chr7-90630598-C-T

Variant names:

• chr7-90630598-C-T
• rs10242197
• NM_001287135.2:c.123+26349C>T

Variant summary

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

The NM_001287135.2(CDK14):​c.123+26349C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.181 in 152,026 control chromosomes in the GnomAD database, including 2,608 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 0.18 (2608 hom., cov: 32)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0310
• Publications: 6 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=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDK14	NM_001287135.2	c.123+26349C>T		intron_variant	Intron 2 of 14	ENST00000380050.8	NP_001274064.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000380050.8	c.123+26349C>T		intron_variant	Intron 2 of 14	1	NM_001287135.2	ENSP00000369390.3

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27444 AN: 151908 Hom.: 2599 Cov.: 32

Gnomad AFR AF: 0.164

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0337

Gnomad SAS AF: 0.194

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.181 AC: 27485 AN: 152026 Hom.: 2608 Cov.: 32 AF XY: 0.181 AC XY: 13440 AN XY: 74290

African (AFR) AF: 0.165 AC: 6835 AN: 41472

American (AMR) AF: 0.144 AC: 2207 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 662 AN: 3472

East Asian (EAS) AF: 0.0337 AC: 175 AN: 5186

South Asian (SAS) AF: 0.193 AC: 928 AN: 4816

European-Finnish (FIN) AF: 0.222 AC: 2336 AN: 10520

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.200 AC: 13581 AN: 67964

Other (OTH) AF: 0.193 AC: 407 AN: 2110

Alfa AF: 0.194 Hom.: 2276

Bravo AF: 0.173

Asia WGS AF: 0.161 AC: 560 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	2.3
DANN	Benign	0.78
PhyloP100		0.031
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs10242197; hg19: chr7-90259912;