20-63940064-AG-A

Position:

• chr20-63940064-AG-A

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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

• Frequency:
  • Genomes: 𝑓 0.50 (13919 hom., cov: 0)
  • Exomes 𝑓: 0.41 (1848 hom.)
  • Failed GnomAD Quality Control
• Consequence: UCKL1 NM_017859.4 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.715

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 20-63940064-AG-A is Benign according to our data. Variant chr20-63940064-AG-A is described in ClinVar as [Benign]. Clinvar id is 769112.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UCKL1	NM_017859.4	c.1568-10delC		intron_variant		ENST00000354216.11	NP_060329.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UCKL1	ENST00000354216.11	c.1568-10delC		intron_variant		1	NM_017859.4	ENSP00000346155.6
UCKL1	ENST00000369908.9	c.1523-10delC		intron_variant		2		ENSP00000358924.5
UCKL1	ENST00000358711.7	c.*357-10delC		intron_variant		2		ENSP00000351546.3
UCKL1	ENST00000632800.1	n.*32delC		downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.497 AC: 60343 AN: 121528 Hom.: 13906 Cov.: 0

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.530

Gnomad AMR AF: 0.535

Gnomad ASJ AF: 0.440

Gnomad EAS AF: 0.731

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.420

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.510

GnomAD3 exomes AF: 0.449 AC: 89665 AN: 199886 Hom.: 624 AF XY: 0.448 AC XY: 49403 AN XY: 110212

Gnomad AFR exome AF: 0.466

Gnomad AMR exome AF: 0.471

Gnomad ASJ exome AF: 0.446

Gnomad EAS exome AF: 0.493

Gnomad SAS exome AF: 0.456

Gnomad FIN exome AF: 0.393

Gnomad NFE exome AF: 0.438

Gnomad OTH exome AF: 0.444

GnomAD4 exome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.410 AC: 552058 AN: 1345282 Hom.: 1848 Cov.: 0 AF XY: 0.412 AC XY: 276444 AN XY: 670928

Gnomad4 AFR exome AF: 0.455

Gnomad4 AMR exome AF: 0.461

Gnomad4 ASJ exome AF: 0.426

Gnomad4 EAS exome AF: 0.485

Gnomad4 SAS exome AF: 0.442

Gnomad4 FIN exome AF: 0.385

Gnomad4 NFE exome AF: 0.402

Gnomad4 OTH exome AF: 0.419

GnomAD4 genome AF: 0.497 AC: 60385 AN: 121600 Hom.: 13919 Cov.: 0 AF XY: 0.500 AC XY: 29091 AN XY: 58198

Gnomad4 AFR AF: 0.605

Gnomad4 AMR AF: 0.535

Gnomad4 ASJ AF: 0.440

Gnomad4 EAS AF: 0.731

Gnomad4 SAS AF: 0.470

Gnomad4 FIN AF: 0.420

Gnomad4 NFE AF: 0.423

Gnomad4 OTH AF: 0.508

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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

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

Other links and lift over

dbSNP: rs35264801; hg19: chr20-62571417;