ENST00000517820.1:c.188+27139G>A

Variant names:

• chr8-116793930-G-A
• rs13250873
• ENST00000517820.1:c.188+27139G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000517820.1(UTP23):​c.188+27139G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.516 in 151,948 control chromosomes in the GnomAD database, including 24,016 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 0.52 (24016 hom., cov: 31)
• Consequence: UTP23 ENST00000517820.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994
• Publications: 5 publications found

Genes affected

UTP23 (HGNC:28224): (UTP23 small subunit processome component) Enables mRNA 3'-UTR binding activity and mRNA 5'-UTR binding activity. Predicted to be involved in rRNA processing. Predicted to act upstream of or within endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA). Predicted to be part of small-subunit processome. Predicted to be active in nucleolus. Implicated in colorectal adenocarcinoma. [provided by Alliance of Genome Resources, Apr 2022]

LOC112268030 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.681 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112268030	XR_002956724.2	n.760+7281G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTP23	ENST00000517820.1	c.188+27139G>A		intron_variant	Intron 1 of 1	3		ENSP00000427767.1
UTP23	ENST00000520733.5	c.45+23564G>A		intron_variant	Intron 1 of 1	3		ENSP00000429384.1
UTP23	ENST00000521703.5	n.*92+7281G>A		intron_variant	Intron 2 of 2	2		ENSP00000428455.1
UTP23	ENST00000524128.1	n.*92+7281G>A		intron_variant	Intron 3 of 3	3		ENSP00000430309.1

Frequencies

GnomAD3 genomes AF: 0.517 AC: 78429 AN: 151830 Hom.: 24016 Cov.: 31

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.892

Gnomad AMR AF: 0.579

Gnomad ASJ AF: 0.566

Gnomad EAS AF: 0.237

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.643

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.687

Gnomad OTH AF: 0.571

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

GnomAD4 genome AF: 0.516 AC: 78434 AN: 151948 Hom.: 24016 Cov.: 31 AF XY: 0.514 AC XY: 38196 AN XY: 74252

African (AFR) AF: 0.192 AC: 7949 AN: 41450

American (AMR) AF: 0.579 AC: 8839 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.566 AC: 1962 AN: 3468

East Asian (EAS) AF: 0.236 AC: 1214 AN: 5142

South Asian (SAS) AF: 0.592 AC: 2854 AN: 4820

European-Finnish (FIN) AF: 0.643 AC: 6778 AN: 10548

Middle Eastern (MID) AF: 0.595 AC: 175 AN: 294

European-Non Finnish (NFE) AF: 0.687 AC: 46650 AN: 67948

Other (OTH) AF: 0.572 AC: 1201 AN: 2100

Alfa AF: 0.631 Hom.: 22688

Bravo AF: 0.497

Asia WGS AF: 0.437 AC: 1520 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.9
DANN	Benign	0.58
PhyloP100		0.99
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs13250873; hg19: chr8-117806169;