8-116785633-A-G

Variant names:

• chr8-116785633-A-G
• rs7837208
• ENST00000517820.1:c.188+18842A>G

Variant summary

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

The ENST00000517820.1(UTP23):​c.188+18842A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.816 in 152,200 control chromosomes in the GnomAD database, including 52,031 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 0.82 (52031 hom., cov: 33)
• Consequence: UTP23 ENST00000517820.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89
• 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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517820.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTP23	ENST00000517820.1	TSL:3	c.188+18842A>G		intron	N/A	ENSP00000427767.1
	UTP23	ENST00000520733.5	TSL:3	c.45+15267A>G		intron	N/A	ENSP00000429384.1
	UTP23	ENST00000521071.1	TSL:2	n.*83-870A>G		intron	N/A	ENSP00000430029.1

Frequencies

GnomAD3 genomes AF: 0.816 AC: 124049 AN: 152082 Hom.: 52010 Cov.: 33

Gnomad AFR AF: 0.598

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.842

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.846

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.861

Gnomad NFE AF: 0.902

Gnomad OTH AF: 0.842

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

GnomAD4 genome AF: 0.816 AC: 124124 AN: 152200 Hom.: 52031 Cov.: 33 AF XY: 0.818 AC XY: 60896 AN XY: 74418

African (AFR) AF: 0.598 AC: 24792 AN: 41474

American (AMR) AF: 0.893 AC: 13662 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.842 AC: 2923 AN: 3470

East Asian (EAS) AF: 0.979 AC: 5073 AN: 5184

South Asian (SAS) AF: 0.846 AC: 4086 AN: 4832

European-Finnish (FIN) AF: 0.886 AC: 9395 AN: 10606

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.902 AC: 61364 AN: 68024

Other (OTH) AF: 0.841 AC: 1776 AN: 2112

Alfa AF: 0.879 Hom.: 28229

Bravo AF: 0.809

Asia WGS AF: 0.866 AC: 3010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.17
DANN	Benign	0.63
PhyloP100		-1.9
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: rs7837208; hg19: chr8-117797872;