Genetic Variant NM_017859.4:c.1568-11_1568-10dupCC (chr20-63940064-A-AGG) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_017859.4(UCKL1):c.1568-11_1568-10dupCC variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0016 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0011 ( 0 hom. )

Consequence

UCKL1
NM_017859.4 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.715

Publications

2 publications found

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 was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_017859.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UCKL1	NM_017859.4	MANE Select	c.1568-11_1568-10dupCC	intron	N/A	NP_060329.2	Q9NWZ5-1
UCKL1	NM_001353475.2		c.1571-11_1571-10dupCC	intron	N/A	NP_001340404.1
UCKL1	NM_001353476.2		c.1568-11_1568-10dupCC	intron	N/A	NP_001340405.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
UCKL1	ENST00000354216.11	TSL:1 MANE Select	c.1568-10_1568-9insCC	intron	N/A	ENSP00000346155.6	Q9NWZ5-1
UCKL1	ENST00000883271.1		c.1598-10_1598-9insCC	intron	N/A	ENSP00000553330.1
UCKL1	ENST00000969434.1		c.1595-10_1595-9insCC	intron	N/A	ENSP00000639493.1

Frequencies

GnomAD3 genomes

AF:

0.00154

AC:

188

AN:

121820

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00182

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000985

Gnomad ASJ

AF:

0.000679

Gnomad EAS

AF:

0.00270

Gnomad SAS

AF:

0.00178

Gnomad FIN

AF:

0.000140

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00168

Gnomad OTH

AF:

0.000603

GnomAD2 exomes

AF:

0.000175

AC:

AN:

199886

AF XY:

0.000154

show subpopulations

Gnomad AFR exome

AF:

0.000166

Gnomad AMR exome

AF:

0.000299

Gnomad ASJ exome

AF:

0.000363

Gnomad EAS exome

AF:

0.000435

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000798

Gnomad OTH exome

AF:

0.000397

GnomAD4 exome

AF:

0.00107

AC:

1487

AN:

1387106

Hom.:

Cov.:

AF XY:

0.000946

AC XY:

654

AN XY:

691426

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.00105

AC:

AN:

32274

American (AMR)

AF:

0.000465

AC:

AN:

42974

Ashkenazi Jewish (ASJ)

AF:

0.000280

AC:

AN:

24958

East Asian (EAS)

AF:

0.00418

AC:

160

AN:

38290

South Asian (SAS)

AF:

0.000348

AC:

AN:

83406

European-Finnish (FIN)

AF:

0.000219

AC:

AN:

45746

Middle Eastern (MID)

AF:

0.000566

AC:

AN:

5298

European-Non Finnish (NFE)

AF:

0.00110

AC:

1167

AN:

1056610

Other (OTH)

AF:

0.000990

AC:

AN:

57550

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.284

Heterozygous variant carriers

129

258

386

515

644

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

112

168

224

280

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.00155

AC:

189

AN:

121890

Hom.:

Cov.:

AF XY:

0.00137

AC XY:

AN XY:

58362

show subpopulations

African (AFR)

AF:

0.00184

AC:

AN:

32548

American (AMR)

AF:

0.000984

AC:

AN:

12200

Ashkenazi Jewish (ASJ)

AF:

0.000679

AC:

AN:

2944

East Asian (EAS)

AF:

0.00271

AC:

AN:

4060

South Asian (SAS)

AF:

0.00179

AC:

AN:

3352

European-Finnish (FIN)

AF:

0.000140

AC:

AN:

7158

Middle Eastern (MID)

AF:

0.00

AC:

AN:

234

European-Non Finnish (NFE)

AF:

0.00168

AC:

AN:

57006

Other (OTH)

AF:

0.000597

AC:

AN:

1674

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.440

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.000473

Hom.:

411

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.71

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over