Variant chr9-33750750-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The ENST00000342836.9(PRSS3):c.-53+23G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.364 in 1,415,278 control chromosomes in the GnomAD database, including 96,576 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.31 ( 8385 hom., cov: 31)

Exomes 𝑓: 0.37 ( 88191 hom. )

Consequence

PRSS3
ENST00000342836.9 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: 0.298

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 -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.86).

BP6

Variant 9-33750750-G-T is Benign according to our data. Variant chr9-33750750-G-T is described in ClinVar as [Benign]. Clinvar id is 1280871.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
UBE2R2-AS1	NR_170204.1 linkuse as main transcript	n.559-12334C>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	Effect	TSL
PRSS3	ENST00000342836.9 linkuse as main transcript	c.-53+23G>T	intron_variant	1
PRSS3	ENST00000361005.10 linkuse as main transcript	c.-285+23G>T	intron_variant	1
UBE2R2-AS1	ENST00000705030.1 linkuse as main transcript	n.644-12334C>A	intron_variant, non_coding_transcript_variant
PRSS3	ENST00000468152.2 linkuse as main transcript	n.49+23G>T	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.313

AC:

47530

AN:

151738

Hom.:

8388

Cov.:

show subpopulations

Gnomad AFR

AF:

0.151

Gnomad AMI

AF:

0.304

Gnomad AMR

AF:

0.389

Gnomad ASJ

AF:

0.389

Gnomad EAS

AF:

0.560

Gnomad SAS

AF:

0.351

Gnomad FIN

AF:

0.295

Gnomad MID

AF:

0.367

Gnomad NFE

AF:

0.371

Gnomad OTH

AF:

0.349

GnomAD3 exomes

AF:

0.348

AC:

11505

AN:

33048

Hom.:

2161

AF XY:

0.349

AC XY:

6121

AN XY:

17552

show subpopulations

Gnomad AFR exome

AF:

0.101

Gnomad AMR exome

AF:

0.369

Gnomad ASJ exome

AF:

0.371

Gnomad EAS exome

AF:

0.526

Gnomad SAS exome

AF:

0.348

Gnomad FIN exome

AF:

0.275

Gnomad NFE exome

AF:

0.343

Gnomad OTH exome

AF:

0.345

GnomAD4 exome

AF:

0.370

AC:

467620

AN:

1263422

Hom.:

88191

Cov.:

AF XY:

0.370

AC XY:

226862

AN XY:

612828

show subpopulations

Gnomad4 AFR exome

AF:

0.131

Gnomad4 AMR exome

AF:

0.378

Gnomad4 ASJ exome

AF:

0.385

Gnomad4 EAS exome

AF:

0.524

Gnomad4 SAS exome

AF:

0.357

Gnomad4 FIN exome

AF:

0.290

Gnomad4 NFE exome

AF:

0.375

Gnomad4 OTH exome

AF:

0.365

GnomAD4 genome

AF:

0.313

AC:

47528

AN:

151856

Hom.:

8385

Cov.:

AF XY:

0.313

AC XY:

23248

AN XY:

74206

show subpopulations

Gnomad4 AFR

AF:

0.151

Gnomad4 AMR

AF:

0.389

Gnomad4 ASJ

AF:

0.389

Gnomad4 EAS

AF:

0.559

Gnomad4 SAS

AF:

0.351

Gnomad4 FIN

AF:

0.295

Gnomad4 NFE

AF:

0.371

Gnomad4 OTH

AF:

0.349

Alfa

AF:

0.220

Hom.:

629

Bravo

AF:

0.317

Asia WGS

AF:

0.419

AC:

1455

AN:

3476

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	Jun 14, 2019	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

8.4

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