ClinVar Miner

Variants from CZECANCA consortium with conflicting interpretations

Location: Czechia  Primary collection method: clinical testing
Minimum review status of the submission from CZECANCA consortium: Collection method of the submission from CZECANCA consortium:
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
103 96 0 17 0 2 10 25

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
CZECANCA consortium pathogenic likely pathogenic uncertain significance risk factor
pathogenic 0 12 3 2
likely pathogenic 5 0 7 0

Submitter to submitter summary #

Total submitters: 27
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
GeneDx 0 84 0 8 0 0 3 11
Quest Diagnostics Nichols Institute San Juan Capistrano 0 68 0 1 0 0 3 4
PreventionGenetics, part of Exact Sciences 0 27 0 1 0 0 2 3
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden 0 30 0 2 0 0 1 3
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital 0 25 0 1 0 0 2 3
CeGaT Center for Human Genetics Tuebingen 0 42 0 2 0 0 1 3
CHEO Genetics Diagnostic Laboratory, Children's Hospital of Eastern Ontario 0 22 0 1 0 0 1 2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 26 0 0 0 0 2 2
Revvity Omics, Revvity 0 39 0 1 0 0 1 2
Fulgent Genetics, Fulgent Genetics 0 17 0 2 0 0 0 2
Illumina Laboratory Services, Illumina 0 4 0 1 0 0 1 2
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 17 0 1 0 0 1 2
Leiden Open Variation Database 0 2 0 0 0 0 2 2
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 5 0 1 0 0 1 2
OMIM 0 2 0 0 0 1 0 1
Genetic Services Laboratory, University of Chicago 0 6 0 1 0 0 0 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 1 0 0 0 1 0 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 0 0 0 0 0 1 1
Mayo Clinic Laboratories, Mayo Clinic 0 23 0 0 0 0 1 1
GeneKor MSA 0 9 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 13 0 0 0 0 1 1
Research Molecular Genetics Laboratory, Women's College Hospital, University of Toronto 0 0 0 0 0 0 1 1
Laboratory of Medical Genetics Unit, Bambino Gesù Children's Hospital 0 0 0 1 0 0 0 1
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 35 0 1 0 0 0 1
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 6 0 1 0 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 12 0 0 0 0 1 1
Clinical Genetics Laboratory, Department of Pathology, Netherlands Cancer Institute 0 20 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 25
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_007194.4(CHEK2):c.190G>A (p.Glu64Lys) rs141568342 0.00015
NM_007194.4(CHEK2):c.444+1G>A rs121908698 0.00009
NM_002878.4(RAD51D):c.694C>T (p.Arg232Ter) rs587780104 0.00004
NM_000059.4(BRCA2):c.5645C>A (p.Ser1882Ter) rs80358785 0.00002
NM_002485.5(NBN):c.37+1G>A rs574673404 0.00002
NM_007194.4(CHEK2):c.980A>G (p.Tyr327Cys) rs587780194 0.00002
NM_000051.4(ATM):c.7630-2A>C rs587779866 0.00001
NM_000059.4(BRCA2):c.7878G>C (p.Trp2626Cys) rs80359013 0.00001
NM_000059.4(BRCA2):c.9371A>T (p.Asn3124Ile) rs28897759 0.00001
NM_000546.6(TP53):c.711G>A (p.Met237Ile) rs587782664 0.00001
NM_007194.4(CHEK2):c.503C>T (p.Thr168Ile) rs730881684 0.00001
NM_058216.3(RAD51C):c.905-2_905-1del rs587781995 0.00001
NM_000051.4(ATM):c.6096-9_6096-5del rs879254095
NM_000059.4(BRCA2):c.8486A>G (p.Gln2829Arg) rs80359100
NM_000314.8(PTEN):c.737C>T (p.Pro246Leu) rs587782350
NM_000465.4(BARD1):c.2300_2301del (p.Val767fs) rs750413473
NM_002485.5(NBN):c.188del (p.Ile63fs) rs876659592
NM_002485.5(NBN):c.657_661del (p.Lys219fs) rs587776650
NM_007194.4(CHEK2):c.1183G>C (p.Val395Leu) rs587780170
NM_007294.4(BRCA1):c.5074+3A>G rs80358181
NM_007294.4(BRCA1):c.5266dup (p.Gln1756fs) rs80357906
NM_032043.3(BRIP1):c.1_2del (p.Met1fs) rs876661246
NM_032043.3(BRIP1):c.2684_2687del (p.Val894_Ser895insTer) rs760551339
NM_058216.3(RAD51C):c.1026+5_1026+7del rs587781410
NM_058216.3(RAD51C):c.502A>T (p.Arg168Ter) rs587781490

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