rs813379

Positions:

• chr7-91152672-G-A
• chr7-91152672-G-C

Variant summary

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

The NM_001287135.2(CDK14):​c.*28+34464G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.95 in 152,294 control chromosomes in the GnomAD database, including 68,684 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 0.95 (68684 hom., cov: 33)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00200

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=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDK14	NM_001287135.2	c.*28+34464G>A		intron_variant		ENST00000380050.8
CDK14	NM_001287136.1	c.*28+34464G>A		intron_variant
CDK14	NM_001287137.1	c.*28+34464G>A		intron_variant
CDK14	NM_012395.3	c.*28+34464G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK14	ENST00000380050.8	c.*28+34464G>A		intron_variant		1	NM_001287135.2	P4
CDK14	ENST00000265741.7	c.*28+34464G>A		intron_variant		1
CDK14	ENST00000406263.5	c.*28+34464G>A		intron_variant		1		A1
CDK14	ENST00000436577.3	c.*28+34464G>A		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.950 AC: 144495 AN: 152176 Hom.: 68630 Cov.: 33

Gnomad AFR AF: 0.961

Gnomad AMI AF: 0.827

Gnomad AMR AF: 0.960

Gnomad ASJ AF: 0.896

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.890

Gnomad FIN AF: 0.951

Gnomad MID AF: 0.956

Gnomad NFE AF: 0.946

Gnomad OTH AF: 0.944

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

GnomAD4 genome AF: 0.950 AC: 144608 AN: 152294 Hom.: 68684 Cov.: 33 AF XY: 0.950 AC XY: 70711 AN XY: 74468

Gnomad4 AFR AF: 0.961

Gnomad4 AMR AF: 0.960

Gnomad4 ASJ AF: 0.896

Gnomad4 EAS AF: 0.991

Gnomad4 SAS AF: 0.889

Gnomad4 FIN AF: 0.951

Gnomad4 NFE AF: 0.945

Gnomad4 OTH AF: 0.945

Alfa AF: 0.941 Hom.: 88631

Bravo AF: 0.952

Asia WGS AF: 0.954 AC: 3317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.5
DANN	Benign	0.73

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: rs813379; hg19: chr7-90781987;