rs2855981

chr7-142768623-A-Cchr7-142768623-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000632998.1(PRSS2):c.41-3426A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.5 in 150,886 control chromosomes in the GnomAD database, including 19,347 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.50 (19347 hom., cov: 28)
• Consequence: PRSS2 ENST00000632998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341

Genes affected

PRSS2 (HGNC:9483): (serine protease 2) This gene belongs to the trypsin family of serine proteases and encodes anionic trypsinogen. It is part of a cluster of trypsinogen genes that are located within the T cell receptor beta locus. Enzymes of this family cleave peptide bonds that follow lysine or arginine residues. This protein is found at high levels in pancreatic juice and its upregulation is a characteristic feature of pancreatitis. This protein has also been found to activate pro-urokinase in ovarian tumors, suggesting a function in tumor invasion. In addition, this enzyme is able to cleave across the type II collagen triple helix in rheumatoid arthritis synovitis tissue, potentially participating in the degradation of type II collagen-rich cartilage matrix. Alternative splicing results in multiple transcript variants.[provided by RefSeq, Jan 2015]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=4.254).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.567 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PRSS2	ENST00000632998.1	c.41-3426A>C		intron_variant		1		A1

Frequencies

GnomAD3 genomes AF: 0.501 AC: 75470 AN: 150768 Hom.: 19344 Cov.: 28

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.550

Gnomad AMR AF: 0.569

Gnomad ASJ AF: 0.583

Gnomad EAS AF: 0.238

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.598

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.572

Gnomad OTH AF: 0.514

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.500 AC: 75487 AN: 150886 Hom.: 19347 Cov.: 28 AF XY: 0.499 AC XY: 36771 AN XY: 73690

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.569

Gnomad4 ASJ AF: 0.583

Gnomad4 EAS AF: 0.238

Gnomad4 SAS AF: 0.338

Gnomad4 FIN AF: 0.598

Gnomad4 NFE AF: 0.572

Gnomad4 OTH AF: 0.508

Alfa AF: 0.256 Hom.: 388

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
Cadd	Benign	4.3

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs2855981; hg19: -;