rs10487120

Variant names:

• chr7-90524639-G-A
• rs10487120
• ENST00000449528.5:c.-177+30209G>A

Variant summary

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

The ENST00000449528.5(CDK14):​c.-177+30209G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0415 in 152,158 control chromosomes in the GnomAD database, including 287 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 0.042 (287 hom., cov: 32)
• Consequence: CDK14 ENST00000449528.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.758
• Publications: 0 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.121 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CDK14	ENST00000449528.5	c.-177+30209G>A		intron_variant	Intron 3 of 7	1		ENSP00000393616.1

Frequencies

GnomAD3 genomes AF: 0.0415 AC: 6307 AN: 152038 Hom.: 287 Cov.: 32

Gnomad AFR AF: 0.0883

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0650

Gnomad ASJ AF: 0.00403

Gnomad EAS AF: 0.129

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.0262

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00182

Gnomad OTH AF: 0.0272

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

GnomAD4 genome AF: 0.0415 AC: 6318 AN: 152158 Hom.: 287 Cov.: 32 AF XY: 0.0438 AC XY: 3258 AN XY: 74354

African (AFR) AF: 0.0884 AC: 3671 AN: 41504

American (AMR) AF: 0.0650 AC: 992 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00403 AC: 14 AN: 3470

East Asian (EAS) AF: 0.129 AC: 668 AN: 5178

South Asian (SAS) AF: 0.106 AC: 512 AN: 4816

European-Finnish (FIN) AF: 0.0262 AC: 277 AN: 10592

Middle Eastern (MID) AF: 0.0136 AC: 4 AN: 294

European-Non Finnish (NFE) AF: 0.00182 AC: 124 AN: 68006

Other (OTH) AF: 0.0265 AC: 56 AN: 2114

Alfa AF: 0.0258 Hom.: 89

Bravo AF: 0.0446

Asia WGS AF: 0.108 AC: 376 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	6.5
DANN	Benign	0.48
PhyloP100		0.76

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs10487120; hg19: chr7-90153953;