7-90756015-G-C

Variant names:

• chr7-90756015-G-C
• rs10281060
• NM_001287135.2:c.464+8240G>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001287135.2(CDK14):​c.464+8240G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.434 in 151,994 control chromosomes in the GnomAD database, including 15,182 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 0.43 (15182 hom., cov: 32)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.114
• 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=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDK14	NM_001287135.2	c.464+8240G>C		intron_variant	Intron 4 of 14	ENST00000380050.8	NP_001274064.1
CDK14	NM_012395.3	c.410+8240G>C		intron_variant	Intron 3 of 13		NP_036527.1
CDK14	NM_001287136.1	c.326+8240G>C		intron_variant	Intron 3 of 13		NP_001274065.1
CDK14	NM_001287137.1	c.77+29203G>C		intron_variant	Intron 2 of 12		NP_001274066.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000380050.8	c.464+8240G>C		intron_variant	Intron 4 of 14	1	NM_001287135.2	ENSP00000369390.3

Frequencies

GnomAD3 genomes AF: 0.435 AC: 66011 AN: 151876 Hom.: 15181 Cov.: 32

Gnomad AFR AF: 0.444

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.451

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.425

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

GnomAD4 genome AF: 0.434 AC: 66035 AN: 151994 Hom.: 15182 Cov.: 32 AF XY: 0.442 AC XY: 32839 AN XY: 74278

African (AFR) AF: 0.443 AC: 18360 AN: 41456

American (AMR) AF: 0.525 AC: 8021 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1347 AN: 3470

East Asian (EAS) AF: 0.816 AC: 4211 AN: 5158

South Asian (SAS) AF: 0.453 AC: 2181 AN: 4818

European-Finnish (FIN) AF: 0.481 AC: 5089 AN: 10570

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25571 AN: 67940

Other (OTH) AF: 0.420 AC: 886 AN: 2108

Alfa AF: 0.270 Hom.: 679

Bravo AF: 0.440

Asia WGS AF: 0.593 AC: 2058 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	2.5
DANN	Benign	0.71
PhyloP100		0.11
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs10281060; hg19: chr7-90385330;