rs766186870
Positions:
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_002769.5(PRSS1):c.592-9T>C variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 41)
Failed GnomAD Quality Control
Consequence
PRSS1
NM_002769.5 splice_polypyrimidine_tract, intron
NM_002769.5 splice_polypyrimidine_tract, intron
Scores
2
Splicing: ADA: 0.00002795
2
Clinical Significance
Conservation
PhyloP100: -0.288
Genes affected
PRSS1 (HGNC:9475): (serine protease 1) This gene encodes a trypsinogen, which is a member of the trypsin family of serine proteases. This enzyme is secreted by the pancreas and cleaved to its active form in the small intestine. It is active on peptide linkages involving the carboxyl group of lysine or arginine. Mutations in this gene are associated with hereditary pancreatitis. This gene and several other trypsinogen genes are localized to the T cell receptor beta locus on chromosome 7. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -4 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.88).
BP6
?
Variant 7-142752859-T-C is Benign according to our data. Variant chr7-142752859-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 258801.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr7-142752859-T-C is described in Lovd as [Likely_benign].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRSS1 | NM_002769.5 | c.592-9T>C | splice_polypyrimidine_tract_variant, intron_variant | ENST00000311737.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRSS1 | ENST00000311737.12 | c.592-9T>C | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_002769.5 | P1 | |||
PRSS1 | ENST00000486171.5 | c.634-9T>C | splice_polypyrimidine_tract_variant, intron_variant | 5 | |||||
PRSS1 | ENST00000492062.1 | c.425-9T>C | splice_polypyrimidine_tract_variant, intron_variant | 2 | |||||
PRSS1 | ENST00000463701.1 | n.1056-9T>C | splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00 AC: 1AN: 152118Hom.: 0 Cov.: 41 FAILED QC
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GnomAD3 exomes AF: 0.0000400 AC: 10AN: 249758Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135068
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GnomAD4 exome Cov.: 47
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GnomAD4 genome ? Data not reliable, filtered out with message: AS_VQSR AF: 0.00000657 AC: 1AN: 152118Hom.: 0 Cov.: 41 AF XY: 0.0000135 AC XY: 1AN XY: 74324
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?
Data not reliable, filtered out with message: AS_VQSR
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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dbscSNV1_ADA
Benign
dbscSNV1_RF
Benign
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at