Total submissions: 18
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Evidence- |
RCV000031057 | SCV000244324 | benign | Breast-ovarian cancer, familial, susceptibility to, 1 | 2015-08-10 | reviewed by expert panel | curation | IARC class based on posterior probability from multifactorial likelihood analysis, thresholds for class as per Plon et al. 2008 (PMID: 18951446). Class 1 based on posterior probability = 0.00000991 |
Labcorp Genetics |
RCV001084418 | SCV000075900 | benign | Hereditary breast ovarian cancer syndrome | 2024-01-10 | criteria provided, single submitter | clinical testing | |
Gene |
RCV000758799 | SCV000108659 | likely benign | not provided | 2019-06-27 | criteria provided, single submitter | clinical testing | This variant is associated with the following publications: (PMID: 21990134, 16518693, 22753008, 17924331, 26306726, 16267036, 23893897, 18273839, 25682074, 18951461, 18779604, 15385441, 25348012, 29453630) |
Ambry Genetics | RCV000162978 | SCV000213466 | 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: 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. |
Color Diagnostics, |
RCV000162978 | SCV000537503 | likely benign | Hereditary cancer-predisposing syndrome | 2015-11-25 | criteria provided, single submitter | clinical testing | |
Genetic Services Laboratory, |
RCV000074574 | SCV000593691 | likely benign | not specified | 2017-04-13 | criteria provided, single submitter | clinical testing | |
Quest Diagnostics Nichols Institute San Juan Capistrano | RCV000758799 | SCV000887646 | likely benign | not provided | 2023-07-19 | criteria provided, single submitter | clinical testing | |
Women's Health and Genetics/Laboratory Corporation of America, |
RCV000074574 | SCV000918734 | benign | not specified | 2019-09-26 | criteria provided, single submitter | clinical testing | Variant summary: BRCA1 c.2584A>G (p.Lys862Glu) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 6e-05 in 251066 control chromosomes (gnomAD). This frequency is not higher than expected for a pathogenic variant in BRCA1 causing Hereditary Breast and Ovarian Cancer (6e-05 vs 0.001), allowing no conclusion about variant significance. c.2584A>G has been reported in the literature in individuals affected with Hereditary Breast and Ovarian Cancer, however these reports do not provide evidence for pathogenicity (Judkins_2005, Wong-Brown_2015, Anczukow_2008, Kurian_2008, Minucci_2015, Peyrat_1998, Li_2018, Kraemer_2019). In addition, multifactorial probability models, performing systematic assessments of variants of unknown significance in the BRCA genes, which included analysis of co-occurrence in trans with known deleterious mutations, personal and family history of cancer, tumor pathology and co-segregation with disease in pedigrees, predicted this variant to be neutral (Easton 2007 and Lindor 2012). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Six other submitters, including one expert panel (ENIGMA), have provided clinical-significance assessments for this variant in ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as likely benign while the expert panel has classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign. |
CHEO Genetics Diagnostic Laboratory, |
RCV001798028 | SCV002043433 | likely benign | Breast and/or ovarian cancer | 2021-04-09 | criteria provided, single submitter | clinical testing | |
ARUP Laboratories, |
RCV000758799 | SCV002049438 | uncertain significance | not provided | 2021-11-09 | criteria provided, single submitter | clinical testing | The BRCA1 c.2584A>G; p.Lys862Glu variant (rs80356927) is reported in the literature in individuals affected with breast and/or ovarian cancer, although it was no demonstrated to be disease-causing (Peyrat 1998). This variant is reported as benign or likely benign by multiple laboratories in ClinVar (Variation ID: 37476), and it is found in the general population with an overall allele frequency of 0.01% (16/282472 alleles) in the Genome Aggregation Database. The lysine at codon 862 is moderately conserved, and computational analyses predict that this variant is deleterious (REVEL: 0.808). However, multifactorial likelihood analysis considering family history of disease, co-occurrence with pathogenic variants, and co-segregation with disease suggest this variant has very low odds of causing disease (Easton 2007, Lindor 2012). However, given the lack of clinical and functional data, the significance of the p.Lys862Glu variant is uncertain at this time. References: Easton DF et al. A systematic genetic assessment of 1,433 sequence variants of unknown clinical significance in the BRCA1 and BRCA2 breast cancer-predisposition genes. Am J Hum Genet. 