ClinVar Miner

Submissions for variant NM_002769.5(PRSS1):c.200+17C>T

dbSNP: rs200688125
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001192440 SCV001360558 benign not specified 2019-10-01 criteria provided, single submitter clinical testing Variant summary: PRSS1 c.200+17C>T alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0041 in 229856 control chromosomes (gnomAD). The observed variant frequency is approximately 820 fold of the estimated maximal expected allele frequency for a pathogenic variant in PRSS1 causing Chronic Pancreatitis Risk phenotype (5e-06), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.200+17C>T in individuals affected with Chronic Pancreatitis Risk and no experimental evidence demonstrating the variant's impact on protein function have been reported. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014. Based on the evidence outlined above, the variant was classified as benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV002069200 SCV002374118 likely benign Hereditary pancreatitis 2025-01-11 criteria provided, single submitter clinical testing
Ambry Genetics RCV002069200 SCV002721562 benign Hereditary pancreatitis 2016-01-11 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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