Variant 9-33797763-G-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_StrongBP6_ModerateBS1

The NM_002771.4(PRSS3):c.201-66G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0027 in 1,486,938 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.027 ( 0 hom., cov: 36)

Exomes 𝑓: 0.00058 ( 0 hom. )

Consequence

PRSS3
NM_002771.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0740

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 -8 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

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

BP6

Variant 9-33797763-G-T is Benign according to our data. Variant chr9-33797763-G-T is described in ClinVar as [Benign]. Clinvar id is 1245449.Status of the report is criteria_provided_single_submitter, 1 stars.

BS1

Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0267 (3213/120268) while in subpopulation AFR AF= 0.0425 (1331/31342). AF 95% confidence interval is 0.0406. There are 0 homozygotes in gnomad4. There are 1709 alleles in male gnomad4 subpopulation. Median coverage is 36. This position pass quality control queck.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PRSS3	NM_002771.4 linkuse as main transcript	c.201-66G>T		intron_variant		ENST00000379405.4
UBE2R2-AS1	NR_170204.1 linkuse as main transcript	n.558+605C>A		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.201-66G>T		intron_variant		1	NM_002771.4	P1	P35030-3
UBE2R2-AS1	ENST00000705030.1 linkuse as main transcript	n.425+605C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes

AF:

0.0266

AC:

3201

AN:

120194

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0422

Gnomad AMI

AF:

0.0180

Gnomad AMR

AF:

0.0258

Gnomad ASJ

AF:

0.0163

Gnomad EAS

AF:

0.00709

Gnomad SAS

AF:

0.0109

Gnomad FIN

AF:

0.0418

Gnomad MID

AF:

0.0254

Gnomad NFE

AF:

0.0190

Gnomad OTH

AF:

0.0286

GnomAD4 exome

AF:

0.000584

AC:

798

AN:

1366670

Hom.:

AF XY:

0.000620

AC XY:

421

AN XY:

679274

show subpopulations

Gnomad4 AFR exome

AF:

0.00197

Gnomad4 AMR exome

AF:

0.000758

Gnomad4 ASJ exome

AF:

0.00139

Gnomad4 EAS exome

AF:

0.000381

Gnomad4 SAS exome

AF:

0.0000121

Gnomad4 FIN exome

AF:

0.00191

Gnomad4 NFE exome

AF:

0.000474

Gnomad4 OTH exome

AF:

0.00114

GnomAD4 genome

AF:

0.0267

AC:

3213

AN:

120268

Hom.:

Cov.:

AF XY:

0.0291

AC XY:

1709

AN XY:

58772

show subpopulations

Gnomad4 AFR

AF:

0.0425

Gnomad4 AMR

AF:

0.0258

Gnomad4 ASJ

AF:

0.0163

Gnomad4 EAS

AF:

0.00733

Gnomad4 SAS

AF:

0.0109

Gnomad4 FIN

AF:

0.0418

Gnomad4 NFE

AF:

0.0190

Gnomad4 OTH

AF:

0.0276

Alfa

AF:

0.283

Hom.:

401

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

BayesDel_noAF

Benign

-0.83

CADD

Benign

2.1

DANN

Benign

0.86

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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