rs3831310

chr9-33796692-TGAG-Tchr9-33796692-TGAG-TGAGGAG

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_Supporting BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.192

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]

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

ACMG classification

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	c.94_96del	p.Glu32del	inframe_deletion	2/5	ENST00000379405.4
UBE2R2-AS1	NR_170204.1	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	c.94_96del	p.Glu32del	inframe_deletion	2/5	1	NM_002771.4	P1
UBE2R2-AS1	ENST00000705030.1	n.425+1673_425+1675del		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.145 AC: 21935 AN: 151580 Hom.: 1082 Cov.: 32

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

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

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.: 32 AF XY: 0.147 AC XY: 10916 AN XY: 74152

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

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 15, 2019

- -

Computational scores

Source: dbNSFP v4.3

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

Other links and lift over

dbSNP: rs3831310; hg19: chr9-33796690;