Total submissions: 10
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Clin |
RCV003460765 | SCV004190217 | benign | RPE65-related recessive retinopathy | 2023-12-22 | reviewed by expert panel | curation | The NM_000329.3:c.1056G>A variant is a synonymous variant in codon 352 of RPE65, and is present in gnomAD v.2.1.1 at a GrpMax allele frequency of 0.3944, with 8033 alleles / 19884 total alleles in the East Asian population with 1627 homozygotes, which is higher than the ClinGen LCA / eoRD VCEP BA1 threshold of >0.008 (BA1). The variant does not have a strong prediction of impact at splicing sites according to SpliceAI, which calculates a delta score of 0.12 for splice acceptor gain. Because this score is higher than the ClinGen LCA / eoRD VCEP BP4 / BP7 threshold of <0.1 and lower than the PP3 threshold of >0.2, no in silico predictive codes are met. In summary, this variant meets the criteria to be classified as benign for RPE65-related recessive retinopathy based on the ACMG/AMP criteria applied, as specified by the ClinGen LCA/eoRD VCEP: BA1. (VCEP specifications version 1.0.0; date of approval 09/21/2023). |
Gene |
RCV000212977 | SCV000171376 | benign | not specified | 2011-08-11 | 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, |
RCV000212977 | SCV000303623 | benign | not specified | criteria provided, single submitter | clinical testing | ||
Illumina Laboratory Services, |
RCV000395443 | SCV000358874 | benign | Retinitis pigmentosa | 2018-01-12 | 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. |
Illumina Laboratory Services, |
RCV000299398 | SCV000358875 | benign | Leber congenital amaurosis 2 | 2018-01-12 | 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. |
Invitae | RCV001522164 | SCV001731648 | benign | Leber congenital amaurosis 2; Retinitis pigmentosa 20 | 2024-02-01 | criteria provided, single submitter | clinical testing | |
Genome- |
RCV000299398 | SCV001750239 | benign | Leber congenital amaurosis 2 | 2021-07-01 | criteria provided, single submitter | clinical testing | |
Genome- |
RCV001533576 | SCV001750240 | benign | Retinitis pigmentosa 87 with choroidal involvement | 2021-07-01 | criteria provided, single submitter | clinical testing | |
Retina International | RCV000085144 | SCV000117281 | not provided | not provided | no assertion provided | not provided | ||
Natera, |
RCV001275329 | SCV001460403 | benign | Leber congenital amaurosis | 2020-09-16 | no assertion criteria provided | clinical testing |