ClinVar Miner

Variants from Department of Molecular Diagnostics, Institute of Oncology Ljubljana with conflicting interpretations

Location: Slovenia  Primary collection method: clinical testing
Minimum review status of the submission from Department of Molecular Diagnostics, Institute of Oncology Ljubljana: Collection method of the submission from Department of Molecular Diagnostics, Institute of Oncology Ljubljana:
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
73 147 0 51 4 3 9 59

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
Department of Molecular Diagnostics, Institute of Oncology Ljubljana pathogenic likely pathogenic uncertain significance likely benign benign association established risk allele pathogenic, low penetrance risk factor
pathogenic 0 28 6 0 0 1 1 0 2
likely pathogenic 21 0 2 0 0 0 0 1 0
uncertain significance 1 1 0 2 0 0 0 0 0
likely benign 0 0 2 0 2 0 0 0 0

Submitter to submitter summary #

Total submitters: 42
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
Myriad Genetics, Inc. 0 44 0 14 2 0 0 16
Baylor Genetics 0 66 0 12 0 0 1 13
Counsyl 0 50 0 13 0 0 0 13
Invitae 0 34 0 8 0 2 1 11
Mendelics 0 22 0 5 1 0 1 7
Institute of Human Genetics, University of Leipzig Medical Center 0 28 0 5 0 0 0 5
Ambry Genetics 0 4 0 3 0 0 0 3
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 12 0 2 1 0 0 3
Sharing Clinical Reports Project (SCRP) 0 47 0 3 0 0 0 3
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 24 0 2 0 1 0 3
Breast Cancer Information Core (BIC) (BRCA1) 0 28 0 1 0 0 2 3
BRCAlab, Lund University 0 50 0 3 0 0 0 3
OMIM 0 18 0 1 0 1 0 2
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) 0 87 0 2 0 0 0 2
Color Diagnostics, LLC DBA Color Health 0 1 0 2 0 0 0 2
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 35 0 2 0 0 0 2
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge 0 80 0 2 0 0 0 2
Genetics and Molecular Pathology, SA Pathology 0 17 0 2 0 0 0 2
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 3 0 0 0 0 2 2
Neuberg Centre For Genomic Medicine, NCGM 0 6 0 1 0 0 1 2
Department of Medical and Surgical Sciences, University of Bologna 0 0 0 2 0 0 0 2
Genetic Services Laboratory, University of Chicago 0 4 0 1 0 0 0 1
GeneDx 0 0 0 0 1 0 0 1
King Laboratory, University of Washington 0 2 0 1 0 0 0 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 1 0 1 0 0 0 1
Breast Cancer Information Core (BIC) (BRCA2) 0 40 0 0 0 0 1 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 14 0 1 0 0 0 1
Medical Genetics, University of Parma 0 2 0 1 0 0 0 1
Cancer Genetics Laboratory, Peter MacCallum Cancer Centre 0 2 0 1 0 0 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 0 0 0 0 0 1 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 10 0 0 0 0 1 1
Leiden Open Variation Database 0 2 0 0 1 0 0 1
Cancer Diagnostics Division, Gene Solutions 0 0 0 1 0 0 0 1
Institute of Human Genetics, Heidelberg University 0 1 0 0 0 0 1 1
Johns Hopkins Genomics, Johns Hopkins University 0 2 0 0 0 0 1 1
deCODE genetics, Amgen 0 2 0 1 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 4 0 1 0 0 0 1
New York Genome Center 0 2 0 0 0 1 0 1
Genomics England Pilot Project, Genomics England 0 2 0 1 0 0 0 1
Human Genetics Bochum, Ruhr University Bochum 0 5 0 1 0 0 0 1
KCCC/NGS Laboratory, Kuwait Cancer Control Center 0 12 0 0 0 0 1 1
All of Us Research Program, National Institutes of Health 0 37 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 59
