ClinVar Miner

Submissions for variant NM_004646.3(NPHS1):c.349G>A (p.Glu117Lys) (rs3814995)

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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000249474 SCV000310578 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001094483 SCV000411589 benign Congenital nephrotic syndrome 2018-03-06 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Athena Diagnostics Inc RCV000364963 SCV000677369 benign Finnish congenital nephrotic syndrome 2017-04-28 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588607 SCV000698504 benign not provided 2016-10-17 criteria provided, single submitter clinical testing Variant summary: The NPHS1 c.349G>A (p.Glu117Lys) variant involves the alteration of a conserved nucleotide. 2/3 in silico tools predict a benign outcome for this variant (SNPs&GO and MutationTaster not captured due to low reliability index). This variant was found in 37468/119026 control chromosomes (6569 homozygotes) at a frequency of 0.3147884, which is approximately 94 times the estimated maximal expected allele frequency of a pathogenic NPHS1 variant (0.0033541), evidence that this variant is a benign polymorphism. In addition, one clinical diagnostic laboratory classified this variant as benign. Taken together, this variant is classified as benign.
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000364963 SCV000743922 benign Finnish congenital nephrotic syndrome 2014-10-09 criteria provided, single submitter clinical testing
GeneDx RCV000588607 SCV000975244 benign not provided 2018-06-19 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen RCV000364963 SCV000733877 benign Finnish congenital nephrotic syndrome no assertion criteria provided clinical testing

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