ClinVar Miner

Variants from Cancer Genetics and Genomics Laboratory, British Columbia Cancer Agency with conflicting interpretations

Location: Canada  Primary collection method: clinical testing
Minimum review status of the submission from Cancer Genetics and Genomics Laboratory, British Columbia Cancer Agency: Collection method of the submission from Cancer Genetics and Genomics Laboratory, British Columbia Cancer Agency:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic) 		Variants with a confidence conflict
(e.g. benign vs likely benign) 		Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects) 		Variants with a clinically significant conflict
(e.g. benign vs pathogenic) 		Variants with any conflict
4 44 19 58 37 0 0 91

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

All submitters
Cancer Genetics and Genomics Laboratory, British Columbia Cancer Agency likely pathogenic uncertain significance likely benign benign
pathogenic 1 0 0 0
uncertain significance 0 0 14 8
likely benign 0 6 0 12
benign 0 11 45 19

Submitter to submitter summary #

Total submitters: 33
Download table as spreadsheet
Submitter Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic) 		Variants with a confidence conflict
(e.g. benign vs likely benign) 		Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects) 		Variants with a clinically significant conflict
(e.g. benign vs pathogenic) 		Variants with any conflict
Biesecker Lab/Clinical Genomics Section, National Institutes of Health 0 2 19 4 2 0 0 25
CeGaT Center for Human Genetics Tuebingen 0 17 0 22 0 0 0 22
Invitae 0 31 0 0 19 0 0 19
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario 0 29 0 17 1 0 0 18
PreventionGenetics, part of Exact Sciences 0 53 0 15 0 0 0 15
Mayo Clinic Laboratories, Mayo Clinic 0 36 0 15 0 0 0 15
Genetic Services Laboratory, University of Chicago 0 17 0 13 0 0 0 13
GeneDx 0 40 0 9 4 0 0 13
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 29 0 4 8 0 0 12
Eurofins Ntd Llc (ga) 0 46 0 10 0 0 0 10
Fulgent Genetics, Fulgent Genetics 0 27 0 10 0 0 0 10
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 25 0 10 0 0 0 10
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 26 0 7 1 0 0 8
Quest Diagnostics Nichols Institute San Juan Capistrano 0 15 0 6 2 0 0 8
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 59 0 7 0 0 0 7
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute 0 59 0 7 0 0 0 7
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital 0 54 0 6 0 0 0 6
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 70 0 5 0 0 0 5
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 7 0 4 0 0 0 4
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 0 7 0 3 1 0 0 4
Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research 0 0 0 1 2 0 0 3
Department of Pathology and Molecular Medicine, Queen's University 0 12 0 2 1 0 0 3
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 6 0 3 0 0 0 3
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden 0 12 0 2 0 0 0 2
King Laboratory, University of Washington 0 1 0 1 0 0 0 1
