rs12704555

Positions:

• chr7-90633909-G-A
• chr7-90633909-G-T

Variant summary

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

The NM_001287135.2(CDK14):​c.123+29660G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.309 in 151,834 control chromosomes in the GnomAD database, including 8,169 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 (8169 hom., cov: 32)
• Consequence: CDK14 NM_001287135.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
CDK14	NM_001287135.2	c.123+29660G>A		intron_variant		ENST00000380050.8	NP_001274064.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000380050.8	c.123+29660G>A		intron_variant		1	NM_001287135.2	ENSP00000369390	P4

Frequencies

GnomAD3 genomes AF: 0.309 AC: 46918 AN: 151716 Hom.: 8156 Cov.: 32

Gnomad AFR AF: 0.379

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.407

Gnomad ASJ AF: 0.250

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.380

Gnomad FIN AF: 0.250

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.305

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

GnomAD4 genome AF: 0.309 AC: 46967 AN: 151834 Hom.: 8169 Cov.: 32 AF XY: 0.316 AC XY: 23455 AN XY: 74198

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.408

Gnomad4 ASJ AF: 0.250

Gnomad4 EAS AF: 0.675

Gnomad4 SAS AF: 0.380

Gnomad4 FIN AF: 0.250

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.304

Alfa AF: 0.268 Hom.: 771

Bravo AF: 0.328

Asia WGS AF: 0.492 AC: 1700 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	1.8
DANN	Benign	0.53

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: rs12704555; hg19: chr7-90263223;