Cov.: 33

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.560

GnomAD4 exome AF: 0.543 AC: 238465 AN: 438882 Hom.: 66352 AF XY: 0.544 AC XY: 124548 AN XY: 229068

Gnomad4 AFR exome AF: 0.596

Gnomad4 AMR exome AF: 0.514

Gnomad4 ASJ exome AF: 0.511

Gnomad4 EAS exome AF: 0.691

Gnomad4 SAS exome AF: 0.532

Gnomad4 FIN exome AF: 0.681

Gnomad4 NFE exome AF: 0.517

Gnomad4 OTH exome AF: 0.539

GnomAD4 genome AF: 0.563 AC: 85604 AN: 152080 Hom.: 24500 Cov.: 33 AF XY: 0.570 AC XY: 42340 AN XY: 74332

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.533

Gnomad4 ASJ AF: 0.510

Gnomad4 EAS AF: 0.703

Gnomad4 SAS AF: 0.560

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.562

Alfa AF: 0.528 Hom.: 27769

Bravo AF: 0.552

Asia WGS AF: 0.635 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.71

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: rs2286696; hg19: chr7-90546764; COSMIC: COSV56056925;