Total submissions: 29
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Labcorp Genetics |
RCV000119106 | SCV000153817 | benign | Ataxia-telangiectasia syndrome | 2024-02-01 | criteria provided, single submitter | clinical testing | |
Gene |
RCV000120166 | SCV000167061 | benign | not specified | 2013-10-25 | 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 | RCV000131001 | SCV000185925 | benign | Hereditary cancer-predisposing syndrome | 2014-11-24 | 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. |
Eurofins Ntd Llc |
RCV000120166 | SCV000231466 | benign | not specified | 2015-03-30 | criteria provided, single submitter | clinical testing | |
Vantari Genetics | RCV000131001 | SCV000266237 | likely benign | Hereditary cancer-predisposing syndrome | 2016-02-04 | criteria provided, single submitter | clinical testing | |
Center for Pediatric Genomic Medicine, |
RCV000223988 | SCV000280714 | benign | not provided | 2014-09-15 | criteria provided, single submitter | clinical testing | |
Color Diagnostics, |
RCV000131001 | SCV000682266 | benign | Hereditary cancer-predisposing syndrome | 2014-11-18 | criteria provided, single submitter | clinical testing | |
Prevention |
RCV000120166 | SCV000805580 | benign | not specified | 2017-02-17 | criteria provided, single submitter | clinical testing | |
Illumina Laboratory Services, |
RCV000119106 | SCV001260305 | likely benign | Ataxia-telangiectasia syndrome | 2017-04-27 | criteria provided, single submitter | clinical testing | This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign. |
ARUP Laboratories, |
RCV000223988 | SCV001477885 | benign | not provided | 2023-08-11 | criteria provided, single submitter | clinical testing | |
Al Jalila Children’s Genomics Center, |
RCV000119106 | SCV001984724 | benign | Ataxia-telangiectasia syndrome | 2020-03-23 | criteria provided, single submitter | clinical testing | |
Quest Diagnostics Nichols Institute San Juan Capistrano | RCV000223988 | SCV002047259 | benign | not provided | 2021-03-30 | criteria provided, single submitter | clinical testing | |
National Health Laboratory Service, |
RCV002225343 | SCV002505003 | benign | Hereditary breast ovarian cancer syndrome | 2022-04-19 | criteria provided, single submitter | clinical testing | |
Mendelics | RCV000120166 | SCV002518013 | benign | not specified | 2022-05-04 | criteria provided, single submitter | clinical testing | |
Sema4, |
RCV000131001 | SCV002528475 | benign | Hereditary cancer-predisposing syndrome | 2020-09-15 | criteria provided, single submitter | curation | |
Center for Genomic Medicine, |
RCV000120166 | SCV002760507 | benign | not specified | 2023-08-15 | criteria provided, single submitter | clinical testing | |
Ce |
RCV000223988 | SCV003916778 | benign | not provided | 2024-08-01 | criteria provided, single submitter | clinical testing | ATM: BP4, BS1, BS2 |
KCCC/NGS Laboratory, |
RCV003315697 | SCV004016586 | benign | Familial cancer of breast | 2023-07-07 | criteria provided, single submitter | clinical testing | |
Myriad Genetics, |
RCV003315697 | SCV005083950 | benign | Familial cancer of breast | 2024-04-19 | criteria provided, single submitter | clinical testing | This variant is considered benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance. |
Breakthrough Genomics, |
RCV000223988 | SCV005213516 | likely benign | not provided | criteria provided, single submitter | not provided | ||
ITMI | RCV000120166 | SCV000084308 | not provided | not specified | 2013-09-19 | no assertion provided | reference population | |
Genome Diagnostics Laboratory, |
RCV000119106 | SCV000745803 | benign | Ataxia-telangiectasia syndrome | 2017-09-27 | no assertion criteria provided | clinical testing | |
True Health Diagnostics | RCV000131001 | SCV000886664 | likely benign | Hereditary cancer-predisposing syndrome | 2018-11-16 | no assertion criteria provided | clinical testing | |
Department of Pathology and Laboratory Medicine, |
RCV001354360 | SCV001548957 | benign | Malignant tumor of breast | no assertion criteria provided | clinical testing | ATM, EXON6, c.544G>C, p.Val182Leu, Heterozygous, Benign The ATM p.Val182Leu variant was identified in 7 of 856 proband chromosomes (frequency: 0.008) from a multiethnic American cohort of individuals or families with breast cancer and in 4 of 852 control chromosomes (frequency: 0.005) from healthy women (Bretsky 2003). The variant was also identified in dbSNP (ID: rs3218707) as “With other allele” and ClinVar (classified as benign by GeneDx, Ambry Genetics, Invitae, Prevention Genetics, and four other submitters; and as likely benign by Vantari Genetics and True Health Diagnostics). The variant was not identified in LOVD 3.0. The variant was identified in control databases in 814 of 273878 chromosomes at a frequency of 0.003 (Genome Aggregation Database Feb 27, 2017), increasing the likelihood this could be a low frequency benign variant. It was observed in the following populations: African in 526 of 23792 chromosomes (freq: 0.02) (1 homozygote in ExAC), Other in 19 of 6360 chromosomes (freq: 0.003), Latino in 159 of 34126 chromosomes (freq: 0.005), European Non-Finnish in 96 of 124726 chromosomes (freq: 0.0008) (1 homozygote in ExAC), Ashkenazi Jewish in 5 of 10042 chromosomes (freq: 0.0005), European Finnish in 7 of 25552 chromosomes (freq: 0.0003), and South Asian in 2 of 30596 chromosomes (freq: 0.00007); it was not observed in the East Asian population. The variant was identified by our laboratory in 6 individuals with breast, colon or endometrial cancers, co-occurring with multiple pathogenic variants: BRCA2, c.2957_2958insG (p.Asn986Lysfs*2) and CHEK2, c.1100del (p.Thr367Metfs*15). The p.Val182 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood the Leu variant impacts 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) 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. Assessment Date: 2019/07/03 References (PMIDs): 11821961, 12917204, 17640065 | |
Clinical Genetics Laboratory, |
RCV000120166 | SCV001906397 | benign | not specified | no assertion criteria provided | clinical testing | ||
Clinical Genetics, |
RCV000120166 | SCV001922882 | benign | not specified | no assertion criteria provided | clinical testing | ||
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, |
RCV000120166 | SCV001951760 | benign | not specified | no assertion criteria provided | clinical testing | ||
Laboratory of Diagnostic Genome Analysis, |
RCV000223988 | SCV002036363 | likely benign | not provided | no assertion criteria provided | clinical testing | ||
Natera, |
RCV000119106 | SCV002094074 | likely benign | Ataxia-telangiectasia syndrome | 2019-10-22 | no assertion criteria provided | clinical testing |