Total submissions: 12
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Eurofins Ntd Llc |
RCV000082564 | SCV000114606 | benign | not specified | 2013-04-23 | criteria provided, single submitter | clinical testing | |
Prevention |
RCV000082564 | SCV000315815 | benign | not specified | criteria provided, single submitter | clinical testing | ||
Illumina Laboratory Services, |
RCV000314583 | SCV000464077 | benign | Autosomal recessive polycystic kidney disease | 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. |
Women's Health and Genetics/Laboratory Corporation of America, |
RCV000589675 | SCV000699870 | benign | not provided | 2016-04-27 | criteria provided, single submitter | clinical testing | Variant summary: The c.5896C>T variant involves the alteration of a conserved nucleotide resulting in a synonymous change. 4/5 in silico tools via Alamut predict no significant effect on splicing. The variant was observed in the large and broad cohorts of the ExAC project at an allele frequency of 3.2%, predominantly observed in the African subpopulation at a frequency of 13.5% including 82 homozygous occurrences. This frequency exceeds the maximal expected allele frequency for a pathogenic variant in PKHD1 (0.71%), suggesting this is a benign polymorphism found primarily in population(s) of African origin. Publications and a clinical lab have classifed the variant as polymorphism/benign. |
Genome Diagnostics Laboratory, |
RCV000314583 | SCV000743914 | benign | Autosomal recessive polycystic kidney disease | 2014-12-01 | criteria provided, single submitter | clinical testing | |
Invitae | RCV000314583 | SCV000754662 | benign | Autosomal recessive polycystic kidney disease | 2024-02-01 | criteria provided, single submitter | clinical testing | |
Pars Genome Lab | RCV001530422 | SCV001745243 | benign | Polycystic kidney disease 4 | 2021-06-19 | criteria provided, single submitter | clinical testing | |
Gene |
RCV000589675 | SCV001751499 | benign | not provided | 2018-07-09 | criteria provided, single submitter | clinical testing | |
Department of Pathology and Laboratory Medicine, |
RCV001291855 | SCV000592898 | benign | Polycystic kidney disease | no assertion criteria provided | clinical testing | The PKHD1 p.Leu1966Leu variant was identified in 2 of 726 proband chromosomes (frequency: 0.003) from individuals or families with ARPKD, and was present in 22 of 920 control chromosomes (frequency: 0.024) from healthy individuals (Bergmann 2005, Furu 2004, Losekoot 2005, Sharp 2005). The variant was also identified in dbSNP (ID: rs1266923) “With benign allele”, in 1000 Genomes Project in 408 of 5006 chromosomes (frequency: 0.0815), in NHLBI GO Exome Sequencing Project in 35 of 8600 (frequency: 0.004) European American and 586 in 4406 (frequency: 0.1285) African American alleles. This variant was identified in the Exome Aggregation Consortium database (March 14, 2016) in 3934 of 121262 chromosomes (frequency: 0.03) from a population (frequency) of African (0.14), East Asian (0.11), Finnish (0.06), South Asian (0.04), Other (0.03), Latino (0.02), and European Non-Finnish (0.006) individuals. Furthermore, the variant is listed in the ClinVar database as benign by Emory Genetics Laboratory, in the GeneInsight COGR database as benign by LMM, and in RWTH Aachen University ARPKD database as a polymorphism. The p.Leu1966Leu variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information, this variant is classified as benign. | |
Diagnostic Laboratory, |
RCV000314583 | SCV000734506 | benign | Autosomal recessive polycystic kidney disease | no assertion criteria provided | clinical testing | ||
Laboratory of Diagnostic Genome Analysis, |
RCV000082564 | SCV002036226 | benign | not specified | no assertion criteria provided | clinical testing | ||
Natera, |
RCV000314583 | SCV002078063 | benign | Autosomal recessive polycystic kidney disease | 2017-05-11 | no assertion criteria provided | clinical testing |