Variant chr12-101291865-C-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2

The ENST00000261637.5(UTP20):c.1015C>A(p.Pro339Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00779 in 1,613,108 control chromosomes in the GnomAD database, including 136 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.018 ( 55 hom., cov: 33)

Exomes 𝑓: 0.0067 ( 81 hom. )

Consequence

UTP20
ENST00000261637.5 missense

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.313

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 made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0028953254).

BP6

Variant 12-101291865-C-A is Benign according to our data. Variant chr12-101291865-C-A is described in ClinVar as [Benign]. Clinvar id is 782332.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0184 (2802/152288) while in subpopulation AFR AF= 0.0478 (1988/41556). AF 95% confidence interval is 0.0461. There are 55 homozygotes in gnomad4. There are 1339 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 55 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTP20	NM_014503.3 linkuse as main transcript	c.1015C>A	p.Pro339Thr	missense_variant	9/62	ENST00000261637.5	NP_055318.2	O75691

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UTP20	ENST00000261637.5 linkuse as main transcript	c.1015C>A	p.Pro339Thr	missense_variant	9/62	1	NM_014503.3	ENSP00000261637.4		O75691

Frequencies

GnomAD3 genomes

AF:

0.0182

AC:

2777

AN:

152170

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0474

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0179

Gnomad ASJ

AF:

0.0164

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00538

Gnomad FIN

AF:

0.000471

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.00579

Gnomad OTH

AF:

0.0248

GnomAD3 exomes

AF:

0.00898

AC:

2248

AN:

250204

Hom.:

AF XY:

0.00839

AC XY:

1134

AN XY:

135194

show subpopulations

Gnomad AFR exome

AF:

0.0503

Gnomad AMR exome

AF:

0.00918

Gnomad ASJ exome

AF:

0.0173

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00523

Gnomad FIN exome

AF:

0.000463

Gnomad NFE exome

AF:

0.00626

Gnomad OTH exome

AF:

0.0106

GnomAD4 exome

AF:

0.00668

AC:

9762

AN:

1460820

Hom.:

Cov.:

AF XY:

0.00656

AC XY:

4763

AN XY:

726598

show subpopulations

Gnomad4 AFR exome

AF:

0.0491

Gnomad4 AMR exome

AF:

0.0105

Gnomad4 ASJ exome

AF:

0.0173

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00568

Gnomad4 FIN exome

AF:

0.000449

Gnomad4 NFE exome

AF:

0.00533

Gnomad4 OTH exome

AF:

0.0105

GnomAD4 genome

AF:

0.0184

AC:

2802

AN:

152288

Hom.:

Cov.:

AF XY:

0.0180

AC XY:

1339

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0478

Gnomad4 AMR

AF:

0.0177

Gnomad4 ASJ

AF:

0.0164

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00559

Gnomad4 FIN

AF:

0.000471

Gnomad4 NFE

AF:

0.00582

Gnomad4 OTH

AF:

0.0246

Alfa

AF:

0.00806

Hom.:

Bravo

AF:

0.0220

TwinsUK

AF:

0.00593

AC:

ALSPAC

AF:

0.00493

AC:

ESP6500AA

AF:

0.0479

AC:

211

ESP6500EA

AF:

0.00674

AC:

ExAC

AF:

0.00931

AC:

1130

EpiCase

AF:

0.00987

EpiControl

AF:

0.00765

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	Labcorp Genetics (formerly Invitae), Labcorp	Jul 31, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.050

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.66

CADD

Benign

3.1

DANN

Benign

0.042

DEOGEN2

Benign

0.0051

Eigen

Benign

-1.1

Eigen_PC

Benign

-0.88

FATHMM_MKL

Benign

0.098

LIST_S2

Benign

0.19

MetaRNN

Benign

0.0029

MetaSVM

Benign

-1.1

MutationAssessor

Benign

-1.6

MutationTaster

Benign

1.0

PrimateAI

Benign

0.34

PROVEAN

Benign

2.4

REVEL

Benign

0.13

Sift

Benign

1.0

Sift4G

Benign

1.0

Polyphen

0.0

Vest4

0.11

MVP

0.32

MPC

0.13

ClinPred

0.0026

GERP RS

3.1

Varity_R

0.025

gMVP

0.13

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