7-142767843-G-T

Variant names:

• chr7-142767843-G-T
• rs2734212
• ENST00000632998.1:c.41-4206G>T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000632998.1(PRSS2):​c.41-4206G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. 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 0.41 (6126 hom., cov: 48)
  • Failed GnomAD Quality Control
• Consequence: PRSS2 ENST00000632998.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.70
• Publications: 2 publications found

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]

TRB (HGNC:12155):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (Cadd=0.054).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000632998.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PRSS2	ENST00000632998.1	TSL:1	c.41-4206G>T		intron	N/A	ENSP00000488789.1

Frequencies

GnomAD3 genomes AF: 0.410 AC: 60107 AN: 146712 Hom.: 6122 Cov.: 48

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.456

Gnomad AMR AF: 0.465

Gnomad ASJ AF: 0.476

Gnomad EAS AF: 0.217

Gnomad SAS AF: 0.303

Gnomad FIN AF: 0.491

Gnomad MID AF: 0.365

Gnomad NFE AF: 0.468

Gnomad OTH AF: 0.431

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.410 AC: 60136 AN: 146820 Hom.: 6126 Cov.: 48 AF XY: 0.409 AC XY: 29390 AN XY: 71870

African (AFR) AF: 0.299 AC: 11603 AN: 38838

American (AMR) AF: 0.465 AC: 6904 AN: 14834

Ashkenazi Jewish (ASJ) AF: 0.476 AC: 1610 AN: 3384

East Asian (EAS) AF: 0.217 AC: 1116 AN: 5154

South Asian (SAS) AF: 0.303 AC: 1452 AN: 4786

European-Finnish (FIN) AF: 0.491 AC: 5026 AN: 10244

Middle Eastern (MID) AF: 0.375 AC: 108 AN: 288

European-Non Finnish (NFE) AF: 0.468 AC: 31045 AN: 66374

Other (OTH) AF: 0.427 AC: 865 AN: 2026

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.054
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs2734212;