ClinVar Miner

Variants from Cancer Genetics Laboratory, Peter MacCallum Cancer Centre with conflicting interpretations

Location: Australia  Primary collection method: case-control
Minimum review status of the submission from Cancer Genetics Laboratory, Peter MacCallum Cancer Centre: Collection method of the submission from Cancer Genetics Laboratory, Peter MacCallum Cancer Centre:
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
7 19 0 37 36 0 0 70

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 Laboratory, Peter MacCallum Cancer Centre pathogenic uncertain significance likely benign benign
likely pathogenic 16 0 0 0
uncertain significance 0 0 21 14
likely benign 0 7 0 21

Submitter to submitter summary #

Total submitters: 21
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
Invitae 0 32 0 29 26 0 0 55
Myriad Genetics, Inc. 0 6 0 24 16 0 0 40
Leiden Open Variation Database 0 10 0 9 6 0 0 15
Counsyl 0 28 0 8 6 0 0 14
Baylor Genetics 0 8 0 11 1 0 0 12
Pathway Genomics 0 0 0 5 3 0 0 8
Institute of Human Genetics, University of Leipzig Medical Center 0 0 0 5 2 0 0 7
Mendelics 0 10 0 1 3 0 0 4
Genetics and Molecular Pathology, SA Pathology 0 3 0 3 1 0 0 4
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 0 0 3 0 0 0 3
ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen 0 1 0 2 1 0 0 3
MGZ Medical Genetics Center 0 0 0 2 0 0 0 2
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 0 0 2 0 0 0 2
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 0 0 2 0 0 0 2
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 0 0 1 0 0 0 1
Department of Molecular Diagnostics, Institute of Oncology Ljubljana 0 2 0 1 0 0 0 1
St. Jude Molecular Pathology, St. Jude Children's Research Hospital 0 0 0 0 1 0 0 1
deCODE genetics, Amgen 0 0 0 1 0 0 0 1
Division of Medical Genetics, University of Washington 0 1 0 1 0 0 0 1
Human Genetics Bochum, Ruhr University Bochum 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 70
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HGVS dbSNP gnomAD frequency
NM_024675.4(PALB2):c.1676A>G (p.Gln559Arg) rs152451 0.12980
NM_024675.4(PALB2):c.3300T>G (p.Thr1100=) rs45516100 0.02529
NM_024675.4(PALB2):c.2014G>C (p.Glu672Gln) rs45532440 0.02171
NM_024675.4(PALB2):c.629C>T (p.Pro210Leu) rs57605939 0.02101
NM_024675.4(PALB2):c.2993G>A (p.Gly998Glu) rs45551636 0.01717
NM_024675.4(PALB2):c.1010T>C (p.Leu337Ser) rs45494092 0.01508
NM_024675.4(PALB2):c.925A>G (p.Ile309Val) rs3809683 0.00919
NM_024675.4(PALB2):c.53A>G (p.Lys18Arg) rs138789658 0.00530
NM_024675.4(PALB2):c.2794G>A (p.Val932Met) rs45624036 0.00449
NM_024675.4(PALB2):c.1572A>G (p.Ser524=) rs45472400 0.00312
NM_024675.4(PALB2):c.2590C>T (p.Pro864Ser) rs45568339 0.00287
NM_024675.4(PALB2):c.400G>A (p.Asp134Asn) rs139555085 0.00160
NM_024675.4(PALB2):c.2742C>T (p.Phe914=) rs115759702 0.00143
NM_024675.4(PALB2):c.2816T>G (p.Leu939Trp) rs45478192 0.00121
NM_024675.4(PALB2):c.1194G>A (p.Val398=) rs61755173 0.00103
NM_024675.4(PALB2):c.1470C>T (p.Pro490=) rs45612837 0.00035
NM_024675.4(PALB2):c.298C>T (p.Leu100Phe) rs61756147 0.00021
NM_024675.4(PALB2):c.656A>G (p.Asp219Gly) rs45594034 0.00021
