Variant rs16888728 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_032334.3(UTP23):c.644C>T(p.Pro215Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.112 in 1,611,740 control chromosomes in the GnomAD database, including 13,253 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.17 ( 3427 hom., cov: 33)

Exomes 𝑓: 0.10 ( 9826 hom. )

Consequence

UTP23
NM_032334.3 missense

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.74

Variant links:

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]

UTP23 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.003584206).

BP6

Variant 8-116771736-C-T is Benign according to our data. Variant chr8-116771736-C-T is described in ClinVar as [Benign]. Clinvar id is 1287707.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UTP23	NM_032334.3 linkuse as main transcript	c.644C>T	p.Pro215Leu	missense_variant	3/3	ENST00000309822.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
UTP23	ENST00000309822.7 linkuse as main transcript	c.644C>T	p.Pro215Leu	missense_variant	3/3	1	NM_032334.3	P1	Q9BRU9-1

Frequencies

GnomAD3 genomes

AF:

0.174

AC:

26415

AN:

151782

Hom.:

3425

Cov.:

show subpopulations

Gnomad AFR

AF:

0.368

Gnomad AMI

AF:

0.123

Gnomad AMR

AF:

0.103

Gnomad ASJ

AF:

0.154

Gnomad EAS

AF:

0.0210

Gnomad SAS

AF:

0.154

Gnomad FIN

AF:

0.114

Gnomad MID

AF:

0.140

Gnomad NFE

AF:

0.0975

Gnomad OTH

AF:

0.149

GnomAD3 exomes

AF:

0.116

AC:

28810

AN:

247972

Hom.:

2451

AF XY:

0.116

AC XY:

15641

AN XY:

134508

show subpopulations

Gnomad AFR exome

AF:

0.375

Gnomad AMR exome

AF:

0.0590

Gnomad ASJ exome

AF:

0.164

Gnomad EAS exome

AF:

0.0163

Gnomad SAS exome

AF:

0.162

Gnomad FIN exome

AF:

0.113

Gnomad NFE exome

AF:

0.0975

Gnomad OTH exome

AF:

0.114

GnomAD4 exome

AF:

0.105

AC:

153269

AN:

1459840

Hom.:

9826

Cov.:

AF XY:

0.106

AC XY:

77249

AN XY:

726168

show subpopulations

Gnomad4 AFR exome

AF:

0.372

Gnomad4 AMR exome

AF:

0.0634

Gnomad4 ASJ exome

AF:

0.159

Gnomad4 EAS exome

AF:

0.0262

Gnomad4 SAS exome

AF:

0.163

Gnomad4 FIN exome

AF:

0.114

Gnomad4 NFE exome

AF:

0.0940

Gnomad4 OTH exome

AF:

0.124

GnomAD4 genome

AF:

0.174

AC:

26454

AN:

151900

Hom.:

3427

Cov.:

AF XY:

0.172

AC XY:

12770

AN XY:

74268

show subpopulations

Gnomad4 AFR

AF:

0.368

Gnomad4 AMR

AF:

0.102

Gnomad4 ASJ

AF:

0.154

Gnomad4 EAS

AF:

0.0212

Gnomad4 SAS

AF:

0.154

Gnomad4 FIN

AF:

0.114

Gnomad4 NFE

AF:

0.0975

Gnomad4 OTH

AF:

0.149

Alfa

AF:

0.106

Hom.:

2434

Bravo

AF:

0.179

TwinsUK

AF:

0.105

AC:

391

ALSPAC

AF:

0.0900

AC:

347

ESP6500AA

AF:

0.357

AC:

1571

ESP6500EA

AF:

0.0981

AC:

843

ExAC

AF:

0.125

AC:

15179

Asia WGS

AF:

0.130

AC:

455

AN:

3476

EpiCase

AF:

0.0966

EpiControl

AF:

0.0937

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 13, 2018	This variant is associated with the following publications: (PMID: 29547645, 26553438) -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.071

BayesDel_addAF

Benign

-0.77

BayesDel_noAF

Benign

-0.74

CADD

Benign

7.3

DANN

Benign

0.72

DEOGEN2

Benign

0.0054

Eigen

Benign

-0.81

Eigen_PC

Benign

-0.75

FATHMM_MKL

Uncertain

0.82

LIST_S2

Benign

0.35

MetaRNN

Benign

0.0036

MetaSVM

Benign

-0.91

MutationAssessor

Benign

0.34

MutationTaster

Benign

1.0

P;P;P;P

PrimateAI

Benign

0.26

PROVEAN

Benign

-1.0

REVEL

Benign

0.047

Sift

Benign

0.31

Sift4G

Benign

0.31

Polyphen

0.0040

Vest4

0.050

MPC

0.24

ClinPred

0.0025

GERP RS

-0.54

Varity_R

0.049

gMVP

0.10

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over