ClinVar Miner

Variants from Genetics Program, Instituto Nacional de Cancer with conflicting interpretations

Location: Brazil  Primary collection method: research
Minimum review status of the submission from Genetics Program, Instituto Nacional de Cancer: Collection method of the submission from Genetics Program, Instituto Nacional de Cancer:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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
12 83 3 64 17 0 0 80

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
Genetics Program, Instituto Nacional de Cancer pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 3 3 0 0 0
likely pathogenic 1 0 0 0 0
uncertain significance 0 0 0 9 5
likely benign 0 0 3 0 46
benign 0 0 2 14 0

Submitter to submitter summary #

Total submitters: 15
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
Labcorp Genetics (formerly Invitae), Labcorp 0 98 1 46 12 0 0 59
National Health Laboratory Service, Universitas Academic Hospital and University of the Free State 0 62 0 19 5 0 0 24
Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C. 0 13 0 18 2 0 0 20
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 68 0 16 0 0 0 16
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia 0 11 0 5 1 0 0 6
Hereditary Cancer Genetics group, Vall d'Hebron Institute of Oncology 0 0 0 2 1 0 0 3
German Consortium for Hereditary Breast and Ovarian Cancer, University Hospital Cologne 0 0 1 1 0 0 0 2
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital 0 0 1 1 0 0 0 2
Mendelics 0 8 0 1 1 0 0 2
CSER _CC_NCGL, University of Washington 0 1 0 1 0 0 0 1
Cancer Variant Interpretation Group UK, Institute of Cancer Research, London 0 0 0 1 0 0 0 1
Clinical Genetics Laboratory, CHRU Nancy 0 0 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 2 0 1 0 0 0 1
GeneKor MSA 0 5 0 1 0 0 0 1
Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto 0 15 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 80
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000059.4(BRCA2):c.5744C>T (p.Thr1915Met) rs4987117 0.01796
NM_007294.4(BRCA1):c.3119G>A (p.Ser1040Asn) rs4986852 0.01109
NM_007294.4(BRCA1):c.3418A>G (p.Ser1140Gly) rs2227945 0.00983
NM_007294.4(BRCA1):c.2458A>G (p.Lys820Glu) rs56082113 0.00964
NM_000059.4(BRCA2):c.7319A>G (p.His2440Arg) rs4986860 0.00910
NM_000059.4(BRCA2):c.3264T>C (p.Pro1088=) rs36060526 0.00793
NM_000059.4(BRCA2):c.7017G>C (p.Lys2339Asn) rs45574331 0.00792
NM_000059.4(BRCA2):c.1788T>C (p.Asp596=) rs11571642 0.00768
NM_000059.4(BRCA2):c.9730G>A (p.Val3244Ile) rs11571831 0.00725
NM_000059.4(BRCA2):c.9976A>T (p.Lys3326Ter) rs11571833 0.00597
NM_007294.4(BRCA1):c.4039A>G (p.Arg1347Gly) rs28897689 0.00419
NM_000059.4(BRCA2):c.1275A>G (p.Glu425=) rs34355306 0.00324
NM_000059.4(BRCA2):c.6412G>T (p.Val2138Phe) rs11571659 0.00318
NM_007294.4(BRCA1):c.557C>A (p.Ser186Tyr) rs55688530 0.00301
NM_000059.4(BRCA2):c.4068G>A (p.Leu1356=) rs28897724 0.00295
NM_000059.4(BRCA2):c.4681C>A (p.His1561Asn) rs2219594 0.00292
NM_000059.4(BRCA2):c.7805+6C>G rs81002819 0.00290
NM_000059.4(BRCA2):c.5640T>G (p.Asn1880Lys) rs11571657 0.00288
NM_000059.4(BRCA2):c.3869G>A (p.Cys1290Tyr) rs41293485 0.00280
NM_000059.4(BRCA2):c.6100C>T (p.Arg2034Cys) rs1799954 0.00268
NM_000059.4(BRCA2):c.6220C>A (p.His2074Asn) rs34309943 0.00247
NM_007294.4(BRCA1):c.4535G>T (p.Ser1512Ile) rs1800744 0.00240
NM_007294.4(BRCA1):c.2167A>G (p.Asn723Asp) rs4986845 0.00209
