dbSNP rs2270861: UTP20:c.4245+14A>G (chr12-101342603-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_014503.3(UTP20):c.4245+14A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.239 in 1,590,188 control chromosomes in the GnomAD database, including 47,029 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 0.23 ( 4328 hom., cov: 32)

Exomes 𝑓: 0.24 ( 42701 hom. )

Consequence

UTP20
NM_014503.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0230

Publications

12 publications found

Variant links:

Genes affected

UTP20 (HGNC:17897): (UTP20 small subunit processome component) UTP20 is a component of the U3 small nucleolar RNA (snoRNA) (SNORD3A; MIM 180710) protein complex (U3 snoRNP) and is involved in 18S rRNA processing (Wang et al., 2007 [PubMed 17498821]).[supplied by OMIM, Jun 2009]

UTP20 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 (BayesDel_noAF=-0.71).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
UTP20	NM_014503.3 link	c.4245+14A>G		intron_variant	Intron 33 of 61	ENST00000261637.5	NP_055318.2	O75691

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
UTP20	ENST00000261637.5 link	c.4245+14A>G		intron_variant	Intron 33 of 61	1	NM_014503.3	ENSP00000261637.4		O75691

Frequencies

GnomAD3 genomes

AF:

0.230

AC:

34952

AN:

151966

Hom.:

4313

Cov.:

show subpopulations

Gnomad AFR

AF:

0.172

Gnomad AMI

AF:

0.389

Gnomad AMR

AF:

0.323

Gnomad ASJ

AF:

0.283

Gnomad EAS

AF:

0.370

Gnomad SAS

AF:

0.253

Gnomad FIN

AF:

0.159

Gnomad MID

AF:

0.250

Gnomad NFE

AF:

0.237

Gnomad OTH

AF:

0.261

GnomAD2 exomes

AF:

0.253

AC:

57739

AN:

228314

AF XY:

0.251

show subpopulations

Gnomad AFR exome

AF:

0.174

Gnomad AMR exome

AF:

0.352

Gnomad ASJ exome

AF:

0.274

Gnomad EAS exome

AF:

0.367

Gnomad FIN exome

AF:

0.167

Gnomad NFE exome

AF:

0.236

Gnomad OTH exome

AF:

0.267

GnomAD4 exome

AF:

0.240

AC:

345252

AN:

1438104

Hom.:

42701

Cov.:

AF XY:

0.240

AC XY:

171817

AN XY:

715016

show subpopulations

African (AFR)

AF:

0.172

AC:

5497

AN:

32026

American (AMR)

AF:

0.342

AC:

13013

AN:

38102

Ashkenazi Jewish (ASJ)

AF:

0.272

AC:

6775

AN:

24908

East Asian (EAS)

AF:

0.388

AC:

15340

AN:

39554

South Asian (SAS)

AF:

0.242

AC:

19840

AN:

81924

European-Finnish (FIN)

AF:

0.169

AC:

8943

AN:

52794

Middle Eastern (MID)

AF:

0.280

AC:

1517

AN:

5422

European-Non Finnish (NFE)

AF:

0.235

AC:

259560

AN:

1104100

Other (OTH)

AF:

0.249

AC:

14767

AN:

59274

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.478

Heterozygous variant carriers

12099

24199

36298

48398

60497

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

8964

17928

26892

35856

44820

<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:

0.230

AC:

35014

AN:

152084

Hom.:

4328

Cov.:

AF XY:

0.230

AC XY:

17126

AN XY:

74340

show subpopulations

African (AFR)

AF:

0.173

AC:

7157

AN:

41488

American (AMR)

AF:

0.324

AC:

4945

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.283

AC:

981

AN:

3470

East Asian (EAS)

AF:

0.370

AC:

1913

AN:

5176

South Asian (SAS)

AF:

0.254

AC:

1223

AN:

4822

European-Finnish (FIN)

AF:

0.159

AC:

1685

AN:

10582

Middle Eastern (MID)

AF:

0.248

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.237

AC:

16134

AN:

67962

Other (OTH)

AF:

0.260

AC:

548

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1367

2734

4100

5467

6834

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

378

756

1134

1512

1890

<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:

0.232

Hom.:

994

Bravo

AF:

0.243

Asia WGS

AF:

0.329

AC:

1141

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.71

CADD

Benign

1.0

(source)

DANN

Benign

0.72

PhyloP100

-0.023

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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