ClinVar Miner

Variants from Geisinger Clinic, Geisinger Health System with conflicting interpretations

Location: United States  Primary collection method: research
Minimum review status of the submission from Geisinger Clinic, Geisinger Health System: Collection method of the submission from Geisinger Clinic, Geisinger Health System:
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
45 27 0 21 0 0 8 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
Geisinger Clinic, Geisinger Health System pathogenic likely pathogenic uncertain significance
pathogenic 0 17 4
likely pathogenic 4 0 4

Submitter to submitter summary #

Total submitters: 17
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
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 5 0 2 0 0 6 8
Genetics and Molecular Pathology, SA Pathology 0 2 0 3 0 0 1 4
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 12 0 4 0 0 0 4
Ambry Genetics 0 2 0 2 0 0 1 3
Institute of Human Genetics Munich, TUM University Hospital 0 2 0 2 0 0 0 2
Translational Genomics Laboratory, University of Maryland School of Medicine 0 2 0 2 0 0 0 2
3billion 0 6 0 1 0 0 0 1
Department of Human Genetics, Hannover Medical School 0 0 0 1 0 0 0 1
Genetic Services Laboratory, University of Chicago 0 3 0 1 0 0 0 1
Genomics And Bioinformatics Analysis Resource, Columbia University 0 0 0 1 0 0 0 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 1 0 1 0 0 0 1
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota 0 0 0 1 0 0 0 1
Molecular Genetics, Royal Melbourne Hospital 0 1 0 1 0 0 0 1
National Newborn Screening Laboratory, Hospital Nacional de Niños 0 1 0 1 0 0 0 1
OMIM 0 3 0 1 0 0 0 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 2 0 1 0 0 0 1
deCODE genetics, Amgen 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 25
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000162.5(GCK):c.106C>T (p.Arg36Trp) rs762263694 0.00003
NM_000162.5(GCK):c.370G>A (p.Asp124Asn) rs759072800 0.00002
NM_000162.5(GCK):c.571C>T (p.Arg191Trp) rs1085307455 0.00001
NM_000162.5(GCK):c.676G>A (p.Val226Met) rs148311934 0.00001
NM_000162.5(GCK):c.951C>G (p.His317Gln) rs1379908545 0.00001
NM_175914.5(HNF4A):c.1198C>T (p.Arg400Ter) rs1413742263 0.00001
NM_175914.5(HNF4A):c.322G>A (p.Val108Ile) rs377476335 0.00001
NM_175914.5(HNF4A):c.925C>T (p.Arg309Cys) rs193922479 0.00001
NM_000162.5(GCK):c.1019G>T (p.Ser340Ile) rs1376631949
NM_000162.5(GCK):c.1174C>T (p.Arg392Cys) rs1167124132
NM_000162.5(GCK):c.1358C>T (p.Ser453Leu) rs193922283
NM_000162.5(GCK):c.208+2T>C rs2128823089
NM_000162.5(GCK):c.316C>T (p.Gln106Ter) rs2096281702
NM_000162.5(GCK):c.391T>C (p.Ser131Pro) rs104894010
NM_000162.5(GCK):c.748C>T (p.Arg250Cys) rs1057524904
NM_000162.5(GCK):c.781G>A (p.Gly261Arg) rs104894008
NM_000162.5(GCK):c.863+1G>A rs1376796469
NM_000162.5(GCK):c.878T>C (p.Ile293Thr) rs2128820046
NM_000162.5(GCK):c.878T>G (p.Ile293Arg) rs2128820046
NM_000545.8(HNF1A):c.343G>T (p.Val115Leu) rs1876667856
NM_000545.8(HNF1A):c.475C>T (p.Arg159Trp) rs765432081
NM_175914.5(HNF4A):c.691C>T (p.Arg231Trp) rs376013528
NM_175914.5(HNF4A):c.869G>A (p.Arg290His) rs1191912908
NM_175914.5(HNF4A):c.926G>T (p.Arg309Leu) rs369429452
NM_175914.5(HNF4A):c.932G>A (p.Arg311His) rs1375557127

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