Revvity Omics, Revvity 0 0 0 0 1 0 0 1
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital 0 0 0 1 0 0 0 1
Illumina Laboratory Services, Illumina 0 1 0 0 1 0 0 1
CSER _CC_NCGL, University of Washington 0 0 0 0 1 0 0 1
Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto 0 24 0 0 1 0 0 1
3DMed Clinical Laboratory Inc 0 0 0 0 1 0 0 1
Breast Center, Key Laboratory of Carcinogenesis and Translational Research 0 0 0 0 1 0 0 1
National Health Laboratory Service, Universitas Academic Hospital and University of the Free State 0 2 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 91
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_007294.4(BRCA1):c.3548A>G (p.Lys1183Arg) rs16942 0.30784
NM_007294.4(BRCA1):c.3113A>G (p.Glu1038Gly) rs16941 0.29115
NM_000059.4(BRCA2):c.1114A>C (p.Asn372His) rs144848 0.23116
NM_007294.4(BRCA1):c.2077G>A (p.Asp693Asn) rs4986850 0.05782
NM_007294.4(BRCA1):c.1067A>G (p.Gln356Arg) rs1799950 0.04695
NM_000059.4(BRCA2):c.2971A>G (p.Asn991Asp) rs1799944 0.04357
NM_000059.4(BRCA2):c.10234A>G (p.Ile3412Val) rs1801426 0.03864
NM_000059.4(BRCA2):c.865A>C (p.Asn289His) rs766173 0.03693
NM_000059.4(BRCA2):c.5744C>T (p.Thr1915Met) rs4987117 0.01834
NM_007294.4(BRCA1):c.4956G>A (p.Met1652Ile) rs1799967 0.01348
NM_007294.4(BRCA1):c.3119G>A (p.Ser1040Asn) rs4986852 0.01109
NM_000059.4(BRCA2):c.7319A>G (p.His2440Arg) rs4986860 0.00984
NM_000059.4(BRCA2):c.7469T>C (p.Ile2490Thr) rs11571707 0.00868
NM_000059.4(BRCA2):c.8851G>A (p.Ala2951Thr) rs11571769 0.00809
NM_000059.4(BRCA2):c.3264T>C (p.Pro1088=) rs36060526 0.00793
NM_000059.4(BRCA2):c.9730G>A (p.Val3244Ile) rs11571831 0.00792
NM_000059.4(BRCA2):c.5418A>G (p.Glu1806=) rs34351119 0.00791
NM_000059.4(BRCA2):c.4258G>T (p.Asp1420Tyr) rs28897727 0.00609
NM_000059.4(BRCA2):c.9257-16T>C rs11571818 0.00597
NM_000059.4(BRCA2):c.9976A>T (p.Lys3326Ter) rs11571833 0.00597
NM_000059.4(BRCA2):c.5199C>T (p.Ser1733=) rs28897734 0.00488
NM_007294.4(BRCA1):c.4039A>G (p.Arg1347Gly) rs28897689 0.00419
NM_000059.4(BRCA2):c.4068G>A (p.Leu1356=) rs28897724 0.00295
NM_000059.4(BRCA2):c.68-7T>A rs81002830 0.00277
NM_000059.4(BRCA2):c.6100C>T (p.Arg2034Cys) rs1799954 0.00268
NM_000059.4(BRCA2):c.6323G>A (p.Arg2108His) rs35029074 0.00260
NM_007294.4(BRCA1):c.4535G>T (p.Ser1512Ile) rs1800744 0.00240
NM_000059.4(BRCA2):c.8182G>A (p.Val2728Ile) rs28897749 0.00239
NM_007294.4(BRCA1):c.114G>A (p.Lys38=) rs1800062 0.00233
NM_000059.4(BRCA2):c.3516G>A (p.Ser1172=) rs1799952 0.00228
NM_000059.4(BRCA2):c.125A>G (p.Tyr42Cys) rs4987046 0.00158
NM_000059.4(BRCA2):c.8567A>C (p.Glu2856Ala) rs11571747 0.00158
NM_007294.4(BRCA1):c.2521C>T (p.Arg841Trp) rs1800709 0.00137
NM_000059.4(BRCA2):c.10110G>A (p.Arg3370=) rs28897762 0.00132
NM_000059.4(BRCA2):c.1938C>T (p.Ser646=) rs28897711 0.00096
NM_000059.4(BRCA2):c.978C>A (p.Ser326Arg) rs28897706 0.00082
NM_000059.4(BRCA2):c.1151C>T (p.Ser384Phe) rs41293475 0.00074
NM_007294.4(BRCA1):c.2733A>G (p.Gly911=) rs1800740 0.00066
NM_007294.4(BRCA1):c.3024G>A (p.Met1008Ile) rs1800704 0.00065
