ClinVar Miner

Submissions for variant NM_004744.5(LRAT):c.*98C>T (rs529360609)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000354005 SCV000447908 uncertain significance Leber congenital amaurosis 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000277933 SCV000447909 likely benign Leber congenital amaurosis 14 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 Clinical Services Laboratory,Illumina RCV000333107 SCV000447910 likely benign Retinitis pigmentosa 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.
Diagnostics Lab (ASPIRE), CSIR - Centre for Cellular and Molecular Biology RCV001090045 SCV001237985 uncertain significance Rod-cone dystrophy 2020-03-23 criteria provided, single submitter clinical testing The c.*98C>T variant is not present in publicly available databases like EVS and ExAC. It is present in 1000 Genomes, gnomAD and dbSNP at a low frequency (MAF<=0.0099), in heterozygous state. The variant is not present in our in-house exome database. The variant was earlier reported to ClinVar as uncertain significance in association with recessive Retinitis pigmentosa (ClinVar Accession: VCV000347852.1). In-silico pathogenicity prediction programs like MutationTaster2, CADD etc. predicted this variant to be likely deleterious. However there are no documented functional studies to prove this. Due to lack of enough evidence the variant has been classified as uncertain significance.

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