NM_000059.4(BRCA2):c.2927C>T (p.Ser976Phe) rs11571656 0.00208
NM_000059.4(BRCA2):c.7150C>A (p.Gln2384Lys) rs55977008 0.00203
NM_000059.4(BRCA2):c.8503T>C (p.Ser2835Pro) rs11571746 0.00202
NM_000059.4(BRCA2):c.2926T>A (p.Ser976Thr) rs144862123 0.00192
NM_000059.4(BRCA2):c.1792A>G (p.Thr598Ala) rs28897710 0.00172
NM_007294.4(BRCA1):c.21C>T (p.Arg7=) rs149402012 0.00165
NM_000059.4(BRCA2):c.125A>G (p.Tyr42Cys) rs4987046 0.00158
NM_000059.4(BRCA2):c.4187A>G (p.Gln1396Arg) rs55969723 0.00156
NM_007294.4(BRCA1):c.4682C>T (p.Thr1561Ile) rs56158747 0.00150
NM_007294.4(BRCA1):c.4600G>A (p.Val1534Met) rs55815649 0.00145
NM_007294.4(BRCA1):c.2521C>T (p.Arg841Trp) rs1800709 0.00137
NM_007294.4(BRCA1):c.4113G>A (p.Gly1371=) rs147448807 0.00135
NM_000059.4(BRCA2):c.10110G>A (p.Arg3370=) rs28897762 0.00132
NM_000546.6(TP53):c.139C>T (p.Pro47Ser) rs1800371 0.00123
NM_007294.4(BRCA1):c.591C>T (p.Cys197=) rs1799965 0.00117
NM_000059.4(BRCA2):c.1040A>G (p.Gln347Arg) rs55800493 0.00109
NM_000059.4(BRCA2):c.1911T>C (p.Gly637=) rs11571652 0.00109
NM_000059.4(BRCA2):c.9235G>A (p.Val3079Ile) rs55933907 0.00106
NM_000059.4(BRCA2):c.175C>G (p.Pro59Ala) rs56091799 0.00098
NM_000059.4(BRCA2):c.5768A>C (p.Asp1923Ala) rs45491005 0.00088
NM_000059.4(BRCA2):c.10121C>T (p.Thr3374Ile) rs56309455 0.00059
NM_007294.4(BRCA1):c.4840C>T (p.Pro1614Ser) rs70953660 0.00059
NM_000059.4(BRCA2):c.2803G>A (p.Asp935Asn) rs28897716 0.00054
NM_000059.4(BRCA2):c.7435+6G>A rs81002852 0.00053
NM_007294.4(BRCA1):c.5348T>C (p.Met1783Thr) rs55808233 0.00051
NM_007294.4(BRCA1):c.301+8T>C rs80358101 0.00049
NM_000059.4(BRCA2):c.7544C>T (p.Thr2515Ile) rs28897744 0.00048
NM_000059.4(BRCA2):c.322A>C (p.Asn108His) rs80358567 0.00034
NM_000059.4(BRCA2):c.223G>C (p.Ala75Pro) rs28897701 0.00032
NM_007294.4(BRCA1):c.3708T>G (p.Asn1236Lys) rs28897687 0.00031
NM_000059.4(BRCA2):c.5312G>A (p.Gly1771Asp) rs80358755 0.00021
NM_007294.4(BRCA1):c.5411T>A (p.Val1804Asp) rs80356920 0.00021
NM_000059.4(BRCA2):c.6803G>A (p.Arg2268Lys) rs80358906 0.00020
NM_000059.4(BRCA2):c.5612G>A (p.Ser1871Asn) rs80358782 0.00019
NM_000059.4(BRCA2):c.9770A>G (p.Lys3257Arg) rs55847618 0.00019
NM_000059.4(BRCA2):c.7712A>G (p.Glu2571Gly) rs55689095 0.00018
NM_007294.4(BRCA1):c.4410A>T (p.Glu1470Asp) rs80357075 0.00016
NM_000059.4(BRCA2):c.5986G>A (p.Ala1996Thr) rs80358833 0.00011
NM_000059.4(BRCA2):c.4977C>T (p.Ser1659=) rs45484897 0.00009
NM_000059.4(BRCA2):c.9501+3A>T rs61757642 0.00007
NM_007294.4(BRCA1):c.5117G>C (p.Gly1706Ala) rs80356860 0.00005
NM_000059.4(BRCA2):c.280C>T (p.Pro94Ser) rs80358531 0.00004
NM_007294.4(BRCA1):c.1881C>G (p.Val627=) rs80356838 0.00003
NM_007294.4(BRCA1):c.5175A>G (p.Glu1725=) rs191373374 0.00003
NM_022552.5(DNMT3A):c.1904G>A (p.Arg635Gln) rs751562376 0.00003
NM_000059.4(BRCA2):c.9728C>T (p.Pro3243Leu) rs80359241 0.00002
NM_007294.4(BRCA1):c.3746C>G (p.Thr1249Ser) rs80357099 0.00002
NM_000059.4(BRCA2):c.8668C>A (p.Leu2890Ile) rs80359127 0.00001
NM_000546.6(TP53):c.1010G>A (p.Arg337His) rs121912664 0.00001
NM_007294.4(BRCA1):c.301+12A>C rs863224757 0.00001
NM_007294.4(BRCA1):c.441+8C>T rs756130118 0.00001
NM_007294.4(BRCA1):c.5096G>A (p.Arg1699Gln) rs41293459 0.00001
NM_000059.4(BRCA2):c.9043A>G (p.Lys3015Glu) rs587781497
NM_000321.3(RB1):c.1215+1G>A rs587776783
NM_000321.3(RB1):c.1960+1G>T rs1949360306
NM_007294.4(BRCA1):c.3600G>T (p.Gln1200His) rs56214134
NM_007294.4(BRCA1):c.4964C>T (p.Ser1655Phe) rs80357390

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