Total submissions: 18
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Gene |
RCV000211893 | SCV000209484 | benign | not specified | 2014-08-29 | 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. |
Ambry Genetics | RCV000159527 | SCV000213274 | likely benign | Hereditary cancer-predisposing syndrome | 2014-08-22 | 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. |
Labcorp Genetics |
RCV000199795 | SCV000252922 | likely benign | Familial adenomatous polyposis 1 | 2024-01-27 | criteria provided, single submitter | clinical testing | |
Counsyl | RCV000199795 | SCV000488938 | likely benign | Familial adenomatous polyposis 1 | 2016-07-25 | criteria provided, single submitter | clinical testing | |
Color Diagnostics, |
RCV000159527 | SCV000681670 | benign | Hereditary cancer-predisposing syndrome | 2016-03-18 | criteria provided, single submitter | clinical testing | |
Quest Diagnostics Nichols Institute San Juan Capistrano | RCV000211893 | SCV000888747 | benign | not specified | 2019-01-24 | criteria provided, single submitter | clinical testing | |
Mendelics | RCV000199795 | SCV001136874 | likely benign | Familial adenomatous polyposis 1 | 2019-05-28 | criteria provided, single submitter | clinical testing | |
Illumina Laboratory Services, |
RCV001156933 | SCV001318473 | uncertain significance | APC-Associated Polyposis Disorders | 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease. |
Sema4, |
RCV000159527 | SCV002534316 | likely benign | Hereditary cancer-predisposing syndrome | 2022-01-30 | criteria provided, single submitter | curation | |
Center for Genomic Medicine, |
RCV000211893 | SCV002760340 | uncertain significance | not specified | 2023-08-15 | criteria provided, single submitter | clinical testing | |
Myriad Genetics, |
RCV000199795 | SCV004018576 | benign | Familial adenomatous polyposis 1 | 2023-02-17 | criteria provided, single submitter | clinical testing | This variant is considered benign. This variant is a silent/synonymous amino acid change and it is not expected to impact splicing. |
All of Us Research Program, |
RCV003998400 | SCV004837274 | benign | Classic or attenuated familial adenomatous polyposis | 2024-01-11 | criteria provided, single submitter | clinical testing | |
Department of Pathology and Laboratory Medicine, |
RCV001353868 | SCV000591031 | likely benign | Carcinoma of colon | no assertion criteria provided | clinical testing | The APC p.Lys150Lys variant was identified in 1 of 3082 proband chromosomes (frequency: 0.0003) from individuals or families being evaluated for FAP (Kerr 2013). The variant was also identified in dbSNP (ID: rs116020626) “With other allele”, Clinvitae database (with conflicting interpretations), InSiGHT Colon Cancer Gene Variant Database (LOVD), ClinVar database (classification benign by GeneDx, and likely benign by Ambry Genetics and Invitae), and UMD (2x with a “likely neutral” classification, and co-occurring with a pathogenic APC mutation, c.1312+3A>G). This variant was also identified in the 1000 Genomes Project in 2 of 5000 chromosomes (frequency: 0.0004); HAPMAP-EUR in 2 of 1006 chromosomes (frequency: 0.002); NHLBI GO Exome Sequencing Project (ESP) in 4 of 8582 European American alleles, and the Exome Aggregation Consortium (ExAC) database (released Jan 13, 2015) in 14 of 66536 chromosomes (frequency: 0.0002) from a population of European (Non-Finnish) individuals. The p.Lys150Lys 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 addition, 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, 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. | |
True Health Diagnostics | RCV000159527 | SCV000787836 | likely benign | Hereditary cancer-predisposing syndrome | 2017-12-01 | no assertion criteria provided | clinical testing | |
Diagnostic Laboratory, |
RCV000759433 | SCV001740730 | likely benign | not provided | no assertion criteria provided | clinical testing | ||
Genome Diagnostics Laboratory, |
RCV000759433 | SCV001807434 | likely benign | not provided | no assertion criteria provided | clinical testing | ||
Clinical Genetics, |
RCV000759433 | SCV001925579 | likely benign | not provided | no assertion criteria provided | clinical testing | ||
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, |
RCV000759433 | SCV001957855 | likely benign | not provided | no assertion criteria provided | clinical testing |