Total submissions: 9
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Invitae | RCV001089387 | SCV000253109 | likely benign | Hereditary nonpolyposis colorectal neoplasms | 2023-11-30 | criteria provided, single submitter | clinical testing | |
| Laboratory for Molecular Medicine, |
RCV000455691 | SCV000539700 | likely benign | not specified | 2016-10-26 | criteria provided, single submitter | clinical testing | Variant identified in a genome or exome case(s) and assessed due to predicted null impact of the variant or pathogenic assertions in the literature or databases. Disclaimer: This variant has not undergone full assessment. The following are preliminary notes: Silent variant. MaxMAF = 0.012% in ExAC. Classified in ClinVar as Likely Benign by Invitae (1 star). |
| Ambry Genetics | RCV000575136 | SCV000662436 | likely benign | Hereditary cancer-predisposing syndrome | 2016-06-29 | criteria provided, single submitter | clinical testing | This alteration is classified as likely 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. |
| Color Diagnostics, |
RCV000575136 | SCV000690364 | likely benign | Hereditary cancer-predisposing syndrome | 2016-04-28 | criteria provided, single submitter | clinical testing | |
| ARUP Laboratories, |
RCV000756350 | SCV000884136 | likely benign | not provided | 2017-06-23 | criteria provided, single submitter | clinical testing | |
| Quest Diagnostics Nichols Institute San Juan Capistrano | RCV000756350 | SCV000888278 | likely benign | not provided | 2018-04-13 | criteria provided, single submitter | clinical testing | |
| Gene |
RCV000756350 | SCV001943381 | likely benign | not provided | 2018-07-09 | criteria provided, single submitter | clinical testing | |
| CHEO Genetics Diagnostic Laboratory, |
RCV001798667 | SCV002042053 | likely benign | Breast and/or ovarian cancer | 2020-01-03 | criteria provided, single submitter | clinical testing | |
| Department of Pathology and Laboratory Medicine, |
RCV001355723 | SCV001550681 | likely benign | Carcinoma of colon | no assertion criteria provided | clinical testing | The MSH6 p.Thr118= variant was not identified in the literature nor was it identified in the COGR, Cosmic, MutDB, UMD-LSDB, Insight Colon Cancer Gene Variant Database, Zhejiang Colon Cancer Database, Mismatch Repair Genes Variant Database, or Insight Hereditary Tumors databases. The variant was identified in dbSNP (ID: rs558590898) as “With Likely benign allele”, ClinVar (as likely benign by Invitae, Partners HealthCare Personalized Medicine, Ambry Genetics, and Color), and Clinvitae (3x). The variant was identified in control databases in 4 of 246272 chromosomes at a frequency of 0.00002 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 1 of 15304 chromosomes (freq: 0.00007), European (Non-Finnish) in 2 of 111720 chromosomes (freq: 0.00002), and East Asian in 1 of 17248 chromosomes (freq: 0.000058); it was not observed in the Other, Latino, Ashkenazi Jewish, Finnish, and South Asian populations. The p.Thr118= 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. |