Total submissions: 19
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
International Society for Gastrointestinal Hereditary Tumours |
RCV000074639 | SCV000107839 | no known pathogenicity | Lynch syndrome | 2013-09-05 | reviewed by expert panel | research | MAF >1% & Multifactorial likelihood analysis posterior probability <0.001 |
Invitae | RCV000524102 | SCV000153934 | benign | Hereditary nonpolyposis colorectal neoplasms | 2024-02-01 | criteria provided, single submitter | clinical testing | |
Ambry Genetics | RCV000130493 | SCV000185362 | benign | Hereditary cancer-predisposing syndrome | 2014-11-18 | criteria provided, single submitter | clinical testing | This alteration is classified as benign based on a combination of the following: 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. |
Eurofins Ntd Llc |
RCV000035317 | SCV000203035 | benign | not specified | 2014-04-11 | criteria provided, single submitter | clinical testing | |
Prevention |
RCV000035317 | SCV000302866 | benign | not specified | criteria provided, single submitter | clinical testing | ||
Illumina Laboratory Services, |
RCV001094632 | SCV000430958 | likely benign | Lynch syndrome 5 | 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. |
Color Diagnostics, |
RCV000130493 | SCV000685173 | benign | Hereditary cancer-predisposing syndrome | 2015-04-01 | criteria provided, single submitter | clinical testing | |
ARUP Laboratories, |
RCV000035317 | SCV001158618 | benign | not specified | 2019-02-06 | criteria provided, single submitter | clinical testing | |
Gene |
RCV001711146 | SCV001940728 | benign | not provided | 2015-03-03 | criteria provided, single submitter | clinical testing | |
Sema4, |
RCV000130493 | SCV002535604 | benign | Hereditary cancer-predisposing syndrome | 2020-01-30 | criteria provided, single submitter | curation | |
Center for Genomic Medicine, |
RCV000035317 | SCV002552289 | benign | not specified | 2023-08-15 | criteria provided, single submitter | clinical testing | |
KCCC/NGS Laboratory, |
RCV001094632 | SCV004015994 | benign | Lynch syndrome 5 | 2023-07-07 | criteria provided, single submitter | clinical testing | |
Laboratory for Molecular Medicine, |
RCV000035317 | SCV000058965 | likely benign | not specified | 2008-07-10 | no assertion criteria provided | clinical testing | |
Mayo Clinic Laboratories, |
RCV000035317 | SCV000257206 | benign | not specified | no assertion criteria provided | research | ||
True Health Diagnostics | RCV000130493 | SCV000788041 | likely benign | Hereditary cancer-predisposing syndrome | 2018-02-20 | no assertion criteria provided | clinical testing | |
Department of Pathology and Laboratory Medicine, |
RCV001356459 | SCV001551636 | benign | Endometrial carcinoma | no assertion criteria provided | clinical testing | The MSH6 p.His388= variant was identified in 4 of 908 proband chromosomes (frequency: 0.004) from cases with high risk breast and colon cancer and was not identified in 332 chromosomes from healthy individuals (Kolodner 1999, Perez-Cabornero 2009, Sanchez 2005, Wasielewski 2009). The variant was identified in the following databases: dbSNP (ID: rs55708305) “With other allele”, ClinVar (classified benign, reviewed by an expert panel 2013, submitters: benign by InSIGHT, Invitae, Ambry Genetics, EGL Genetic Diagnostics, Prevention Genetics and Mayo Clinic, and likely benign by Illumina and the Laboratory for Molecular Medicine), Clinvitae (4x), UMD-LSDB (8x neutral), Insight Colon Cancer Gene Variant Database (4x), Mismatch Repair Genes Variant Database (3x), Insight Hereditary Tumors Database (4x) and was not identified in Cosmic, MutDB, and Zhejiang Colon Cancer Database. The variant was identified in control databases in 1240 (29 homozygous) of 276736 chromosomes at a frequency of 0.004 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). Observations by population include African in 1060 of 24012 chromosomes (freq: 0.04), Other in 18 of 6454 chromosomes (freq: 0.003), Latino in 125 of 34402 chromosomes (freq: 0.004), European Non-Finnish in 37 of 126300 chromosomes (freq: 0.0003); it was not observed in the Ashkenazi Jewish, East Asian, European Finnish, and South Asian populations. The p.His388= 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 this variant meets our laboratory's criteria to be classified as benign. | |
Genome Diagnostics Laboratory, |
RCV000035317 | SCV001809328 | benign | not specified | no assertion criteria provided | clinical testing | ||
Clinical Genetics, |
RCV000035317 | SCV001917768 | benign | not specified | no assertion criteria provided | clinical testing | ||
Laboratory of Diagnostic Genome Analysis, |
RCV000035317 | SCV002036563 | benign | not specified | no assertion criteria provided | clinical testing |