NM_007294.4(BRCA1):c.981A>G (p.Thr327=) rs1800063 0.00065
NM_000059.4(BRCA2):c.7544C>T (p.Thr2515Ile) rs28897744 0.00048
NM_007294.4(BRCA1):c.2566T>C (p.Tyr856His) rs80356892 0.00046
NM_007294.4(BRCA1):c.1036C>T (p.Pro346Ser) rs80357015 0.00032
NM_000059.4(BRCA2):c.5785A>G (p.Ile1929Val) rs79538375 0.00031
NM_000059.4(BRCA2):c.1395A>C (p.Val465=) rs11571641 0.00026
NM_000059.4(BRCA2):c.1786G>C (p.Asp596His) rs56328701 0.00025
NM_000059.4(BRCA2):c.440A>G (p.Gln147Arg) rs80358674 0.00025
NM_000059.4(BRCA2):c.5070A>C (p.Lys1690Asn) rs56087561 0.00023
NM_007294.4(BRCA1):c.4484+14A>G rs80358022 0.00019
NM_000059.4(BRCA2):c.3445A>G (p.Met1149Val) rs80358589 0.00013
NM_000059.4(BRCA2):c.2919G>A (p.Ser973=) rs45525041 0.00012
NM_000059.4(BRCA2):c.2538A>C (p.Ser846=) rs11571654 0.00009
NM_000059.4(BRCA2):c.4614T>C (p.Ser1538=) rs45520945 0.00009
NM_007294.4(BRCA1):c.5332+13G>T rs372391060 0.00007
NM_000059.4(BRCA2):c.1362A>G (p.Lys454=) rs55919657 0.00006
NM_007294.4(BRCA1):c.1392C>T (p.Thr464=) rs533802049 0.00006
NM_007294.4(BRCA1):c.795T>C (p.Ser265=) rs201441987 0.00006
NM_000059.4(BRCA2):c.2550A>G (p.Gln850=) rs80359785 0.00005
NM_000059.4(BRCA2):c.9087G>A (p.Ala3029=) rs368576266 0.00005
NM_007294.4(BRCA1):c.199G>T (p.Asp67Tyr) rs80357102 0.00005
NM_000059.4(BRCA2):c.4531G>A (p.Glu1511Lys) rs376338226 0.00004
NM_007294.4(BRCA1):c.75C>T (p.Pro25=) rs80356839 0.00004
NM_000059.4(BRCA2):c.1744A>C (p.Thr582Pro) rs80358457 0.00003
NM_007294.4(BRCA1):c.396C>A (p.Asn132Lys) rs80357413 0.00003
NM_007294.4(BRCA1):c.5152+15A>G rs750905289 0.00003
NM_007294.4(BRCA1):c.5310G>A (p.Gly1770=) rs273901761 0.00003
NM_007294.4(BRCA1):c.5347A>C (p.Met1783Leu) rs80357012 0.00003
NM_007294.4(BRCA1):c.594-2A>C rs80358033 0.00003
NM_007294.4(BRCA1):c.81-6T>C rs80358179 0.00003
NM_000059.4(BRCA2):c.10150C>T (p.Arg3384Ter) rs397507568 0.00001
NM_007294.4(BRCA1):c.154C>T (p.Leu52Phe) rs80357084 0.00001
NM_007294.4(BRCA1):c.3416G>T (p.Ser1139Ile) rs80357228 0.00001
NM_007294.4(BRCA1):c.886A>G (p.Arg296Gly) rs748675395 0.00001
NM_000059.4(BRCA2):c.10253_10256del (p.Ile3418fs) rs80359259
NM_000059.4(BRCA2):c.1056C>T (p.Tyr352=) rs786201858
NM_000059.4(BRCA2):c.1077A>G (p.Glu359=) rs1135401832
NM_000059.4(BRCA2):c.1909+22del rs276174816
NM_000059.4(BRCA2):c.1909+22dup rs276174816
NM_000059.4(BRCA2):c.3786A>T (p.Ser1262=) rs1042077901
NM_000059.4(BRCA2):c.4928T>C (p.Val1643Ala) rs28897731
NM_000059.4(BRCA2):c.627C>A (p.Leu209=) rs28897704
NM_000059.4(BRCA2):c.8850G>T (p.Lys2950Asn) rs28897754
NM_000059.4(BRCA2):c.9104A>C (p.Tyr3035Ser) rs80359165
NM_007294.4(BRCA1):c.2612C>T (p.Pro871Leu) rs799917
NM_007294.4(BRCA1):c.426C>T (p.Pro142=) rs542687218
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) rs1799966
NM_007294.4(BRCA1):c.4860T>C (p.Thr1620=) rs750938749
NM_007294.4(BRCA1):c.4868C>G (p.Ala1623Gly) rs80356862
NM_007294.4(BRCA1):c.81-14C>T rs80358006
NM_007294.4(BRCA1):c.823G>A (p.Gly275Ser) rs8176153
NM_007294.4(BRCA1):c.889A>C (p.Met297Leu) rs80357196

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