Variant 9-33794842-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The ENST00000342836.9(PRSS3):c.45G>A(p.Ala15=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0145 in 1,402,726 control chromosomes in the GnomAD database, including 1,619 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.10 ( 854 hom., cov: 33)

Exomes 𝑓: 0.0069 ( 765 hom. )

Consequence

PRSS3
ENST00000342836.9 synonymous

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.323

Variant links:

Genes affected

PRSS3 (HGNC:9486): (serine protease 3) This gene encodes a trypsinogen, which is a member of the trypsin family of serine proteases. This enzyme is expressed in the brain and pancreas and is resistant to common trypsin inhibitors. It is active on peptide linkages involving the carboxyl group of lysine or arginine. This gene is localized to the locus of T cell receptor beta variable orphans on chromosome 9. Four transcript variants encoding different isoforms have been described for this gene. [provided by RefSeq, Oct 2010]

PRSS3 links:

UBE2R2-AS1 (HGNC:49911): (UBE2R2 antisense RNA 1)

UBE2R2-AS1 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

BP6

Variant 9-33794842-G-A is Benign according to our data. Variant chr9-33794842-G-A is described in ClinVar as [Benign]. Clinvar id is 1271011.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-0.323 with no splicing effect.

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.283 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
UBE2R2-AS1	NR_170204.1 linkuse as main transcript	n.558+3526C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
UBE2R2-AS1	ENST00000705030.1 linkuse as main transcript	n.425+3526C>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.104

AC:

11360

AN:

109732

Hom.:

846

Cov.:

show subpopulations

Gnomad AFR

AF:

0.287

Gnomad AMI

AF:

0.0205

Gnomad AMR

AF:

0.0610

Gnomad ASJ

AF:

0.0241

Gnomad EAS

AF:

0.00579

Gnomad SAS

AF:

0.0119

Gnomad FIN

AF:

0.0398

Gnomad MID

AF:

0.0294

Gnomad NFE

AF:

0.0254

Gnomad OTH

AF:

0.0805

GnomAD3 exomes

AF:

0.0125

AC:

1856

AN:

148268

Hom.:

134

AF XY:

0.00955

AC XY:

762

AN XY:

79760

show subpopulations

Gnomad AFR exome

AF:

0.207

Gnomad AMR exome

AF:

0.0125

Gnomad ASJ exome

AF:

0.000120

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000489

Gnomad FIN exome

AF:

0.000243

Gnomad NFE exome

AF:

0.00157

Gnomad OTH exome

AF:

0.00927

GnomAD4 exome

AF:

0.00691

AC:

8928

AN:

1292910

Hom.:

765

Cov.:

AF XY:

0.00602

AC XY:

3845

AN XY:

638184

show subpopulations

Gnomad4 AFR exome

AF:

0.224

Gnomad4 AMR exome

AF:

0.0155

Gnomad4 ASJ exome

AF:

0.000308

Gnomad4 EAS exome

AF:

0.000117

Gnomad4 SAS exome

AF:

0.00104

Gnomad4 FIN exome

AF:

0.000925

Gnomad4 NFE exome

AF:

0.000658

Gnomad4 OTH exome

AF:

0.0176

GnomAD4 genome

AF:

0.104

AC:

11408

AN:

109816

Hom.:

854

Cov.:

AF XY:

0.102

AC XY:

5479

AN XY:

53722

show subpopulations

Gnomad4 AFR

AF:

0.288

Gnomad4 AMR

AF:

0.0609

Gnomad4 ASJ

AF:

0.0241

Gnomad4 EAS

AF:

0.00580

Gnomad4 SAS

AF:

0.0119

Gnomad4 FIN

AF:

0.0398

Gnomad4 NFE

AF:

0.0254

Gnomad4 OTH

AF:

0.0786

Alfa

AF:

0.0918

Hom.:

169

Asia WGS

AF:

0.0140

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	GeneDx	Aug 15, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

1.2

DANN

Benign

0.75

Splicing

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