Variant 12-101290282-A-C details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2

The ENST00000261637.5(UTP20):c.735+8A>C variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00674 in 1,583,346 control chromosomes in the GnomAD database, including 74 homozygotes. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.0060 ( 8 hom., cov: 32)

Exomes 𝑓: 0.0068 ( 66 hom. )

Consequence

UTP20
ENST00000261637.5 splice_region, intron

Scores

Splicing: ADA: 0.00003658

Clinical Significance

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

Conservation

PhyloP100: -0.0660

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:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -16 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.83).

BP6

Variant 12-101290282-A-C is Benign according to our data. Variant chr12-101290282-A-C is described in ClinVar as [Benign]. Clinvar id is 773548.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BS2

High Homozygotes in GnomAd4 at 8 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UTP20	NM_014503.3 linkuse as main transcript	c.735+8A>C		splice_region_variant, intron_variant		ENST00000261637.5	NP_055318.2

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris
UTP20	ENST00000261637.5 linkuse as main transcript	c.735+8A>C	splice_region_variant, intron_variant	1	NM_014503.3	ENSP00000261637	P1
UTP20	ENST00000551825.1 linkuse as main transcript	n.890+8A>C	splice_region_variant, intron_variant, non_coding_transcript_variant	1
UTP20	ENST00000551998.1 linkuse as main transcript	n.372+8A>C	splice_region_variant, intron_variant, non_coding_transcript_variant	3

Frequencies

GnomAD3 genomes

AF:

0.00602

AC:

916

AN:

152216

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00116

Gnomad AMI

AF:

0.00768

Gnomad AMR

AF:

0.00713

Gnomad ASJ

AF:

0.00403

Gnomad EAS

AF:

0.000192

Gnomad SAS

AF:

0.0116

Gnomad FIN

AF:

0.00687

Gnomad MID

AF:

0.00949

Gnomad NFE

AF:

0.00867

Gnomad OTH

AF:

0.00717

GnomAD3 exomes

AF:

0.00673

AC:

1541

AN:

228834

Hom.:

AF XY:

0.00720

AC XY:

891

AN XY:

123828

show subpopulations

Gnomad AFR exome

AF:

0.000773

Gnomad AMR exome

AF:

0.00350

Gnomad ASJ exome

AF:

0.00391

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.0111

Gnomad FIN exome

AF:

0.00589

Gnomad NFE exome

AF:

0.00892

Gnomad OTH exome

AF:

0.00604

GnomAD4 exome

AF:

0.00682

AC:

9757

AN:

1431012

Hom.:

Cov.:

AF XY:

0.00713

AC XY:

5063

AN XY:

710346

show subpopulations

Gnomad4 AFR exome

AF:

0.00124

Gnomad4 AMR exome

AF:

0.00349

Gnomad4 ASJ exome

AF:

0.00411

Gnomad4 EAS exome

AF:

0.0000256

Gnomad4 SAS exome

AF:

0.0119

Gnomad4 FIN exome

AF:

0.00575

Gnomad4 NFE exome

AF:

0.00707

Gnomad4 OTH exome

AF:

0.00646

GnomAD4 genome

AF:

0.00601

AC:

915

AN:

152334

Hom.:

Cov.:

AF XY:

0.00619

AC XY:

461

AN XY:

74502

show subpopulations

Gnomad4 AFR

AF:

0.00115

Gnomad4 AMR

AF:

0.00712

Gnomad4 ASJ

AF:

0.00403

Gnomad4 EAS

AF:

0.000193

Gnomad4 SAS

AF:

0.0114

Gnomad4 FIN

AF:

0.00687

Gnomad4 NFE

AF:

0.00867

Gnomad4 OTH

AF:

0.00710

Alfa

AF:

0.00662

Hom.:

Bravo

AF:

0.00535

Asia WGS

AF:

0.00318

AC:

AN:

3478

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	Dec 31, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.83

CADD

Benign

0.58

DANN

Benign

0.47

Splicing

Name

Calibrated prediction

Score

Prediction

dbscSNV1_ADA

Benign

0.000037

dbscSNV1_RF

Benign

0.0

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