Total submissions: 9
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Prevention |
RCV000251699 | SCV000305793 | likely benign | not specified | criteria provided, single submitter | clinical testing | ||
Athena Diagnostics | RCV000251699 | SCV000614546 | benign | not specified | 2017-03-13 | criteria provided, single submitter | clinical testing | |
ARUP Laboratories, |
RCV000757637 | SCV000885937 | benign | Polycystic kidney disease, adult type | 2019-03-08 | criteria provided, single submitter | clinical testing | |
Ambry Genetics | RCV003258716 | SCV003955286 | likely benign | Inborn genetic diseases | 2023-05-19 | criteria provided, single submitter | clinical testing | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. |
Ce |
RCV001727657 | SCV004142836 | likely benign | not provided | 2024-11-01 | criteria provided, single submitter | clinical testing | PKD1: BP4, BP7 |
Breakthrough Genomics, |
RCV001727657 | SCV005217047 | likely benign | not provided | criteria provided, single submitter | not provided | ||
Department of Pathology and Laboratory Medicine, |
RCV001292040 | SCV001480656 | likely benign | Polycystic kidney disease | no assertion criteria provided | clinical testing | The PKD1 p.Ser2788= variant was identified in 1 of 460 proband chromosomes (freq 0.002) from individuals or families with PKD (Rossetti 2012). The variant was also identified in dbSNP (ID: rs145176597) as “With Likely benign allele”, in Clinvitae and ClinVar (as likely benign by PreventionGenetics), ADPKD Mutation Database (as likely neutral), and PKD1-LOVD 3.0 (2x, unclassified with the probability of no functional affect), the 1000 Genomes Project in 4 of 5008 chromosomes (freq 0.0008), the NHLBI GO Exome Sequencing Project in 20 of 8446 European American alleles (freq 0.0023) and 2 in 4306 African American alleles (freq 0.00045), the genome Aggregation Database (beta, October 19th 2016) in 286 (1 homozygous) of 271612 chromosomes (freq. 0.001), the Exome Aggregation Consortium database (August 8th 2016) in 108 (1 homozygous) of 113342 chromosomes (freq. 0.001) in the following populations: European in 84 of 61652 chromosomes (freq. 0.001), South Asian in 13 of 16422 chromosomes (freq. 0.0008), Latino in 8 of 11282 chromosomes (freq. 0.0007), African in 2 of 8270 chromosomes (freq. 0.00024), and East Asian in 1 of 8378 chromosomes (freq. 0.0001), but was not seen in Finnish and other populations, increasing the likelihood this could be a low frequency benign variant. In addition we cannot be certain that data from control databases is specific to PKD1 and not from one of the six PKD1 pseudogenes. This variant was not identified in GeneInsight-COGR, MutDB, and PKD1-LOVD databases. The p.Ser2788= 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. The variant occurs outside of the splicing consensus sequence and 1 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. | |
Genome Diagnostics Laboratory, |
RCV000251699 | SCV001927558 | benign | not specified | no assertion criteria provided | clinical testing | ||
Clinical Genetics DNA and cytogenetics Diagnostics Lab, |
RCV001727657 | SCV001973896 | likely benign | not provided | no assertion criteria provided | clinical testing |