ClinVar Miner

Submissions for variant NM_014625.3(NPHS2):c.59C>T (p.Pro20Leu) (rs74315344)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Integrated Genetics/Laboratory Corporation of America RCV000588524 SCV000699383 likely benign not provided 2016-03-04 criteria provided, single submitter clinical testing Variant summary: The c.59C>T variant affects a non-conserved nucleotide, resulting in amino acid change from Pro to Leu. 2/3 in-silico tools predict this variant to be damaging (SNPs&GO, MutationTaster not captured due to low reliability index). This variant is found in 92/7048 control chromosomes (1 homozygote) at a frequency of 0.0130533, which is about 7 times of maximal expected frequency of a pathogenic allele (0.0017678), suggesting this variant is benign. Although this variant was classified as pathogenic by OMIM via ClinVar, multiple recent literatures suggested this variant was a polymorphism based on the evidence of co-occurrences with a pathogenic variant and homozygous occurrences in controls. Taken together, this variant was classified as likely benign.
Athena Diagnostics Inc RCV000588524 SCV000842931 benign not provided 2018-01-25 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000005696 SCV001254354 benign Nephrotic syndrome, idiopathic, steroid-resistant 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
OMIM RCV000005696 SCV000025878 pathogenic Nephrotic syndrome, idiopathic, steroid-resistant 2003-05-01 no assertion criteria provided literature only

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