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001048174.2(MUTYH):c.1103G>A (p.Gly368Asp) rs36053993 0.00341
NM_001048174.2(MUTYH):c.452A>G (p.Tyr151Cys) rs34612342 0.00168
NM_024675.4(PALB2):c.3495G>A (p.Ser1165=) rs45439097 0.00121
NM_000038.6(APC):c.3920T>A (p.Ile1307Lys) rs1801155 0.00116
NM_007194.4(CHEK2):c.1427C>T (p.Thr476Met) rs142763740 0.00032
NM_007194.4(CHEK2):c.1283C>T (p.Ser428Phe) rs137853011 0.00026
NM_001048174.2(MUTYH):c.650G>A (p.Arg217His) rs140342925 0.00009
NM_007194.4(CHEK2):c.349A>G (p.Arg117Gly) rs28909982 0.00009
NM_007194.4(CHEK2):c.444+1G>A rs121908698 0.00009
NM_024675.4(PALB2):c.2379C>T (p.Gly793=) rs377626805 0.00009
NM_006767.4(LZTR1):c.2062C>T (p.Arg688Cys) rs587777178 0.00006
NM_000051.4(ATM):c.7816A>G (p.Ile2606Val) rs376824528 0.00004
NM_000051.4(ATM):c.8147T>C (p.Val2716Ala) rs587782652 0.00004
NM_001048174.2(MUTYH):c.241C>T (p.Arg81Trp) rs765123255 0.00004
NM_007294.4(BRCA1):c.116G>A (p.Cys39Tyr) rs80357498 0.00003
NM_000051.4(ATM):c.6095G>A (p.Arg2032Lys) rs139770721 0.00001
NM_000051.4(ATM):c.8494C>T (p.Arg2832Cys) rs587779872 0.00001
NM_000059.4(BRCA2):c.9371A>T (p.Asn3124Ile) rs28897759 0.00001
NM_000077.5(CDKN2A):c.71G>C (p.Arg24Pro) rs104894097 0.00001
NM_007194.4(CHEK2):c.319+1G>A rs765080766 0.00001
NM_007194.4(CHEK2):c.85C>T (p.Gln29Ter) rs761494650 0.00001
NM_024675.4(PALB2):c.3549C>G (p.Tyr1183Ter) rs118203998 0.00001
NM_058216.3(RAD51C):c.905-2_905-1del rs587781995 0.00001
NM_000038.6(APC):c.1908_1909dup (p.Gly637fs) rs1764733583
NM_000038.6(APC):c.3927_3931del (p.Glu1309fs) rs121913224
NM_000038.6(APC):c.531+1G>A rs876659973
NM_000051.4(ATM):c.3802del (p.Glu1267_Val1268insTer) rs587779834
NM_000051.4(ATM):c.4110-1G>A rs1060501692
NM_000051.4(ATM):c.6082del (p.Gln2028fs) rs1565499093
NM_000051.4(ATM):c.7789-3T>G rs864622185
NM_000051.4(ATM):c.8425C>T (p.Gln2809Ter) rs1555137973
NM_000059.3(BRCA2):c.2808_2811del (p.Ala938Profs) rs80359351
NM_000059.4(BRCA2):c.5851_5854del (p.Ser1951fs) rs80359543
NM_000059.4(BRCA2):c.631+1G>A rs81002897
NM_000059.4(BRCA2):c.7806-2A>G rs81002836
NM_000059.4(BRCA2):c.8755-1G>A rs81002812
NM_000179.3(MSH6):c.2092C>T (p.Gln698Ter) rs63750832
NM_000179.3(MSH6):c.718C>T (p.Arg240Ter) rs63750019
NM_000249.4(MLH1):c.199G>A (p.Gly67Arg) rs63750206
NM_000249.4(MLH1):c.62C>T (p.Ala21Val) rs63750706
NM_000251.3(MSH2):c.1015C>T (p.Gln339Ter) rs1558466577
NM_000251.3(MSH2):c.1661G>A (p.Ser554Asn) rs63750597
NM_000455.5(STK11):c.863-5_863-3del rs764739106
NM_000546.6(TP53):c.1009C>T (p.Arg337Cys) rs587782529
NM_000551.4(VHL):c.224TCT[1] (p.Phe76del) rs5030648
NM_001042492.3(NF1):c.6921+1G>A rs1060500355
NM_001048174.2(MUTYH):c.1435-2A>T rs1553123105
NM_002485.5(NBN):c.657_661del (p.Lys219fs) rs587776650
NM_002528.7(NTHL1):c.211dup (p.Ala71fs) rs745671590
NM_004360.5(CDH1):c.832+1G>A rs878854697
NM_007294.4(BRCA1):c.191G>A (p.Cys64Tyr) rs55851803
NM_007294.4(BRCA1):c.3756_3759del (p.Ser1253fs) rs80357868
NM_007294.4(BRCA1):c.4065_4068del (p.Asn1355fs) rs80357508
NM_007294.4(BRCA1):c.4986+3G>C rs80358023
NM_007294.4(BRCA1):c.5509T>C (p.Trp1837Arg) rs80356959
NM_024675.4(PALB2):c.172_175del (p.Gln60fs) rs180177143
NM_024675.4(PALB2):c.2192T>G (p.Leu731Ter) rs1567217898
NM_024675.4(PALB2):c.48G>A (p.Lys16=) rs587776405
NM_058216.3(RAD51C):c.572-1G>C rs1413872299

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