Submissions for variant NM_153240.5(NPHP3):c.154G>A (p.Ala52Thr)

gnomAD frequency: 0.01037  dbSNP: rs145643112

Total submissions: 16

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Eurofins Ntd Llc (ga)	RCV000082661	SCV000114703	benign	not specified	2013-11-14	criteria provided, single submitter	clinical testing
Invitae	RCV001083406	SCV000291537	benign	Nephronophthisis	2024-01-31	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV000082661	SCV000316255	benign	not specified		criteria provided, single submitter	clinical testing
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics	RCV000434124	SCV000510834	benign	not provided	2017-01-31	criteria provided, single submitter	clinical testing
GeneDx	RCV000082661	SCV000518594	benign	not specified	2017-09-06	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.
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine	RCV000082661	SCV000539956	likely benign	not specified	2016-03-29	criteria provided, single submitter	clinical testing	Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: frequency in ExAC 2.38% in european population with 3 homozygotes). Also Benign in Clinvar (by Emory)
Mendelics	RCV000987337	SCV001136605	benign	Renal-hepatic-pancreatic dysplasia 1	2019-05-28	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000987337	SCV001308213	uncertain significance	Renal-hepatic-pancreatic dysplasia 1	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). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Laboratory Services, Illumina	RCV001148319	SCV001309209	likely benign	Nephronophthisis 3	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 determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Illumina Laboratory Services, Illumina	RCV001148320	SCV001309210	likely benign	NPHP3-related Meckel-like syndrome	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). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000082661	SCV002051034	likely benign	not specified	2021-12-10	criteria provided, single submitter	clinical testing
CeGaT Center for Human Genetics Tuebingen	RCV000434124	SCV002497226	benign	not provided	2023-12-01	criteria provided, single submitter	clinical testing	NPHP3: BS1, BS2
Genome Diagnostics Laboratory, The Hospital for Sick Children	RCV002294022	SCV002587214	likely benign	Kidney disorder	2016-12-12	criteria provided, single submitter	clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC)	RCV000434124	SCV001798994	likely benign	not provided		no assertion criteria provided	clinical testing
Genome Diagnostics Laboratory, University Medical Center Utrecht	RCV000082661	SCV001929343	benign	not specified		no assertion criteria provided	clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center	RCV000434124	SCV001964077	likely benign	not provided		no assertion criteria provided	clinical testing