rs10488004

chr7-91128921-A-Gchr7-91128921-A-T

Variant summary

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

The NM_001287135.2(CDK14):c.*28+10713A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.565 in 152,046 control chromosomes in the GnomAD database, including 27,855 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 (27855 hom., cov: 32)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CDK14	NM_001287135.2	c.*28+10713A>G		intron_variant		ENST00000380050.8
CDK14	NM_001287136.1	c.*28+10713A>G		intron_variant
CDK14	NM_001287137.1	c.*28+10713A>G		intron_variant
CDK14	NM_012395.3	c.*28+10713A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CDK14	ENST00000380050.8	c.*28+10713A>G		intron_variant		1	NM_001287135.2	P4
CDK14	ENST00000265741.7	c.*28+10713A>G		intron_variant		1
CDK14	ENST00000406263.5	c.*28+10713A>G		intron_variant		1		A1
CDK14	ENST00000436577.3	c.*28+10713A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.565 AC: 85879 AN: 151928 Hom.: 27857 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.871

Gnomad AMR AF: 0.541

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.468

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.720

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.746

Gnomad OTH AF: 0.580

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

GnomAD4 genome AF: 0.565 AC: 85888 AN: 152046 Hom.: 27855 Cov.: 32 AF XY: 0.562 AC XY: 41794 AN XY: 74314

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.541

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.468

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.720

Gnomad4 NFE AF: 0.746

Gnomad4 OTH AF: 0.575

Alfa AF: 0.707 Hom.: 84369

Bravo AF: 0.541

Asia WGS AF: 0.474 AC: 1643 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	0.13
Dann	Benign	0.58

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: rs10488004; hg19: chr7-90758236;