rs3831310
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PM4_SupportingBP6_ModerateBA1
The NM_002771.4(PRSS3):βc.94_96delβ(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 (β ).
Frequency
Genomes: π 0.14 ( 1087 hom., cov: 32)
Exomes π: 0.17 ( 3565 hom. )
Consequence
PRSS3
NM_002771.4 inframe_deletion
NM_002771.4 inframe_deletion
Scores
Not classified
Clinical Significance
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]
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ACMG classification
Classification made for transcript
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: 21935AN: 151580Hom.: 1082 Cov.: 32
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GnomAD3 exomes AF: 0.171 AC: 42943AN: 250786Hom.: 1204 AF XY: 0.178 AC XY: 24167AN XY: 135494
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GnomAD4 exome AF: 0.170 AC: 248064AN: 1459164Hom.: 3565 AF XY: 0.174 AC XY: 125966AN XY: 725796
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GnomAD4 genome ? AF: 0.145 AC: 21947AN: 151700Hom.: 1087 Cov.: 32 AF XY: 0.147 AC XY: 10916AN XY: 74152
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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
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at