rs6951213

chr7-90783786-G-Achr7-90783786-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.465-6787G>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 151,908 control chromosomes in the GnomAD database, including 15,199 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 (15199 hom., cov: 32)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.365

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDK14	NM_001287135.2	c.465-6787G>A		intron_variant		ENST00000380050.8
CDK14	NM_001287136.1	c.327-6787G>A		intron_variant
CDK14	NM_001287137.1	c.78-6787G>A		intron_variant
CDK14	NM_012395.3	c.411-6787G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK14	ENST00000380050.8	c.465-6787G>A		intron_variant		1	NM_001287135.2	P4

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66112 AN: 151790 Hom.: 15198 Cov.: 32

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.818

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.354

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: 66137 AN: 151908 Hom.: 15199 Cov.: 32 AF XY: 0.443 AC XY: 32856 AN XY: 74244

Gnomad4 AFR AF: 0.444

Gnomad4 AMR AF: 0.525

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.818

Gnomad4 SAS AF: 0.448

Gnomad4 FIN AF: 0.473

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.424

Alfa AF: 0.437 Hom.: 2574

Bravo AF: 0.442

Asia WGS AF: 0.589 AC: 2047 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	3.4
Dann	Benign	0.50

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: rs6951213; hg19: chr7-90413101;