7-142749475-C-G
Variant names:
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_002769.5(PRSS1):c.-10C>G variant causes a 5 prime UTR 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.000013 ( 0 hom., cov: 34)
Failed GnomAD Quality Control
Consequence
PRSS1
NM_002769.5 5_prime_UTR
NM_002769.5 5_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.743
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 -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.9).
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PRSS1 | ENST00000311737 | c.-10C>G | 5_prime_UTR_variant | Exon 1 of 5 | 1 | NM_002769.5 | ENSP00000308720.7 | |||
PRSS1 | ENST00000486171 | c.-10C>G | 5_prime_UTR_variant | Exon 1 of 6 | 5 | ENSP00000417854.1 | ||||
PRSS1 | ENST00000485223.1 | n.4C>G | non_coding_transcript_exon_variant | Exon 1 of 2 | 2 | |||||
PRSS1 | ENST00000497041.1 | n.-6C>G | upstream_gene_variant | 2 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 2AN: 152156Hom.: 0 Cov.: 34 FAILED QC
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34
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GnomAD4 exome Cov.: 47
GnomAD4 exome
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47
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000131 AC: 2AN: 152156Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 74334
GnomAD4 genome
Data not reliable, filtered out with message: AS_VQSR
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34
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74334
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at