ClinVar Miner

Submissions for variant NM_014625.4(NPHS2):c.725C>T (p.Ala242Val)

gnomAD frequency: 0.02224  dbSNP: rs61747727
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000243949 SCV000312203 benign not specified criteria provided, single submitter clinical testing
Athena Diagnostics RCV000712439 SCV000842934 benign not provided 2018-06-19 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000243949 SCV000917912 benign not specified 2018-11-02 criteria provided, single submitter clinical testing Variant summary: NPHS2 c.725C>T (p.Ala242Val) results in a non-conservative amino acid change located in the Band 7 domain of the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0069 in 276216 control chromosomes, predominantly within the African subpopulation at a frequency of 0.073 in the gnomAD database, including 67 homozygotes. The observed variant frequency within African control individuals in the gnomAD database is approximately 41-fold above the estimated maximal expected allele frequency for a pathogenic variant in NPHS2 causing Nephrotic Syndrome, Type 2 phenotype (0.0018), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
Labcorp Genetics (formerly Invitae), Labcorp RCV000712439 SCV001092676 benign not provided 2024-01-31 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001101695 SCV001258324 benign Nephrotic syndrome, type 2 2017-04-28 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.
Institute of Human Genetics, University of Leipzig Medical Center RCV001101695 SCV001440191 uncertain significance Nephrotic syndrome, type 2 2019-01-01 criteria provided, single submitter clinical testing
GeneDx RCV000712439 SCV001852146 benign not provided 2020-12-19 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 32691731, 30450462, 26211502, 12707396, 20981092)
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002294175 SCV002587227 benign Focal segmental glomerulosclerosis 2022-03-14 criteria provided, single submitter clinical testing
Natera, Inc. RCV001273613 SCV001456813 benign Steroid-resistant nephrotic syndrome 2020-09-16 no assertion criteria provided clinical testing

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