7-90819060-G-A

Variant names:

• chr7-90819060-G-A
• rs3824039
• NM_001287135.2:c.544+28408G>A

Variant summary

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

The NM_001287135.2(CDK14):​c.544+28408G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.435 in 151,794 control chromosomes in the GnomAD database, including 15,195 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 (15195 hom., cov: 31)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.476
• 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=-0.63).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.796 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001287135.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK14	NM_001287135.2	MANE Select	c.544+28408G>A		intron	N/A	NP_001274064.1
	CDK14	NM_012395.3		c.490+28408G>A		intron	N/A	NP_036527.1
	CDK14	NM_001287136.1		c.406+28408G>A		intron	N/A	NP_001274065.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK14	ENST00000380050.8	TSL:1 MANE Select	c.544+28408G>A		intron	N/A	ENSP00000369390.3
	CDK14	ENST00000265741.7	TSL:1	c.490+28408G>A		intron	N/A	ENSP00000265741.3
	CDK14	ENST00000406263.5	TSL:1	c.406+28408G>A		intron	N/A	ENSP00000385034.1

Frequencies

GnomAD3 genomes AF: 0.436 AC: 66079 AN: 151678 Hom.: 15194 Cov.: 31

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.525

Gnomad ASJ AF: 0.398

Gnomad EAS AF: 0.817

Gnomad SAS AF: 0.448

Gnomad FIN AF: 0.473

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.379

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.435 AC: 66102 AN: 151794 Hom.: 15195 Cov.: 31 AF XY: 0.442 AC XY: 32813 AN XY: 74156

African (AFR) AF: 0.444 AC: 18386 AN: 41404

American (AMR) AF: 0.526 AC: 8010 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.398 AC: 1381 AN: 3470

East Asian (EAS) AF: 0.817 AC: 4227 AN: 5174

South Asian (SAS) AF: 0.449 AC: 2162 AN: 4814

European-Finnish (FIN) AF: 0.473 AC: 4962 AN: 10494

Middle Eastern (MID) AF: 0.357 AC: 105 AN: 294

European-Non Finnish (NFE) AF: 0.379 AC: 25713 AN: 67888

Other (OTH) AF: 0.423 AC: 889 AN: 2104

Alfa AF: 0.396 Hom.: 6436

Bravo AF: 0.442

Asia WGS AF: 0.591 AC: 2050 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.63
CADD	Benign	13
DANN	Benign	0.61
PhyloP100		0.48
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: rs3824039; hg19: chr7-90448375;