ClinVar Miner

Variants from Constitutional Genetics Lab, Leon Berard Cancer Center with conflicting interpretations

Location: France  Primary collection method: clinical testing
Minimum review status of the submission from Constitutional Genetics Lab, Leon Berard Cancer Center: Collection method of the submission from Constitutional Genetics Lab, Leon Berard Cancer Center:
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
54 56 0 13 7 0 11 30

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
Constitutional Genetics Lab, Leon Berard Cancer Center pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 9 5 0 0
likely pathogenic 4 0 5 1 0
uncertain significance 1 1 0 2 6

Submitter to submitter summary #

Total submitters: 16
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
Labcorp Genetics (formerly Invitae), Labcorp 0 68 0 6 7 0 4 17
Quest Diagnostics Nichols Institute San Juan Capistrano 0 32 0 3 1 0 3 7
Department of Pathology and Laboratory Medicine, Sinai Health System 0 5 0 0 0 0 6 6
GeneDx 0 44 0 2 1 0 3 6
Mayo Clinic Laboratories, Mayo Clinic 0 25 0 2 0 0 2 4
CeGaT Center for Human Genetics Tuebingen 0 16 0 2 0 0 1 3
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden 0 5 0 2 0 0 1 3
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 4 0 0 1 0 2 3
Genetics Laboratory, Great Ormond Street Hospital NHS Foundation Trust, North Thames Genomic Laboratory Hub 0 3 0 2 0 0 0 2
Revvity Omics, Revvity 0 18 0 2 0 0 0 2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 11 0 0 1 0 0 1
Breakthrough Genomics, Breakthrough Genomics 0 0 0 0 0 0 1 1
Cambridge Genomics Laboratory, East Genomic Laboratory Hub, NHS Genomic Medicine Service 0 3 0 1 0 0 0 1
Dasa 0 4 0 0 1 0 0 1
Mendelics 0 0 0 0 1 0 0 1
PreventionGenetics, part of Exact Sciences 0 12 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 30
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000535.7(PMS2):c.1004A>G (p.Asn335Ser) rs200513014 0.00026
NM_000179.3(MSH6):c.1730G>A (p.Arg577His) rs376220212 0.00009
NM_000535.7(PMS2):c.1399G>A (p.Val467Ile) rs373611083 0.00008
NM_000249.4(MLH1):c.1154G>A (p.Arg385His) rs63750430 0.00005
NM_000179.3(MSH6):c.362G>A (p.Arg121His) rs769279475 0.00003
NM_000179.3(MSH6):c.2419G>A (p.Glu807Lys) rs587779923 0.00002
NM_000251.3(MSH2):c.1570C>T (p.Arg524Cys) rs755818010 0.00002
NM_000249.4(MLH1):c.790+1G>A rs267607789 0.00001
NM_000179.3(MSH6):c.1483C>T (p.Arg495Ter) rs587779212
NM_000179.3(MSH6):c.1615C>T (p.Leu539Phe) rs1553412999
NM_000179.3(MSH6):c.1721C>G (p.Ser574Ter) rs1669365820
NM_000179.3(MSH6):c.2555AGA[2] (p.Lys854del) rs587782858
NM_000179.3(MSH6):c.2677_2678del (p.Leu893fs) rs1572728112
NM_000179.3(MSH6):c.3416dup (p.Lys1140fs) rs587781544
NM_000179.3(MSH6):c.3724_3726del (p.Arg1242del) rs63749942
NM_000179.3(MSH6):c.3964G>T (p.Glu1322Ter) rs1553333707
NM_000179.3(MSH6):c.67G>A (p.Ala23Thr) rs730881810
NM_000249.4(MLH1):c.1038+1G>C rs267607816
NM_000249.4(MLH1):c.152T>A (p.Val51Asp) rs1553638767
NM_000249.4(MLH1):c.1667G>A (p.Ser556Asn) rs63751596
NM_000249.4(MLH1):c.2104-1G>A rs587778978
NM_000249.4(MLH1):c.545+1G>T rs267607765
NM_000249.4(MLH1):c.588del (p.Lys196fs) rs63751653
NM_000249.4(MLH1):c.676C>T (p.Arg226Ter) rs63751615
NM_000249.4(MLH1):c.677G>T (p.Arg226Leu) rs63751711
NM_000251.3(MSH2):c.1076G>C (p.Arg359Thr) rs63751604
NM_000251.3(MSH2):c.1147C>T (p.Arg383Ter) rs63749849
NM_000251.3(MSH2):c.2038C>T (p.Arg680Ter) rs63749932
NM_000251.3(MSH2):c.2228C>T (p.Ser743Leu) rs63751155
NM_000251.3(MSH2):c.490G>A (p.Gly164Arg) rs63750582

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