Total submissions: 12
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Eurofins Ntd Llc |
RCV000082531 | SCV000114573 | benign | not specified | 2013-03-26 | criteria provided, single submitter | clinical testing | |
Prevention |
RCV000082531 | SCV000315777 | benign | not specified | criteria provided, single submitter | clinical testing | ||
Invitae | RCV000468175 | SCV000557657 | benign | Autosomal recessive polycystic kidney disease | 2024-02-01 | criteria provided, single submitter | clinical testing | |
Genome Diagnostics Laboratory, |
RCV000468175 | SCV000743918 | benign | Autosomal recessive polycystic kidney disease | 2014-10-09 | criteria provided, single submitter | clinical testing | |
SIB Swiss Institute of Bioinformatics | RCV000468175 | SCV000803552 | benign | Autosomal recessive polycystic kidney disease | 2018-05-31 | criteria provided, single submitter | curation | This variant is interpreted as a Benign, for Polycystic kidney disease 4 with or without polycystic liver disease, in Autosomal Recessive manner. The following ACMG Tag(s) were applied: BS1 => Allele frequency is greater than expected for disorder. BS2 => Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age. |
Illumina Laboratory Services, |
RCV000468175 | SCV001320520 | likely benign | Autosomal recessive polycystic kidney disease | 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. |
Pars Genome Lab | RCV001530442 | SCV001745270 | benign | Polycystic kidney disease 4 | 2021-06-19 | criteria provided, single submitter | clinical testing | |
Gene |
RCV001719848 | SCV001949052 | benign | not provided | 2020-10-12 | criteria provided, single submitter | clinical testing | This variant is associated with the following publications: (PMID: 25701400) |
Diagnostic Laboratory, |
RCV000468175 | SCV000734509 | benign | Autosomal recessive polycystic kidney disease | no assertion criteria provided | clinical testing | ||
Department of Pathology and Laboratory Medicine, |
RCV001292255 | SCV001480890 | likely benign | Polycystic kidney disease | no assertion criteria provided | clinical testing | The PKHD1 p.Thr579Met variant was identified in 8 of 1110 proband chromosomes (frequency: 0.007) from individuals or families with ADPKD and was present in 3 of 200 control chromosomes (frequency: 0.015) from healthy individuals (Sharp 2005, Losekoot 2005, Bergmann 2005, Edrees 2016, Obeidova 2015). The variant was also identified in dbSNP (ID: rs45500692) as “With Benign allele”, ClinVar (classified as benign by Invitae and Prevention Genetics), RWTH AAachen University ARPKD database (classified as polynorphism), databases. The variant was not identified in Genesight-COGR, LOVD 3.0, databases. The variant was identified in control databases in 6712 of 276722 chromosomes at a frequency of 0.024255 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). The p.Thr579 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein, in addition the variant amino acid Methionine (Met) is present in northern white cheeked gibbon, increasing the likelihood that this variant does not have clinical significance. The variant occurs outside of the splicing consensus sequence and 2 of 5 in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) predict a greater than 10% difference in splicing; this is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign. | |
Laboratory of Diagnostic Genome Analysis, |
RCV000082531 | SCV002035505 | benign | not specified | no assertion criteria provided | clinical testing | ||
Natera, |
RCV000468175 | SCV002081065 | benign | Autosomal recessive polycystic kidney disease | 2017-05-11 | no assertion criteria provided | clinical testing |