dbSNP rs1133950: UTP23:p.Lys195Gln (chr8-116771675-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -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.

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

Publications

22 publications found

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 was made for transcript

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
UTP23	NM_032334.3 link	c.583A>C	p.Lys195Gln	missense_variant	Exon 3 of 3	ENST00000309822.7	NP_115710.2	Q9BRU9-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTP23	ENST00000309822.7 link	c.583A>C	p.Lys195Gln	missense_variant	Exon 3 of 3	1	NM_032334.3	ENSP00000308332.2		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

GnomAD2 exomes

AF:

0.0538

AC:

13293

AN:

247232

AF XY:

0.0560

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 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

African (AFR)

AF:

0.115

AC:

3816

AN:

33058

American (AMR)

AF:

0.0296

AC:

1303

AN:

44006

Ashkenazi Jewish (ASJ)

AF:

0.101

AC:

2631

AN:

26032

East Asian (EAS)

AF:

0.000353

AC:

AN:

39660

South Asian (SAS)

AF:

0.0877

AC:

7477

AN:

85238

European-Finnish (FIN)

AF:

0.0670

AC:

3574

AN:

53366

Middle Eastern (MID)

AF:

0.107

AC:

615

AN:

5744

European-Non Finnish (NFE)

AF:

0.0405

AC:

45055

AN:

1111286

Other (OTH)

AF:

0.0545

AC:

3280

AN:

60206

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.457

Heterozygous variant carriers

3568

7135

10703

14270

17838

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

1768

3536

5304

7072

8840

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0655

AC:

9974

AN:

152260

Hom.:

412

Cov.:

AF XY:

0.0665

AC XY:

4952

AN XY:

74444

show subpopulations

African (AFR)

AF:

0.113

AC:

4693

AN:

41538

American (AMR)

AF:

0.0491

AC:

751

AN:

15300

Ashkenazi Jewish (ASJ)

AF:

0.0922

AC:

320

AN:

3470

East Asian (EAS)

AF:

0.000578

AC:

AN:

5186

South Asian (SAS)

AF:

0.0805

AC:

389

AN:

4830

European-Finnish (FIN)

AF:

0.0667

AC:

706

AN:

10592

Middle Eastern (MID)

AF:

0.0890

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0429

AC:

2920

AN:

68026

Other (OTH)

AF:

0.0648

AC:

137

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

472

943

1415

1886

2358

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

114

228

342

456

570

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.0512

Hom.:

892

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

(source)

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

PhyloP100

8.6

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

Mutation Taster

=88/12

polymorphism (auto)

(source)

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over