rs2855981
Variant names:
Your query was ambiguous. Multiple possible variants found:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
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
ENST00000632998.1 intron
Scores
Not classified
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.341
Publications
3 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]
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TRB | n.142768623A>C | intragenic_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRSS2 | ENST00000632998.1 | c.41-3426A>C | intron_variant | Intron 1 of 4 | 1 | ENSP00000488789.1 |
Frequencies
GnomAD3 genomes AF: 0.501 AC: 75470AN: 150768Hom.: 19344 Cov.: 28 show subpopulations
GnomAD3 genomes
AF:
AC:
75470
AN:
150768
Hom.:
Cov.:
28
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.500 AC: 75487AN: 150886Hom.: 19347 Cov.: 28 AF XY: 0.499 AC XY: 36771AN XY: 73690 show subpopulations
GnomAD4 genome
AF:
AC:
75487
AN:
150886
Hom.:
Cov.:
28
AF XY:
AC XY:
36771
AN XY:
73690
show subpopulations
African (AFR)
AF:
AC:
15501
AN:
41160
American (AMR)
AF:
AC:
8609
AN:
15128
Ashkenazi Jewish (ASJ)
AF:
AC:
2009
AN:
3448
East Asian (EAS)
AF:
AC:
1228
AN:
5166
South Asian (SAS)
AF:
AC:
1611
AN:
4772
European-Finnish (FIN)
AF:
AC:
6201
AN:
10374
Middle Eastern (MID)
AF:
AC:
135
AN:
294
European-Non Finnish (NFE)
AF:
AC:
38637
AN:
67556
Other (OTH)
AF:
AC:
1060
AN:
2086
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.512
Heterozygous variant carriers
0
1792
3583
5375
7166
8958
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Alfa
AF:
Hom.:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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