Total submissions: 19
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
International Society for Gastrointestinal Hereditary Tumours |
RCV000030366 | SCV000108331 | no known pathogenicity | Lynch syndrome | 2013-09-05 | reviewed by expert panel | research | MAF >1% |
Eurofins Ntd Llc |
RCV000153747 | SCV000203314 | benign | not specified | 2018-03-21 | criteria provided, single submitter | clinical testing | |
Invitae | RCV000857365 | SCV000252714 | benign | Hereditary nonpolyposis colorectal neoplasms | 2024-02-01 | criteria provided, single submitter | clinical testing | |
Preventiongenetics, |
RCV000153747 | SCV000304728 | benign | not specified | criteria provided, single submitter | clinical testing | ||
Illumina Laboratory Services, |
RCV000625383 | SCV000469719 | benign | Lynch syndrome 4 | 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. |
ARUP Laboratories, |
RCV001668144 | SCV000604894 | benign | not provided | 2023-10-23 | criteria provided, single submitter | clinical testing | |
Clinical Genetics DNA and cytogenetics Diagnostics Lab, |
RCV000625383 | SCV000745186 | benign | Lynch syndrome 4 | 2017-05-31 | criteria provided, single submitter | clinical testing | |
Counsyl | RCV000625383 | SCV000785198 | benign | Lynch syndrome 4 | 2017-06-13 | criteria provided, single submitter | clinical testing | |
Gene |
RCV001668144 | SCV001891188 | benign | not provided | 2015-03-03 | criteria provided, single submitter | clinical testing | |
Ambry Genetics | RCV002415437 | SCV002719549 | benign | Hereditary cancer-predisposing syndrome | 2014-09-15 | 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. |
KCCC/NGS Laboratory, |
RCV000625383 | SCV004016581 | benign | Lynch syndrome 4 | 2023-07-07 | criteria provided, single submitter | clinical testing | |
Myriad Genetics, |
RCV000625383 | SCV004019871 | benign | Lynch syndrome 4 | 2023-04-05 | criteria provided, single submitter | clinical testing | This variant is considered benign. This variant is intronic and is not expected to impact mRNA splicing. |
Color Diagnostics, |
RCV002415437 | SCV004359576 | benign | Hereditary cancer-predisposing syndrome | 2015-03-31 | criteria provided, single submitter | clinical testing | |
Women's Health and Genetics/Laboratory Corporation of America, |
RCV000030366 | SCV000053033 | benign | Lynch syndrome | 2013-12-27 | no assertion criteria provided | clinical testing | |
Department of Pathology and Laboratory Medicine, |
RCV001353925 | SCV000592943 | benign | Endometrial carcinoma | no assertion criteria provided | clinical testing | The PMS2 c.2007-7C>T variant was identified in 24 of 1372 proband chromosomes (frequency: 0.017) from individuals or families with Lynch syndrome, but was classified as a benign polymorphism (Hansen 2014, Hendriks 2006, Niessen 2009, Sheng 2010, van der Klift 2016). The variant was also identified in dbSNP (rs55954143) with benign allele, ClinVar 6x (classified as benign, reviewed by an expert panel), Genesight-COGR, Insight Colon Cancer Gene Variant Database (as benign), and Mismatch Repair Genes Variant Database. The variant was not identified in Cosmic, MutDB, Zhejiang Colon Cancer Database, MMR Gene Unclassified Variants Database, or Insight Hereditary Tumors Database. The variant was identified in control databases in 14684 of 174456 chromosomes (776 homozygous) at a frequency of 0.08 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Consortium Feb 27, 2017). The variant was identified in the following populations at a frequency greater than 1%: African in 3950 of 15996 chromosomes (freq: 0.247), East Asian in 1045 of 11848 chromosomes (freq: 0.088), European (Finnish) in 1617 of 19226 chromosomes (freq: 0.084), South Asian in 1722 of 20892 chromosomes (freq: 0.082), Other in 326 of 4640 chromosomes (freq: 0.07), European (Non-Finnish) in 4958 of 72394 chromosomes (freq: 0.068), Ashkenazi Jewish* in 329 of 7828 chromosomes (freq: 0.042). In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign. | |
Mayo Clinic Laboratories, |
RCV000153747 | SCV000691963 | benign | not specified | no assertion criteria provided | clinical testing | ||
Clinical Genetics Laboratory, |
RCV000153747 | SCV001905926 | benign | not specified | no assertion criteria provided | clinical testing | ||
Clinical Genetics, |
RCV000153747 | SCV001921665 | benign | not specified | no assertion criteria provided | clinical testing | ||
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, |
RCV000153747 | SCV001953515 | benign | not specified | no assertion criteria provided | clinical testing |