rs73147065

Positions:

• chr20-63942653-A-C
• chr20-63942653-A-G
• chr20-63942653-A-T

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The NM_017859.4(UCKL1):​c.923+1000T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00733 in 510,766 control chromosomes in the GnomAD database, including 35 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.0064 (6 hom., cov: 32)
  • Exomes 𝑓: 0.0077 (29 hom.)
• Consequence: UCKL1 NM_017859.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.121

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]

MIR647 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS2: High Homozygotes in GnomAd4 at 6 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UCKL1	NM_017859.4	c.923+1000T>G		intron_variant		ENST00000354216.11	NP_060329.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UCKL1	ENST00000354216.11	c.923+1000T>G		intron_variant		1	NM_017859.4	ENSP00000346155.6

Frequencies

GnomAD3 genomes AF: 0.00643 AC: 976 AN: 151754 Hom.: 6 Cov.: 32

Gnomad AFR AF: 0.00194

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00269

Gnomad ASJ AF: 0.00663

Gnomad EAS AF: 0.000194

Gnomad SAS AF: 0.00871

Gnomad FIN AF: 0.00427

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0108

Gnomad OTH AF: 0.00383

GnomAD3 exomes AF: 0.00676 AC: 1357 AN: 200626 Hom.: 11 AF XY: 0.00721 AC XY: 784 AN XY: 108732

Gnomad AFR exome AF: 0.00170

Gnomad AMR exome AF: 0.00173

Gnomad ASJ exome AF: 0.00839

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00689

Gnomad FIN exome AF: 0.00606

Gnomad NFE exome AF: 0.0103

Gnomad OTH exome AF: 0.00765

GnomAD4 exome AF: 0.00771 AC: 2766 AN: 358894 Hom.: 29 Cov.: 4 AF XY: 0.00784 AC XY: 1560 AN XY: 198962

Gnomad4 AFR exome AF: 0.00155

Gnomad4 AMR exome AF: 0.00187

Gnomad4 ASJ exome AF: 0.00814

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.00711

Gnomad4 FIN exome AF: 0.00538

Gnomad4 NFE exome AF: 0.0101

Gnomad4 OTH exome AF: 0.00689

GnomAD4 genome AF: 0.00643 AC: 976 AN: 151872 Hom.: 6 Cov.: 32 AF XY: 0.00605 AC XY: 449 AN XY: 74206

Gnomad4 AFR AF: 0.00193

Gnomad4 AMR AF: 0.00269

Gnomad4 ASJ AF: 0.00663

Gnomad4 EAS AF: 0.000194

Gnomad4 SAS AF: 0.00872

Gnomad4 FIN AF: 0.00427

Gnomad4 NFE AF: 0.0108

Gnomad4 OTH AF: 0.00379

Alfa AF: 0.00483 Hom.: 348

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.76

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		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: rs73147065; hg19: chr20-62574006;