NM_001287135.2:c.124-55301A>G

Variant names:

• chr7-90671266-A-G
• rs10271241
• NM_001287135.2:c.124-55301A>G

Variant summary

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

The NM_001287135.2(CDK14):​c.124-55301A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.308 in 151,690 control chromosomes in the GnomAD database, including 8,029 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 0.31 (8029 hom., cov: 30)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.815

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 = 0.655 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDK14	NM_001287135.2	c.124-55301A>G		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.124-55301A>G		intron_variant	Intron 2 of 14	1	NM_001287135.2	ENSP00000369390.3

Frequencies

GnomAD3 genomes AF: 0.308 AC: 46618 AN: 151578 Hom.: 8019 Cov.: 30

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.187

Gnomad AMR AF: 0.408

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.383

Gnomad FIN AF: 0.251

Gnomad MID AF: 0.283

Gnomad NFE AF: 0.232

Gnomad OTH AF: 0.308

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

GnomAD4 genome AF: 0.308 AC: 46656 AN: 151690 Hom.: 8029 Cov.: 30 AF XY: 0.313 AC XY: 23209 AN XY: 74086

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.673

Gnomad4 SAS AF: 0.383

Gnomad4 FIN AF: 0.251

Gnomad4 NFE AF: 0.232

Gnomad4 OTH AF: 0.307

Alfa AF: 0.283 Hom.: 2213

Bravo AF: 0.326

Asia WGS AF: 0.493 AC: 1714 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	5.4
DANN	Benign	0.46

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: rs10271241; hg19: chr7-90300580;