ClinVar Miner

Variants from ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen with conflicting interpretations

Location: United States  Primary collection method: curation
Minimum review status of the submission from ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen: Collection method of the submission from ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen:
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
20 46 0 19 5 0 5 27

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
ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 9 1 0 0
likely pathogenic 7 0 0 0 0
uncertain significance 1 3 0 2 0
likely benign 0 0 0 0 2
benign 0 0 3 2 0

Submitter to submitter summary #

Total submitters: 13
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 24 0 6 0 0 4 10
Myriad Genetics, Inc. 0 32 0 8 1 0 1 10
Leiden Open Variation Database 0 2 0 4 2 0 1 7
Baylor Genetics 0 29 0 3 0 0 0 3
Cancer Genetics Laboratory, Peter MacCallum Cancer Centre 0 1 0 2 1 0 0 3
Counsyl 0 7 0 0 1 0 1 2
Mendelics 0 2 0 2 0 0 0 2
Institute of Human Genetics, University of Leipzig Medical Center 0 2 0 1 1 0 0 2
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 2 0 1 0 0 0 1
University Health Network, Princess Margaret Cancer Centre 0 0 0 1 0 0 0 1
Division of Medical Genetics, University of Washington 0 1 0 0 1 0 0 1
ClinGen Hereditary Breast, Ovarian and Pancreatic Cancer Variant Curation Expert Panel, ClinGen 92 0 0 1 0 0 0 1
BRCAlab, Lund University 0 3 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 27
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_024675.4(PALB2):c.2014G>C (p.Glu672Gln) rs45532440 0.02171
NM_000051.4(ATM):c.1066-6T>G rs201686625 0.00139
NM_024675.4(PALB2):c.3054G>C (p.Glu1018Asp) rs183489969 0.00016
NM_024675.4(PALB2):c.1794G>A (p.Leu598=) rs182494675 0.00015
NM_024675.4(PALB2):c.109C>A (p.Arg37Ser) rs200048921 0.00006
NM_024675.4(PALB2):c.3249G>C (p.Glu1083Asp) rs147045425 0.00005
NM_024675.4(PALB2):c.212-33A>C rs515726079 0.00003
NM_000051.4(ATM):c.8786+1G>A rs17174393 0.00002
NM_024675.4(PALB2):c.3113G>A (p.Trp1038Ter) rs180177132 0.00002
NM_000051.4(ATM):c.1607+1G>T rs772926890 0.00001
NM_000051.4(ATM):c.3078-1G>A rs750663117 0.00001
NM_000051.4(ATM):c.332-1G>A rs747855862 0.00001
NM_000051.4(ATM):c.6807G>A (p.Gln2269=) rs587780638 0.00001
NM_000051.4(ATM):c.8494C>T (p.Arg2832Cys) rs587779872 0.00001
NM_000051.4(ATM):c.875C>T (p.Pro292Leu) rs747727055 0.00001
NM_024675.4(PALB2):c.2559C>T (p.Gly853=) rs180177115 0.00001
NM_000051.4(ATM):c.8575TCT[1] (p.Ser2860del) rs786203976
NM_024675.4(PALB2):c.104T>C (p.Leu35Pro) rs141047069
NM_024675.4(PALB2):c.1684+1G>A rs1555461148
NM_024675.4(PALB2):c.2074C>T (p.Gln692Ter) rs587776415
NM_024675.4(PALB2):c.3049G>A (p.Ala1017Thr) rs759795184
NM_024675.4(PALB2):c.3350+4A>G rs180177136
NM_024675.4(PALB2):c.3350G>A (p.Arg1117Lys) rs876659859
NM_024675.4(PALB2):c.3362del (p.Gly1121fs) rs515726117
NM_024675.4(PALB2):c.3543del (p.Phe1181fs) rs1567204928
NM_024675.4(PALB2):c.49-2A>T rs786203245
Single allele

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