7-90917449-A-G

Variant names:

• chr7-90917449-A-G
• rs2286696
• NM_001287135.2:c.703-152A>G

Variant summary

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

The NM_001287135.2(CDK14):​c.703-152A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.548 in 590,962 control chromosomes in the GnomAD database, including 90,852 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 0.56 (24500 hom., cov: 33)
  • Exomes 𝑓: 0.54 (66352 hom.)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 3 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=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.684 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK14	NM_001287135.2	MANE Select	c.703-152A>G		intron	N/A	NP_001274064.1	O94921-1
	CDK14	NM_012395.3		c.649-152A>G		intron	N/A	NP_036527.1	O94921-2
	CDK14	NM_001287136.1		c.565-152A>G		intron	N/A	NP_001274065.1	O94921-3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CDK14	ENST00000380050.8	TSL:1 MANE Select	c.703-152A>G		intron	N/A	ENSP00000369390.3	O94921-1
	CDK14	ENST00000265741.7	TSL:1	c.649-152A>G		intron	N/A	ENSP00000265741.3	O94921-2
	CDK14	ENST00000406263.5	TSL:1	c.565-152A>G		intron	N/A	ENSP00000385034.1	O94921-3

Frequencies

GnomAD3 genomes AF: 0.563 AC: 85545 AN: 151960 Hom.: 24485 Cov.: 33

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.342

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.510

Gnomad EAS AF: 0.703

Gnomad SAS AF: 0.561

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.437

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.560

GnomAD4 exome AF: 0.543 AC: 238465 AN: 438882 Hom.: 66352 AF XY: 0.544 AC XY: 124548 AN XY: 229068

African (AFR) AF: 0.596 AC: 7483 AN: 12564

American (AMR) AF: 0.514 AC: 9011 AN: 17536

Ashkenazi Jewish (ASJ) AF: 0.511 AC: 5951 AN: 11648

East Asian (EAS) AF: 0.691 AC: 20061 AN: 29052

South Asian (SAS) AF: 0.532 AC: 16215 AN: 30474

European-Finnish (FIN) AF: 0.681 AC: 19635 AN: 28828

Middle Eastern (MID) AF: 0.510 AC: 869 AN: 1704

European-Non Finnish (NFE) AF: 0.517 AC: 146764 AN: 283914

Other (OTH) AF: 0.539 AC: 12476 AN: 23162

GnomAD4 genome AF: 0.563 AC: 85604 AN: 152080 Hom.: 24500 Cov.: 33 AF XY: 0.570 AC XY: 42340 AN XY: 74332

African (AFR) AF: 0.598 AC: 24813 AN: 41492

American (AMR) AF: 0.533 AC: 8135 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.510 AC: 1769 AN: 3470

East Asian (EAS) AF: 0.703 AC: 3639 AN: 5176

South Asian (SAS) AF: 0.560 AC: 2699 AN: 4818

European-Finnish (FIN) AF: 0.687 AC: 7256 AN: 10556

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35668 AN: 67976

Other (OTH) AF: 0.562 AC: 1188 AN: 2114

Alfa AF: 0.529 Hom.: 31982

Bravo AF: 0.552

Asia WGS AF: 0.635 AC: 2207 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	6.7
DANN	Benign	0.71
PhyloP100		-0.064
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: rs2286696; hg19: chr7-90546764; COSMIC: COSV56056925;