Genetic Variant UCKL1:c.1568-12_1568-10delCCC (chr20-63940064-AGGG-A) – ACMG Classification: Benign (-10 pts)

Variant summary

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

The NM_017859.4(UCKL1):c.1568-12_1568-10delCCC variant causes a intron change involving the alteration of a non-conserved nucleotide. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.070 ( 426 hom., cov: 0)

Exomes 𝑓: 0.072 ( 4164 hom. )

Failed GnomAD Quality Control

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP6

Variant 20-63940064-AGGG-A is Benign according to our data. Variant chr20-63940064-AGGG-A is described in ClinVar as [Benign]. Clinvar id is 774359.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0916 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UCKL1	NM_017859.4 link	c.1568-12_1568-10delCCC		intron_variant	Intron 14 of 14	ENST00000354216.11	NP_060329.2	Q9NWZ5-1Q53HM1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
UCKL1	ENST00000354216.11 link	c.1568-12_1568-10delCCC	intron_variant	Intron 14 of 14	1	NM_017859.4	ENSP00000346155.6	Q9NWZ5-1
UCKL1	ENST00000369908.9 link	c.1523-12_1523-10delCCC	intron_variant	Intron 14 of 14	2		ENSP00000358924.5	Q9NWZ5-4
UCKL1	ENST00000358711.7 link	c.357-12_357-10delCCC	intron_variant	Intron 12 of 12	2		ENSP00000351546.3	Q9NWZ5-2
UCKL1	ENST00000632800.1 link	n.30_32delCCC	downstream_gene_variant		5

Frequencies

GnomAD3 genomes

AF:

0.0700

AC:

8534

AN:

121858

Hom.:

424

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0185

Gnomad AMI

AF:

0.0672

Gnomad AMR

AF:

0.0487

Gnomad ASJ

AF:

0.0543

Gnomad EAS

AF:

0.00393

Gnomad SAS

AF:

0.0462

Gnomad FIN

AF:

0.209

Gnomad MID

AF:

0.0238

Gnomad NFE

AF:

0.0938

Gnomad OTH

AF:

0.0645

GnomAD3 exomes

AF:

0.0614

AC:

12279

AN:

199886

Hom.:

612

AF XY:

0.0607

AC XY:

6691

AN XY:

110212

show subpopulations

Gnomad AFR exome

AF:

0.0179

Gnomad AMR exome

AF:

0.0283

Gnomad ASJ exome

AF:

0.0432

Gnomad EAS exome

AF:

0.00360

Gnomad SAS exome

AF:

0.0399

Gnomad FIN exome

AF:

0.187

Gnomad NFE exome

AF:

0.0768

Gnomad OTH exome

AF:

0.0641

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0724

AC:

100315

AN:

1385706

Hom.:

4164

AF XY:

0.0716

AC XY:

49484

AN XY:

690848

show subpopulations

Gnomad4 AFR exome

AF:

0.0198

Gnomad4 AMR exome

AF:

0.0299

Gnomad4 ASJ exome

AF:

0.0452

Gnomad4 EAS exome

AF:

0.00385

Gnomad4 SAS exome

AF:

0.0408

Gnomad4 FIN exome

AF:

0.173

Gnomad4 NFE exome

AF:

0.0776

Gnomad4 OTH exome

AF:

0.0659

GnomAD4 genome

AF:

0.0700

AC:

8539

AN:

121928

Hom.:

426

Cov.:

AF XY:

0.0738

AC XY:

4309

AN XY:

58390

show subpopulations

Gnomad4 AFR

AF:

0.0187

Gnomad4 AMR

AF:

0.0485

Gnomad4 ASJ

AF:

0.0543

Gnomad4 EAS

AF:

0.00394

Gnomad4 SAS

AF:

0.0462

Gnomad4 FIN

AF:

0.209

Gnomad4 NFE

AF:

0.0937

Gnomad4 OTH

AF:

0.0651

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Dec 31, 2019

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

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