NM_024675.4(PALB2):c.1492G>T (p.Asp498Tyr) rs75023630 0.00020
NM_024675.4(PALB2):c.2135C>T (p.Ala712Val) rs141458731 0.00017
NM_024675.4(PALB2):c.3054G>C (p.Glu1018Asp) rs183489969 0.00016
NM_024675.4(PALB2):c.232G>A (p.Val78Ile) rs515726085 0.00013
NM_024675.4(PALB2):c.1250C>A (p.Ser417Tyr) rs45510998 0.00011
NM_024675.4(PALB2):c.11C>T (p.Pro4Leu) rs45619737 0.00010
NM_024675.4(PALB2):c.12T>C (p.Pro4=) rs567706422 0.00009
NM_024675.4(PALB2):c.1431C>T (p.Thr477=) rs515726068 0.00009
NM_024675.4(PALB2):c.1544A>G (p.Lys515Arg) rs515726072 0.00009
NM_024675.4(PALB2):c.1623G>A (p.Arg541=) rs745665968 0.00009
NM_024675.4(PALB2):c.2379C>T (p.Gly793=) rs377626805 0.00009
NM_024675.4(PALB2):c.344G>T (p.Gly115Val) rs145598272 0.00009
NM_024675.4(PALB2):c.2200A>T (p.Thr734Ser) rs45543843 0.00007
NM_024675.4(PALB2):c.3428T>A (p.Leu1143His) rs62625284 0.00006
NM_024675.4(PALB2):c.768C>T (p.Ser256=) rs45487491 0.00006
NM_024675.4(PALB2):c.1699C>T (p.His567Tyr) rs370422990 0.00004
NM_024675.4(PALB2):c.194C>T (p.Pro65Leu) rs62625272 0.00004
NM_024675.4(PALB2):c.2067G>A (p.Ser689=) rs371149159 0.00004
NM_024675.4(PALB2):c.2082A>G (p.Thr694=) rs781440401 0.00004
NM_024675.4(PALB2):c.2289G>C (p.Leu763Phe) rs373478248 0.00004
NM_024675.4(PALB2):c.2674G>A (p.Glu892Lys) rs45476495 0.00004
NM_024675.4(PALB2):c.1189A>T (p.Thr397Ser) rs367578415 0.00003
NM_024675.4(PALB2):c.2106A>G (p.Ile702Met) rs730881886 0.00003
NM_024675.4(PALB2):c.3146T>C (p.Met1049Thr) rs138273800 0.00003
NM_024675.4(PALB2):c.94C>G (p.Leu32Val) rs151316635 0.00003
NM_024675.4(PALB2):c.2228A>G (p.Tyr743Cys) rs141749524 0.00002
NM_024675.4(PALB2):c.2360C>T (p.Thr787Ile) rs201042302 0.00002
NM_024675.4(PALB2):c.2417C>T (p.Pro806Leu) rs45464991 0.00002
NM_024675.4(PALB2):c.3113G>A (p.Trp1038Ter) rs180177132 0.00002
NM_024675.4(PALB2):c.3256C>T (p.Arg1086Ter) rs587776527 0.00002
NM_024675.4(PALB2):c.1145G>T (p.Ser382Ile) rs515726063 0.00001
NM_024675.4(PALB2):c.196C>T (p.Gln66Ter) rs180177083 0.00001
NM_024675.4(PALB2):c.2386G>T (p.Gly796Ter) rs180177112 0.00001
NM_024675.4(PALB2):c.2478C>T (p.Asn826=) rs786201885 0.00001
NM_024675.4(PALB2):c.353T>C (p.Ile118Thr) rs370404126 0.00001
NM_024675.4(PALB2):c.3549C>G (p.Tyr1183Ter) rs118203998 0.00001
NM_024675.4(PALB2):c.758dup (p.Ser254fs) rs515726126 0.00001
NM_024675.4(PALB2):c.899C>T (p.Thr300Ile) rs528541334 0.00001
NM_024675.4(PALB2):c.1478C>T (p.Pro493Leu) rs770965402
NM_024675.4(PALB2):c.172_175del (p.Gln60fs) rs180177143
NM_024675.4(PALB2):c.1947dup (p.Glu650fs) rs515726075
NM_024675.4(PALB2):c.2391del (p.Gln797fs) rs1555460360
NM_024675.4(PALB2):c.2959_2966dup (p.Glu990fs) rs875989792
NM_024675.4(PALB2):c.2982dup (p.Ala995fs) rs180177127
NM_024675.4(PALB2):c.3116del (p.Asn1039fs) rs180177133
NM_024675.4(PALB2):c.3307G>A (p.Val1103Met) rs201657283
NM_024675.4(PALB2):c.3362del (p.Gly1121fs) rs515726117
NM_024675.4(PALB2):c.3507_3508del (p.His1170fs) rs587776428
NM_024675.4(PALB2):c.508A>G (p.Arg170Gly) rs864622622
NM_024675.4(PALB2):c.557A>T (p.Asn186Ile) rs587782164
NM_024675.4(PALB2):c.693dup (p.Gly232fs) rs875989791
NM_024675.4(PALB2):c.860dup (p.Ser288fs) rs864622301

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