2007 Nov;81(5):873-83. PMID: 17924331. Lindor NM et al. A review of a multifactorial probability-based model for classification of BRCA1 and BRCA2 variants of uncertain significance (VUS). Hum Mutat. 2012 Jan;33(1):8-21. PMID: 21990134 Peyrat JP et al. Germline BRCA1 mutations in patients from 84 families with breast and/or ovarian cancers in northern France. Eur J Cancer Prev. 1998 Feb;7 Suppl 1:S7-12. PMID: 10866029. |
Sema4, |
RCV000162978 | SCV002538136 | likely benign | Hereditary cancer-predisposing syndrome | 2021-06-22 | criteria provided, single submitter | curation | |
KCCC/NGS Laboratory, |
RCV000031057 | SCV004016763 | benign | Breast-ovarian cancer, familial, susceptibility to, 1 | 2023-07-07 | criteria provided, single submitter | clinical testing | |
Prevention |
RCV004554623 | SCV004740207 | likely benign | BRCA1-related disorder | 2019-09-24 | criteria provided, single submitter | clinical testing | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). |
Sharing Clinical Reports Project |
RCV000031057 | SCV000053652 | benign | Breast-ovarian cancer, familial, susceptibility to, 1 | 2010-02-10 | no assertion criteria provided | clinical testing | |
Breast Cancer Information Core |
RCV000031057 | SCV000144481 | uncertain significance | Breast-ovarian cancer, familial, susceptibility to, 1 | 2002-05-29 | no assertion criteria provided | clinical testing | |
Department of Pathology and Laboratory Medicine, |
RCV001357913 | SCV001553513 | likely benign | Malignant tumor of breast | no assertion criteria provided | clinical testing | The BRCA1 p.Lys862Glu variant was identified in 8 of 111260 proband chromosomes (frequency: 0.00007) from individuals or families with breast cancer (Judkins 2005). The variant was also identified in dbSNP (ID: rs80356927) as “With Likely benign allele”, Clinvitae database (classified as benign by ClinVar; classified as likely benign by ClinVar, Invitae), Fanconi Anemia Mutation Database (LOVD), ARUP Laboratories BRCA Mutations Database (classified as not pathogenic or of no clinical significance), the ClinVar database (classified as benign by ENIGMA, Ambry genetics, SCRP; classified as likely benign by Invitae, GeneDx; classified as uncertain significance by BIC), the BIC database (5x with unknown clinical importance), and UMD (12x with a “likely neutral” classification). This variant was identified in the Exome Aggregation Consortium database (August 8th 2016) in 12 of 121328 chromosomes (freq. 0.0001) in the following populations: European in 8 of 66696 chromosomes (freq. 0.0001), Asian in 3 of 16502 chromosomes (freq. 0.0002), Finnish in 1 of 6614 chromosomes (freq. 0.0002), but was not seen in African, Latino and Other populations. The p.Lys862 residue is not conserved in mammals and four out of five computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; however, this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. The variant was also classified as neutral with odds in favor of neutrality 2059 in a study utilizing evidence of co-occurrence with a pathogenic variant, family history and if available segregation of the variant with disease (Easton 2007). The variant was also found to have a probability of being deleterious of 9.91√ó10‚à Ã6 in a similar study (Lindor 2012). In addition, a study by Burk-Herrick (2005) found the variant has no effect by analyzing 19 marsupials and 94 eutherian mammal sequences, which were used to rank oncogenic risk of missence mutations based on conservation. 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. | |
Clinical Genetics Laboratory, |
RCV000758799 | SCV001905900 | likely benign | not provided | no assertion criteria provided | clinical testing | ||
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, |
RCV000074574 | SCV001957180 | benign | not specified | no assertion criteria provided | clinical testing |