chr8-116789909-T-C

Position:

• chr8-116789909-T-C

Variant summary

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

The XR_002956724.2(LOC112268030):​n.760+3260T>C 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 0.818 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: LOC112268030 XR_002956724.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0830

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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.957 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC112268030	XR_002956724.2	n.760+3260T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTP23	ENST00000517820.1	c.188+23118T>C		intron_variant		3		ENSP00000427767
UTP23	ENST00000520733.5	c.45+19543T>C		intron_variant		3		ENSP00000429384
UTP23	ENST00000521703.5	c.*92+3260T>C		intron_variant, NMD_transcript_variant		2		ENSP00000428455
UTP23	ENST00000524128.1	c.*92+3260T>C		intron_variant, NMD_transcript_variant		3		ENSP00000430309

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

Gnomad4 AFR AF: 0.603

Gnomad4 AMR AF: 0.896

Gnomad4 ASJ AF: 0.882

Gnomad4 EAS AF: 0.979

Gnomad4 SAS AF: 0.840

Gnomad4 FIN AF: 0.886

Gnomad4 NFE AF: 0.903

Gnomad4 OTH AF: 0.845

Alfa AF: 0.882 Hom.: 32251

Bravo AF: 0.813

Asia WGS AF: 0.864 AC: 3001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.1
DANN	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6983626; hg19: chr8-117802148;