ClinVar Miner

Submissions for variant NM_017739.4(POMGNT1):c.1257G>A (p.Leu419=)

gnomAD frequency: 0.01062  dbSNP: rs41292143
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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000118028 SCV000196857 benign not specified 2014-10-17 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.
PreventionGenetics, part of Exact Sciences RCV000118028 SCV000307098 benign not specified criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001083592 SCV000649953 benign Autosomal recessive limb-girdle muscular dystrophy type 2O; Muscular dystrophy-dystroglycanopathy (congenital with intellectual disability), type B3 2024-01-31 criteria provided, single submitter clinical testing
Athena Diagnostics RCV000712840 SCV000843375 benign not provided 2017-11-29 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV001101550 SCV001258168 likely benign Autosomal recessive limb-girdle muscular dystrophy type 2O 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 and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Illumina Laboratory Services, Illumina RCV001101551 SCV001258169 likely benign Congenital Muscular Dystrophy, alpha-dystroglycan related 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 and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
Breakthrough Genomics, Breakthrough Genomics RCV000712840 SCV005260363 likely benign not provided criteria provided, single submitter not provided
Genetic Services Laboratory, University of Chicago RCV000118028 SCV000152346 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Natera, Inc. RCV001275233 SCV001460160 benign Muscle eye brain disease 2020-09-16 no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000118028 SCV001920814 benign not specified no assertion criteria provided clinical testing
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center RCV000118028 SCV001964222 benign not specified no assertion criteria provided clinical testing
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) RCV000712840 SCV002035444 likely benign not provided no assertion criteria provided clinical testing

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