Variant rs1133950 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_032334.3(UTP23):c.583A>C(p.Lys195Gln) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0483 in 1,610,856 control chromosomes in the GnomAD database, including 2,429 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. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.

Frequency

Genomes: 𝑓 0.066 ( 412 hom., cov: 33)

Exomes 𝑓: 0.046 ( 2017 hom. )

Consequence

UTP23
NM_032334.3 missense

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 8.55

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.001796186).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.11 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTP23	NM_032334.3 linkuse as main transcript	c.583A>C	p.Lys195Gln	missense_variant	3/3	ENST00000309822.7	NP_115710.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTP23	ENST00000309822.7 linkuse as main transcript	c.583A>C	p.Lys195Gln	missense_variant	3/3	1	NM_032334.3	ENSP00000308332	P1	Q9BRU9-1

Frequencies

GnomAD3 genomes

AF:

0.0656

AC:

9976

AN:

152142

Hom.:

413

Cov.:

show subpopulations

Gnomad AFR

AF:

0.113

Gnomad AMI

AF:

0.0318

Gnomad AMR

AF:

0.0492

Gnomad ASJ

AF:

0.0922

Gnomad EAS

AF:

0.000577

Gnomad SAS

AF:

0.0809

Gnomad FIN

AF:

0.0667

Gnomad MID

AF:

0.0924

Gnomad NFE

AF:

0.0429

Gnomad OTH

AF:

0.0660

GnomAD3 exomes

AF:

0.0538

AC:

13293

AN:

247232

Hom.:

505

AF XY:

0.0560

AC XY:

7495

AN XY:

133756

show subpopulations

Gnomad AFR exome

AF:

0.112

Gnomad AMR exome

AF:

0.0281

Gnomad ASJ exome

AF:

0.107

Gnomad EAS exome

AF:

0.000608

Gnomad SAS exome

AF:

0.0885

Gnomad FIN exome

AF:

0.0661

Gnomad NFE exome

AF:

0.0450

Gnomad OTH exome

AF:

0.0618

GnomAD4 exome

AF:

0.0465

AC:

67765

AN:

1458596

Hom.:

2017

Cov.:

AF XY:

0.0479

AC XY:

34759

AN XY:

725500

show subpopulations

Gnomad4 AFR exome

AF:

0.115

Gnomad4 AMR exome

AF:

0.0296

Gnomad4 ASJ exome

AF:

0.101

Gnomad4 EAS exome

AF:

0.000353

Gnomad4 SAS exome

AF:

0.0877

Gnomad4 FIN exome

AF:

0.0670

Gnomad4 NFE exome

AF:

0.0405

Gnomad4 OTH exome

AF:

0.0545

GnomAD4 genome

AF:

0.0655

AC:

9974

AN:

152260

Hom.:

412

Cov.:

AF XY:

0.0665

AC XY:

4952

AN XY:

74444

show subpopulations

Gnomad4 AFR

AF:

0.113

Gnomad4 AMR

AF:

0.0491

Gnomad4 ASJ

AF:

0.0922

Gnomad4 EAS

AF:

0.000578

Gnomad4 SAS

AF:

0.0805

Gnomad4 FIN

AF:

0.0667

Gnomad4 NFE

AF:

0.0429

Gnomad4 OTH

AF:

0.0648

Alfa

AF:

0.0479

Hom.:

436

Bravo

AF:

0.0638

TwinsUK

AF:

0.0515

AC:

191

ALSPAC

AF:

0.0355

AC:

137

ESP6500AA

AF:

0.107

AC:

470

ESP6500EA

AF:

0.0405

AC:

348

ExAC

AF:

0.0572

AC:

6944

Asia WGS

AF:

0.0380

AC:

136

AN:

3478

EpiCase

AF:

0.0445

EpiControl

AF:

0.0439

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.21

BayesDel_addAF

Benign

-0.56

BayesDel_noAF

Benign

-0.49

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.33

Eigen

Pathogenic

0.72

Eigen_PC

Pathogenic

0.70

FATHMM_MKL

Pathogenic

0.99

LIST_S2

Benign

0.74

MetaRNN

Benign

0.0018

MetaSVM

Benign

-1.1

MutationAssessor

Benign

2.0

MutationTaster

Benign

0.000075

P;P;P;P

PrimateAI

Benign

0.44

PROVEAN

Uncertain

-2.7

REVEL

Benign

0.17

Sift

Uncertain

0.014

Sift4G

Uncertain

0.0090

Polyphen

0.98

Vest4

0.12

MPC

0.52

ClinPred

0.034

GERP RS

5.6

Varity_R

0.50

gMVP

0.37

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over