20-63940064-AGGG-A

Variant names:

• chr20-63940064-AGGG-A
• rs35264801
• NM_017859.4:c.1568-12_1568-10delCCC

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 0.715
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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 VariationId 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.

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UCKL1	NM_017859.4	MANE Select	c.1568-12_1568-10delCCC		intron	N/A	NP_060329.2	Q9NWZ5-1
	UCKL1	NM_001353475.2		c.1571-12_1571-10delCCC		intron	N/A	NP_001340404.1
	UCKL1	NM_001353476.2		c.1568-12_1568-10delCCC		intron	N/A	NP_001340405.1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UCKL1	ENST00000354216.11	TSL:1 MANE Select	c.1568-12_1568-10delCCC		intron	N/A	ENSP00000346155.6	Q9NWZ5-1
	UCKL1	ENST00000883271.1		c.1598-12_1598-10delCCC		intron	N/A	ENSP00000553330.1
	UCKL1	ENST00000969434.1		c.1595-12_1595-10delCCC		intron	N/A	ENSP00000639493.1

Frequencies

GnomAD3 genomes AF: 0.0700 AC: 8534 AN: 121858 Hom.: 424 Cov.: 0

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

GnomAD2 exomes AF: 0.0614 AC: 12279 AN: 199886 AF XY: 0.0607

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 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

African (AFR) AF: 0.0198 AC: 635 AN: 32108

American (AMR) AF: 0.0299 AC: 1284 AN: 42892

Ashkenazi Jewish (ASJ) AF: 0.0452 AC: 1127 AN: 24950

East Asian (EAS) AF: 0.00385 AC: 148 AN: 38442

South Asian (SAS) AF: 0.0408 AC: 3405 AN: 83366

European-Finnish (FIN) AF: 0.173 AC: 7901 AN: 45664

Middle Eastern (MID) AF: 0.0285 AC: 151 AN: 5290

European-Non Finnish (NFE) AF: 0.0776 AC: 81874 AN: 1055480

Other (OTH) AF: 0.0659 AC: 3790 AN: 57514

GnomAD4 genome AF: 0.0700 AC: 8539 AN: 121928 Hom.: 426 Cov.: 0 AF XY: 0.0738 AC XY: 4309 AN XY: 58390

African (AFR) AF: 0.0187 AC: 608 AN: 32558

American (AMR) AF: 0.0485 AC: 592 AN: 12202

Ashkenazi Jewish (ASJ) AF: 0.0543 AC: 160 AN: 2948

East Asian (EAS) AF: 0.00394 AC: 16 AN: 4062

South Asian (SAS) AF: 0.0462 AC: 155 AN: 3354

European-Finnish (FIN) AF: 0.209 AC: 1501 AN: 7166

Middle Eastern (MID) AF: 0.0214 AC: 5 AN: 234

European-Non Finnish (NFE) AF: 0.0937 AC: 5345 AN: 57016

Other (OTH) AF: 0.0651 AC: 109 AN: 1674

Alfa AF: 0.0781 Hom.: 411

ClinVar

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		0.71
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs35264801; hg19: chr20-62571417;