20-63940064-AGGGGGGGG-AGGGGGGGGGG

Variant names:

• chr20-63940064-A-AGG
• rs35264801
• NM_017859.4:c.1568-11_1568-10dupCC

Variant summary

Our verdict is Uncertain significance. Variant got 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
• Clinical Significance: Not reported in ClinVar
• 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 Uncertain_significance. Variant got 0 ACMG points.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UCKL1	NM_017859.4	c.1568-11_1568-10dupCC		intron_variant	Intron 14 of 14	ENST00000354216.11	NP_060329.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UCKL1	ENST00000354216.11	c.1568-10_1568-9insCC		intron_variant	Intron 14 of 14	1	NM_017859.4	ENSP00000346155.6
UCKL1	ENST00000369908.9	c.1523-10_1523-9insCC		intron_variant	Intron 14 of 14	2		ENSP00000358924.5
UCKL1	ENST00000358711.7	c.*357-10_*357-9insCC		intron_variant	Intron 12 of 12	2		ENSP00000351546.3
UCKL1	ENST00000632800.1	n.*32_*33insCC		downstream_gene_variant		5

Frequencies

GnomAD3 genomes AF: 0.00154 AC: 188 AN: 121820 Hom.: 0 Cov.: 0

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

GnomAD3 exomes AF: 0.000175 AC: 35 AN: 199886 Hom.: 0 AF XY: 0.000154 AC XY: 17 AN XY: 110212

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 SAS exome AF: 0.000190

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.: 0 Cov.: 0 AF XY: 0.000946 AC XY: 654 AN XY: 691426

Gnomad4 AFR exome AF: 0.00105

Gnomad4 AMR exome AF: 0.000465

Gnomad4 ASJ exome AF: 0.000280

Gnomad4 EAS exome AF: 0.00418

Gnomad4 SAS exome AF: 0.000348

Gnomad4 FIN exome AF: 0.000219

Gnomad4 NFE exome AF: 0.00110

Gnomad4 OTH exome AF: 0.000990

GnomAD4 genome AF: 0.00155 AC: 189 AN: 121890 Hom.: 0 Cov.: 0 AF XY: 0.00137 AC XY: 80 AN XY: 58362

Gnomad4 AFR AF: 0.00184

Gnomad4 AMR AF: 0.000984

Gnomad4 ASJ AF: 0.000679

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.00179

Gnomad4 FIN AF: 0.000140

Gnomad4 NFE AF: 0.00168

Gnomad4 OTH AF: 0.000597

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Splicing

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;