Variant 20-63940064-A-AG details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_017859.4(UCKL1):c.1568-10dupC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.10 ( 868 hom., cov: 0)

Exomes 𝑓: 0.061 ( 2 hom. )

Consequence

UCKL1
NM_017859.4 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.715

Variant links:

Genes affected

UCKL1 (HGNC:15938): (uridine-cytidine kinase 1 like 1) The protein encoded by this gene is a uridine kinase. Uridine kinases catalyze the phosphorylation of uridine to uridine monophosphate. This protein has been shown to bind to Epstein-Barr nuclear antigen 3 as well as natural killer lytic-associated molecule. Ubiquitination of this protein is enhanced by the presence of natural killer lytic-associated molecule. In addition, protein levels decrease in the presence of natural killer lytic-associated molecule, suggesting that association with natural killer lytic-associated molecule results in ubiquitination and subsequent degradation of this protein. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Nov 2014]

UCKL1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 20-63940064-A-AG is Benign according to our data. Variant chr20-63940064-A-AG is described in ClinVar as [Benign]. Clinvar id is 774968.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UCKL1	NM_017859.4 linkuse as main transcript	c.1568-10dupC		intron_variant		ENST00000354216.11	NP_060329.2	Q9NWZ5-1Q53HM1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
UCKL1	ENST00000354216.11 linkuse as main transcript	c.1568-10_1568-9insC	intron_variant	1	NM_017859.4	ENSP00000346155.6	Q9NWZ5-1
UCKL1	ENST00000369908.9 linkuse as main transcript	c.1523-10_1523-9insC	intron_variant	2		ENSP00000358924.5	Q9NWZ5-4
UCKL1	ENST00000358711.7 linkuse as main transcript	c.357-10_357-9insC	intron_variant	2		ENSP00000351546.3	Q9NWZ5-2
UCKL1	ENST00000632800.1 linkuse as main transcript	n.32_33insC	downstream_gene_variant	5

Frequencies

GnomAD3 genomes

AF:

0.101

AC:

12291

AN:

121370

Hom.:

868

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0553

Gnomad AMI

AF:

0.0140

Gnomad AMR

AF:

0.105

Gnomad ASJ

AF:

0.175

Gnomad EAS

AF:

0.0145

Gnomad SAS

AF:

0.0802

Gnomad FIN

AF:

0.0559

Gnomad MID

AF:

0.0847

Gnomad NFE

AF:

0.138

Gnomad OTH

AF:

0.0912

GnomAD3 exomes

AF:

0.0216

AC:

4315

AN:

199886

Hom.:

AF XY:

0.0209

AC XY:

2304

AN XY:

110212

show subpopulations

Gnomad AFR exome

AF:

0.0135

Gnomad AMR exome

AF:

0.0280

Gnomad ASJ exome

AF:

0.0381

Gnomad EAS exome

AF:

0.00571

Gnomad SAS exome

AF:

0.0207

Gnomad FIN exome

AF:

0.00897

Gnomad NFE exome

AF:

0.0237

Gnomad OTH exome

AF:

0.0298

GnomAD4 exome

AF:

0.0608

AC:

82684

AN:

1360274

Hom.:

Cov.:

AF XY:

0.0589

AC XY:

39953

AN XY:

678188

show subpopulations

Gnomad4 AFR exome

AF:

0.0289

Gnomad4 AMR exome

AF:

0.0345

Gnomad4 ASJ exome

AF:

0.0609

Gnomad4 EAS exome

AF:

0.00935

Gnomad4 SAS exome

AF:

0.0355

Gnomad4 FIN exome

AF:

0.0257

Gnomad4 NFE exome

AF:

0.0688

Gnomad4 OTH exome

AF:

0.0550

GnomAD4 genome

AF:

0.101

AC:

12293

AN:

121440

Hom.:

868

Cov.:

AF XY:

0.0947

AC XY:

5507

AN XY:

58124

show subpopulations

Gnomad4 AFR

AF:

0.0552

Gnomad4 AMR

AF:

0.105

Gnomad4 ASJ

AF:

0.175

Gnomad4 EAS

AF:

0.0145

Gnomad4 SAS

AF:

0.0802

Gnomad4 FIN

AF:

0.0559

Gnomad4 NFE

AF:

0.138

Gnomad4 OTH

AF:

0.0904

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over