rs13250873

chr8-116793930-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_002956724.2(LOC112268030):n.760+7281G>A variant causes a intron, non coding transcript 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: LOC112268030 XR_002956724.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.994

Genes affected

LOC112268030 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC112268030	XR_002956724.2	n.760+7281G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UTP23	ENST00000517820.1	c.188+27139G>A		intron_variant		3
UTP23	ENST00000520733.5	c.45+23564G>A		intron_variant		3
UTP23	ENST00000521703.5	c.*92+7281G>A		intron_variant, NMD_transcript_variant		2
UTP23	ENST00000524128.1	c.*92+7281G>A		intron_variant, NMD_transcript_variant		3

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

Gnomad4 AFR AF: 0.192

Gnomad4 AMR AF: 0.579

Gnomad4 ASJ AF: 0.566

Gnomad4 EAS AF: 0.236

Gnomad4 SAS AF: 0.592

Gnomad4 FIN AF: 0.643

Gnomad4 NFE AF: 0.687

Gnomad4 OTH AF: 0.572

Alfa AF: 0.621 Hom.: 13845

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13250873; hg19: chr8-117806169;