8-116789909-T-C

Variant names:

• chr8-116789909-T-C
• rs6983626
• ENST00000517820.1:c.188+23118T>C

Variant summary

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

The ENST00000517820.1(UTP23):​c.188+23118T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.818 in 152,182 control chromosomes in the GnomAD database, including 52,319 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 (52319 hom., cov: 32)
• Consequence: UTP23 ENST00000517820.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830
• Publications: 12 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	UTP23	ENST00000517820.1	TSL:3	c.188+23118T>C		intron	N/A	ENSP00000427767.1
	UTP23	ENST00000520733.5	TSL:3	c.45+19543T>C		intron	N/A	ENSP00000429384.1
	UTP23	ENST00000521703.5	TSL:2	n.*92+3260T>C		intron	N/A	ENSP00000428455.1

Frequencies

GnomAD3 genomes AF: 0.818 AC: 124424 AN: 152062 Hom.: 52299 Cov.: 32

Gnomad AFR AF: 0.602

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.896

Gnomad ASJ AF: 0.882

Gnomad EAS AF: 0.979

Gnomad SAS AF: 0.841

Gnomad FIN AF: 0.886

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.903

Gnomad OTH AF: 0.847

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

GnomAD4 genome AF: 0.818 AC: 124498 AN: 152182 Hom.: 52319 Cov.: 32 AF XY: 0.821 AC XY: 61076 AN XY: 74394

African (AFR) AF: 0.603 AC: 24999 AN: 41486

American (AMR) AF: 0.896 AC: 13687 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.882 AC: 3062 AN: 3472

East Asian (EAS) AF: 0.979 AC: 5079 AN: 5188

South Asian (SAS) AF: 0.840 AC: 4055 AN: 4826

European-Finnish (FIN) AF: 0.886 AC: 9397 AN: 10610

Middle Eastern (MID) AF: 0.871 AC: 256 AN: 294

European-Non Finnish (NFE) AF: 0.903 AC: 61379 AN: 68004

Other (OTH) AF: 0.845 AC: 1784 AN: 2110

Alfa AF: 0.884 Hom.: 47553

Bravo AF: 0.813

Asia WGS AF: 0.864 AC: 3001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.64
PhyloP100		-0.083
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: rs6983626; hg19: chr8-117802148;