rs855581
Positions:
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_002771.4(PRSS3):āc.391A>Gā(p.Thr131Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.70 ( 27687 hom., cov: 38)
Exomes š: 0.73 ( 316286 hom. )
Failed GnomAD Quality Control
Consequence
PRSS3
NM_002771.4 missense
NM_002771.4 missense
Scores
2
14
Clinical Significance
Conservation
PhyloP100: -0.108
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 Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=1.1308639E-6).
BP6
?
Variant 9-33798019-A-G is Benign according to our data. Variant chr9-33798019-A-G is described in ClinVar as [Benign]. Clinvar id is 2786908.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRSS3 | NM_002771.4 | c.391A>G | p.Thr131Ala | missense_variant | 3/5 | ENST00000379405.4 | |
UBE2R2-AS1 | NR_170204.1 | n.558+349T>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRSS3 | ENST00000379405.4 | c.391A>G | p.Thr131Ala | missense_variant | 3/5 | 1 | NM_002771.4 | P1 | |
UBE2R2-AS1 | ENST00000705030.1 | n.425+349T>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 95619AN: 135884Hom.: 27684 Cov.: 38 FAILED QC
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?
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GnomAD3 exomes AF: 0.960 AC: 233319AN: 243014Hom.: 111817 AF XY: 0.962 AC XY: 126489AN XY: 131442
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GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR;InbreedingCoeff AF: 0.726 AC: 1015042AN: 1397528Hom.: 316286 Cov.: 100 AF XY: 0.730 AC XY: 508137AN XY: 696372
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GnomAD4 genome ? Data not reliable, filtered out with message: InbreedingCoeff AF: 0.704 AC: 95682AN: 136004Hom.: 27687 Cov.: 38 AF XY: 0.703 AC XY: 46813AN XY: 66578
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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 | Invitae | Jan 17, 2024 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationTaster
Benign
P;P;P;P
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N
REVEL
Uncertain
Sift
Benign
T;T;T;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
B;B;.;.;B
Vest4
MPC
0.24
ClinPred
T
GERP RS
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gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at