Variant 20-63940064-AGG-A 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.1568-11_1568-10delCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.139 in 1,482,034 control chromosomes in the GnomAD database, including 73 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.020 ( 60 hom., cov: 0)

Exomes 𝑓: 0.15 ( 13 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-AGG-A is Benign according to our data. Variant chr20-63940064-AGG-A is described in ClinVar as [Benign]. Clinvar id is 770004.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0593 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.1568-11_1568-10delCC		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.1568-11_1568-10delCC	intron_variant	1	NM_017859.4	ENSP00000346155.6	Q9NWZ5-1
UCKL1	ENST00000369908.9 linkuse as main transcript	c.1523-11_1523-10delCC	intron_variant	2		ENSP00000358924.5	Q9NWZ5-4
UCKL1	ENST00000358711.7 linkuse as main transcript	c.357-11_357-10delCC	intron_variant	2		ENSP00000351546.3	Q9NWZ5-2
UCKL1	ENST00000632800.1 linkuse as main transcript	n.31_32delCC	downstream_gene_variant	5

Frequencies

GnomAD3 genomes

AF:

0.0199

AC:

2426

AN:

121666

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0613

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0136

Gnomad ASJ

AF:

0.00102

Gnomad EAS

AF:

0.00982

Gnomad SAS

AF:

0.00562

Gnomad FIN

AF:

0.00748

Gnomad MID

AF:

0.00794

Gnomad NFE

AF:

0.00223

Gnomad OTH

AF:

0.0163

GnomAD3 exomes

AF:

0.218

AC:

43636

AN:

199886

Hom.:

AF XY:

0.216

AC XY:

23767

AN XY:

110212

show subpopulations

Gnomad AFR exome

AF:

0.327

Gnomad AMR exome

AF:

0.266

Gnomad ASJ exome

AF:

0.189

Gnomad EAS exome

AF:

0.351

Gnomad SAS exome

AF:

0.194

Gnomad FIN exome

AF:

0.165

Gnomad NFE exome

AF:

0.184

Gnomad OTH exome

AF:

0.183

GnomAD4 exome

AF:

0.150

AC:

204284

AN:

1360302

Hom.:

AF XY:

0.150

AC XY:

101713

AN XY:

678216

show subpopulations

Gnomad4 AFR exome

AF:

0.283

Gnomad4 AMR exome

AF:

0.243

Gnomad4 ASJ exome

AF:

0.154

Gnomad4 EAS exome

AF:

0.313

Gnomad4 SAS exome

AF:

0.137

Gnomad4 FIN exome

AF:

0.128

Gnomad4 NFE exome

AF:

0.138

Gnomad4 OTH exome

AF:

0.159

GnomAD4 genome

AF:

0.0200

AC:

2439

AN:

121732

Hom.:

Cov.:

AF XY:

0.0197

AC XY:

1146

AN XY:

58270

show subpopulations

Gnomad4 AFR

AF:

0.0616

Gnomad4 AMR

AF:

0.0137

Gnomad4 ASJ

AF:

0.00102

Gnomad4 EAS

AF:

0.00985

Gnomad4 SAS

AF:

0.00537

Gnomad4 FIN

AF:

0.00748

Gnomad4 NFE

AF:

0.00223

Gnomad4 OTH

AF:

0.0162

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)

0.0

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

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