Variant 9-33796914-A-G 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 NM_002771.4(PRSS3):c.200+112A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.96 in 151,580 control chromosomes in the GnomAD database, including 69,883 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.96 ( 69883 hom., cov: 31)

Exomes 𝑓: 0.99 ( 686750 hom. )

Failed GnomAD Quality Control

Consequence

PRSS3
NM_002771.4 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.925

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=-0.96).

BP6

Variant 9-33796914-A-G is Benign according to our data. Variant chr9-33796914-A-G is described in ClinVar as [Benign]. Clinvar id is 1291262.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.99 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PRSS3	NM_002771.4 linkuse as main transcript	c.200+112A>G		intron_variant		ENST00000379405.4	NP_002762.3
UBE2R2-AS1	NR_170204.1 linkuse as main transcript	n.558+1454T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PRSS3	ENST00000379405.4 linkuse as main transcript	c.200+112A>G		intron_variant		1	NM_002771.4	ENSP00000368715	P1	P35030-3
UBE2R2-AS1	ENST00000705030.1 linkuse as main transcript	n.425+1454T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.960

AC:

145409

AN:

151470

Hom.:

69838

Cov.:

show subpopulations

Gnomad AFR

AF:

0.901

Gnomad AMI

AF:

1.00

Gnomad AMR

AF:

0.960

Gnomad ASJ

AF:

0.992

Gnomad EAS

AF:

0.911

Gnomad SAS

AF:

0.972

Gnomad FIN

AF:

0.958

Gnomad MID

AF:

0.990

Gnomad NFE

AF:

0.996

Gnomad OTH

AF:

0.975

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.987

AC:

1391056

AN:

1409588

Hom.:

686750

AF XY:

0.987

AC XY:

693518

AN XY:

702798

show subpopulations

Gnomad4 AFR exome

AF:

0.897

Gnomad4 AMR exome

AF:

0.958

Gnomad4 ASJ exome

AF:

0.989

Gnomad4 EAS exome

AF:

0.867

Gnomad4 SAS exome

AF:

0.978

Gnomad4 FIN exome

AF:

0.959

Gnomad4 NFE exome

AF:

0.997

Gnomad4 OTH exome

AF:

0.981

GnomAD4 genome

AF:

0.960

AC:

145509

AN:

151580

Hom.:

69883

Cov.:

AF XY:

0.958

AC XY:

70975

AN XY:

74090

show subpopulations

Gnomad4 AFR

AF:

0.901

Gnomad4 AMR

AF:

0.960

Gnomad4 ASJ

AF:

0.992

Gnomad4 EAS

AF:

0.910

Gnomad4 SAS

AF:

0.972

Gnomad4 FIN

AF:

0.958

Gnomad4 NFE

AF:

0.996

Gnomad4 OTH

AF:

0.975

Alfa

AF:

0.926

Hom.:

7119

Bravo

AF:

0.958

Asia WGS

AF:

0.922

AC:

3206

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

-0.96

CADD

Benign

0.55

DANN

Benign

0.69

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