7-90865604-C-T

Variant names:

• chr7-90865604-C-T
• rs758706
• NM_001287135.2:c.639+2335C>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.639+2335C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 151,876 control chromosomes in the GnomAD database, including 13,623 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 0.41 (13623 hom., cov: 32)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855
• Publications: 4 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CDK14	NM_001287135.2	c.639+2335C>T		intron_variant	Intron 6 of 14	ENST00000380050.8	NP_001274064.1
CDK14	NM_012395.3	c.585+2335C>T		intron_variant	Intron 5 of 13		NP_036527.1
CDK14	NM_001287136.1	c.501+2335C>T		intron_variant	Intron 5 of 13		NP_001274065.1
CDK14	NM_001287137.1	c.252+2335C>T		intron_variant	Intron 4 of 12		NP_001274066.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000380050.8	c.639+2335C>T		intron_variant	Intron 6 of 14	1	NM_001287135.2	ENSP00000369390.3

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62996 AN: 151758 Hom.: 13621 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.407

Gnomad EAS AF: 0.663

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.354

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.427

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

GnomAD4 genome AF: 0.415 AC: 63021 AN: 151876 Hom.: 13623 Cov.: 32 AF XY: 0.422 AC XY: 31321 AN XY: 74218

African (AFR) AF: 0.352 AC: 14557 AN: 41396

American (AMR) AF: 0.451 AC: 6881 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.407 AC: 1411 AN: 3464

East Asian (EAS) AF: 0.663 AC: 3434 AN: 5176

South Asian (SAS) AF: 0.448 AC: 2158 AN: 4818

European-Finnish (FIN) AF: 0.542 AC: 5707 AN: 10528

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

European-Non Finnish (NFE) AF: 0.407 AC: 27639 AN: 67922

Other (OTH) AF: 0.424 AC: 895 AN: 2112

Alfa AF: 0.409 Hom.: 43488

Bravo AF: 0.405

Asia WGS AF: 0.499 AC: 1732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.20
DANN	Benign	0.42
PhyloP100		-0.85
Mutation Taster		=97/3	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: rs758706; hg19: chr7-90494919;