Variant 9-33796692-TGAG-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBA1

The NM_002771.4(PRSS3):c.94_96del(p.Glu32del) variant causes a inframe deletion change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.168 in 1,610,864 control chromosomes in the GnomAD database, including 4,652 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.14 ( 1087 hom., cov: 32)

Exomes 𝑓: 0.17 ( 3565 hom. )

Consequence

PRSS3
NM_002771.4 inframe_deletion

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.192

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 -9 ACMG points.

PM4

Nonframeshift variant in NON repetitive region in NM_002771.4. Strenght limited to Supporting due to length of the change: 1aa.

BP6

Variant 9-33796692-TGAG-T is Benign according to our data. Variant chr9-33796692-TGAG-T is described in ClinVar as [Benign]. Clinvar id is 1225003.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRSS3	NM_002771.4 linkuse as main transcript	c.94_96del	p.Glu32del	inframe_deletion	2/5	ENST00000379405.4
UBE2R2-AS1	NR_170204.1 linkuse as main transcript	n.558+1673_558+1675del		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRSS3	ENST00000379405.4 linkuse as main transcript	c.94_96del	p.Glu32del	inframe_deletion	2/5	1	NM_002771.4	P1	P35030-3
UBE2R2-AS1	ENST00000705030.1 linkuse as main transcript	n.425+1673_425+1675del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.145

AC:

21935

AN:

151580

Hom.:

1082

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0639

Gnomad AMI

AF:

0.104

Gnomad AMR

AF:

0.156

Gnomad ASJ

AF:

0.138

Gnomad EAS

AF:

0.0854

Gnomad SAS

AF:

0.309

Gnomad FIN

AF:

0.192

Gnomad MID

AF:

0.118

Gnomad NFE

AF:

0.178

Gnomad OTH

AF:

0.150

GnomAD3 exomes

AF:

0.171

AC:

42943

AN:

250786

Hom.:

1204

AF XY:

0.178

AC XY:

24167

AN XY:

135494

show subpopulations

Gnomad AFR exome

AF:

0.0642

Gnomad AMR exome

AF:

0.166

Gnomad ASJ exome

AF:

0.136

Gnomad EAS exome

AF:

0.0801

Gnomad SAS exome

AF:

0.285

Gnomad FIN exome

AF:

0.201

Gnomad NFE exome

AF:

0.170

Gnomad OTH exome

AF:

0.169

GnomAD4 exome

AF:

0.170

AC:

248064

AN:

1459164

Hom.:

3565

AF XY:

0.174

AC XY:

125966

AN XY:

725796

show subpopulations

Gnomad4 AFR exome

AF:

0.0591

Gnomad4 AMR exome

AF:

0.162

Gnomad4 ASJ exome

AF:

0.133

Gnomad4 EAS exome

AF:

0.0823

Gnomad4 SAS exome

AF:

0.281

Gnomad4 FIN exome

AF:

0.202

Gnomad4 NFE exome

AF:

0.168

Gnomad4 OTH exome

AF:

0.168

GnomAD4 genome

AF:

0.145

AC:

21947

AN:

151700

Hom.:

1087

Cov.:

AF XY:

0.147

AC XY:

10916

AN XY:

74152

show subpopulations

Gnomad4 AFR

AF:

0.0637

Gnomad4 AMR

AF:

0.157

Gnomad4 ASJ

AF:

0.138

Gnomad4 EAS

AF:

0.0856

Gnomad4 SAS

AF:

0.308

Gnomad4 FIN

AF:

0.192

Gnomad4 NFE

AF:

0.178

Gnomad4 OTH

AF:

0.151

Alfa

AF:

0.170

Hom.:

221

Asia WGS

AF:

0.172

AC:

600

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.11

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