ClinVar Miner

Submissions for variant NM_025114.4(CEP290):c.6787A>G (p.Ser2263Gly)

gnomAD frequency: 0.00022  dbSNP: rs77778467
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Total submissions: 15
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory,University of Chicago RCV000193732 SCV000246998 likely benign not specified 2019-03-15 criteria provided, single submitter clinical testing
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center RCV000490488 SCV000267248 uncertain significance Leber congenital amaurosis 10 2016-03-18 criteria provided, single submitter reference population
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics RCV000132681 SCV000609629 uncertain significance not provided 2017-06-02 criteria provided, single submitter clinical testing
GeneDx RCV000193732 SCV000730551 likely benign not specified 2017-08-31 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.
Eurofins NTD LLC (GA) RCV000132681 SCV000857575 uncertain significance not provided 2017-11-02 criteria provided, single submitter clinical testing
Invitae RCV001083794 SCV001007353 benign Joubert syndrome; Meckel-Gruber syndrome; Nephronophthisis 2021-12-13 criteria provided, single submitter clinical testing
Mendelics RCV000988879 SCV001138777 benign Joubert syndrome 1 2019-05-28 criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV001109949 SCV001267333 uncertain significance Senior-Loken syndrome 6 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 RCV001109950 SCV001267334 uncertain significance Bardet-Biedl syndrome 14 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 RCV000490488 SCV001268204 uncertain significance Leber congenital amaurosis 10 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. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Illumina Laboratory Services,Illumina RCV001110731 SCV001268205 uncertain significance Meckel syndrome, type 4 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 RCV001110732 SCV001268206 uncertain significance Joubert syndrome 5 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000193732 SCV002500783 uncertain significance not specified 2022-03-30 criteria provided, single submitter clinical testing Variant summary: CEP290 c.6787A>G (p.Ser2263Gly) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00065 in 249100 control chromosomes in the gnomAD database, including 1 homozygotes. c.6787A>G has been reported in the literature in individuals affected with Leber congenital amaurosis and unexplained epilepsy, without strong evidence for causality (eg. Li_2011, Oishi_2014, Wang_2019, Xu_2016). These reports do not provide unequivocal conclusions about association of the variant with CEP290-Related Disorders. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Nine clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Four submitters classified the variant as VUS while five classified the variant as likely benign/benign. Based on the evidence outlined above, the variant was classified as uncertain significance.
Department of Ophthalmology and Visual Sciences Kyoto University RCV000132681 SCV000172634 probable-non-pathogenic not provided no assertion criteria provided not provided Converted during submission to Likely benign.
Natera, Inc. RCV001272010 SCV001453638 benign Leber congenital amaurosis 2020-01-10 no assertion criteria provided clinical testing

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