7-90787863-A-G

Position:

• chr7-90787863-A-G

Variant summary

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

The NM_001287135.2(CDK14):​c.465-2710A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.436 in 151,896 control chromosomes in the GnomAD database, including 15,234 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 (15234 hom., cov: 31)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.720

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]

CDK14 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• 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/exons	MANE	Protein	UniProt
CDK14	NM_001287135.2	c.465-2710A>G		intron_variant		ENST00000380050.8	NP_001274064.1
CDK14	NM_012395.3	c.411-2710A>G		intron_variant			NP_036527.1
CDK14	NM_001287136.1	c.327-2710A>G		intron_variant			NP_001274065.1
CDK14	NM_001287137.1	c.78-2710A>G		intron_variant			NP_001274066.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000380050.8	c.465-2710A>G		intron_variant		1	NM_001287135.2	ENSP00000369390.3

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66187 AN: 151778 Hom.: 15233 Cov.: 31

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.526

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.816

Gnomad SAS AF: 0.445

Gnomad FIN AF: 0.471

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.429

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

GnomAD4 genome AF: 0.436 AC: 66211 AN: 151896 Hom.: 15234 Cov.: 31 AF XY: 0.443 AC XY: 32853 AN XY: 74214

Gnomad4 AFR AF: 0.447

Gnomad4 AMR AF: 0.526

Gnomad4 ASJ AF: 0.398

Gnomad4 EAS AF: 0.816

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.471

Gnomad4 NFE AF: 0.379

Gnomad4 OTH AF: 0.424

Alfa AF: 0.400 Hom.: 5856

Bravo AF: 0.443

Asia WGS AF: 0.589 AC: 2042 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.42
DANN	Benign	0.77

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: rs1110457; hg19: chr7-90417178;