Genetic Variant NM_014503.3: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

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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