ClinVar Miner

Submissions for variant NM_153240.5(NPHP3):c.2769C>T (p.Phe923=)

gnomAD frequency: 0.00066  dbSNP: rs116174472
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000303773 SCV000343935 likely benign not specified 2016-07-15 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001094791 SCV000441100 uncertain significance Nephronophthisis 3 2018-01-13 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV000364771 SCV000441101 uncertain significance Renal-hepatic-pancreatic dysplasia 1 2018-01-13 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Illumina Laboratory Services, Illumina RCV000274968 SCV000441102 uncertain significance NPHP3-related Meckel-like syndrome 2018-01-13 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Invitae RCV000310058 SCV000759581 benign Nephronophthisis 2024-01-29 criteria provided, single submitter clinical testing
GeneDx RCV000838628 SCV000980502 likely benign not provided 2020-08-04 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000838628 SCV004155566 likely benign not provided 2022-06-01 criteria provided, single submitter clinical testing NPHP3: BP4, BP7
Genome Diagnostics Laboratory, University Medical Center Utrecht RCV000303773 SCV001928831 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000838628 SCV001967650 likely benign not provided no assertion criteria provided clinical testing

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