rs73147065

Variant names:

• chr20-63942653-A-C
• rs73147065
• NM_017859.4:c.923+1000T>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 13 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]

MIR647 (HGNC:32903): (microRNA 647) microRNAs (miRNAs) are short (20-24 nt) non-coding RNAs that are involved in post-transcriptional regulation of gene expression in multicellular organisms by affecting both the stability and translation of mRNAs. miRNAs are transcribed by RNA polymerase II as part of capped and polyadenylated primary transcripts (pri-miRNAs) that can be either protein-coding or non-coding. The primary transcript is cleaved by the Drosha ribonuclease III enzyme to produce an approximately 70-nt stem-loop precursor miRNA (pre-miRNA), which is further cleaved by the cytoplasmic Dicer ribonuclease to generate the mature miRNA and antisense miRNA star (miRNA*) products. The mature miRNA is incorporated into a RNA-induced silencing complex (RISC), which recognizes target mRNAs through imperfect base pairing with the miRNA and most commonly results in translational inhibition or destabilization of the target mRNA. The RefSeq represents the predicted microRNA stem-loop. [provided by RefSeq, Sep 2009]

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

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

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.923+1000T>G		intron	N/A	NP_060329.2	Q9NWZ5-1
	UCKL1	NM_001353475.2		c.907-164T>G		intron	N/A	NP_001340404.1
	UCKL1	NM_001353476.2		c.904-164T>G		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.923+1000T>G		intron	N/A	ENSP00000346155.6	Q9NWZ5-1
	UCKL1	ENST00000883271.1		c.931-161T>G		intron	N/A	ENSP00000553330.1
	UCKL1	ENST00000969434.1		c.931-164T>G		intron	N/A	ENSP00000639493.1

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

GnomAD2 exomes AF: 0.00676 AC: 1357 AN: 200626 AF XY: 0.00721

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 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

African (AFR) AF: 0.00155 AC: 15 AN: 9650

American (AMR) AF: 0.00187 AC: 60 AN: 32160

Ashkenazi Jewish (ASJ) AF: 0.00814 AC: 89 AN: 10934

East Asian (EAS) AF: 0.00 AC: 0 AN: 10928

South Asian (SAS) AF: 0.00711 AC: 445 AN: 62592

European-Finnish (FIN) AF: 0.00538 AC: 155 AN: 28792

Middle Eastern (MID) AF: 0.00733 AC: 20 AN: 2728

European-Non Finnish (NFE) AF: 0.0101 AC: 1877 AN: 185876

Other (OTH) AF: 0.00689 AC: 105 AN: 15234

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

African (AFR) AF: 0.00193 AC: 80 AN: 41384

American (AMR) AF: 0.00269 AC: 41 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.00663 AC: 23 AN: 3468

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5154

South Asian (SAS) AF: 0.00872 AC: 42 AN: 4818

European-Finnish (FIN) AF: 0.00427 AC: 45 AN: 10546

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0108 AC: 733 AN: 67952

Other (OTH) AF: 0.00379 AC: 8 AN: 2112

Alfa AF: 0.00483 Hom.: 348

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.6
DANN	Benign	0.76
PhyloP100		-0.12
Mutation Taster		=100/0	polymorphism

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

Other links and lift over

dbSNP: rs73147065; hg19: chr20-62574006;