rs2275293

Positions:

• chr20-63945066-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_017859.4(UCKL1):​c.655-332T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0779 in 152,278 control chromosomes in the GnomAD database, including 547 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 0.078 (547 hom., cov: 33)
• Consequence: UCKL1 NM_017859.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.68

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0787 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UCKL1	NM_017859.4	c.655-332T>C		intron_variant		ENST00000354216.11	NP_060329.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UCKL1	ENST00000354216.11	c.655-332T>C		intron_variant		1	NM_017859.4	ENSP00000346155
UCKL1	ENST00000358711.7	c.655-332T>C		intron_variant		2		ENSP00000351546
UCKL1	ENST00000369908.9	c.610-332T>C		intron_variant		2		ENSP00000358924	P1
UCKL1	ENST00000632800.1	n.542-332T>C		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.0778 AC: 11843 AN: 152160 Hom.: 540 Cov.: 33

Gnomad AFR AF: 0.0753

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.0484

Gnomad ASJ AF: 0.0435

Gnomad EAS AF: 0.0558

Gnomad SAS AF: 0.0377

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0805

Gnomad OTH AF: 0.0694

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0779 AC: 11859 AN: 152278 Hom.: 547 Cov.: 33 AF XY: 0.0803 AC XY: 5983 AN XY: 74466

Gnomad4 AFR AF: 0.0755

Gnomad4 AMR AF: 0.0482

Gnomad4 ASJ AF: 0.0435

Gnomad4 EAS AF: 0.0553

Gnomad4 SAS AF: 0.0373

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.0805

Gnomad4 OTH AF: 0.0739

Alfa AF: 0.0736 Hom.: 647

Bravo AF: 0.0675

Asia WGS AF: 0.0530 AC: 182 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.18
DANN	Benign	0.35

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: rs2275293; hg19: chr20-62576419;