8-116785633-A-G

Position:

• chr8-116785633-A-G

Variant summary

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

The XR_002956724.2(LOC112268030):​n.614-870A>G 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 0.816 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: LOC112268030 XR_002956724.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.89

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=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.956 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112268030	XR_002956724.2	n.614-870A>G		intron_variant, non_coding_transcript_variant
LOC112268030	XR_007061065.1	n.130-870A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTP23	ENST00000517820.1	c.188+18842A>G		intron_variant		3		ENSP00000427767
UTP23	ENST00000520733.5	c.45+15267A>G		intron_variant		3		ENSP00000429384
UTP23	ENST00000521071.1	c.*83-870A>G		intron_variant, NMD_transcript_variant		2		ENSP00000430029

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

Gnomad4 AFR AF: 0.598

Gnomad4 AMR AF: 0.893

Gnomad4 ASJ AF: 0.842

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.902

Gnomad4 OTH AF: 0.841

Alfa AF: 0.873 Hom.: 16115

Bravo AF: 0.809

Asia WGS AF: 0.866 AC: 3010 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.17
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7837208; hg19: chr8-117797872;