ClinVar Miner

Variants from Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand with conflicting interpretations

Location: South Africa  Primary collection method: research
Minimum review status of the submission from Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand: Collection method of the submission from Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand:
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
73 67 0 24 0 0 10 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
Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand pathogenic likely pathogenic uncertain significance
pathogenic 0 19 7
likely pathogenic 5 0 2
uncertain significance 0 1 0

Submitter to submitter summary #

Total submitters: 30
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 52 0 4 0 0 3 7
Center for Medical Genetics Ghent, University of Ghent 0 0 0 1 0 0 3 4
Genome-Nilou Lab 0 13 0 4 0 0 0 4
Centre of Medical Genetics, University of Antwerp 0 0 0 3 0 0 0 3
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 18 0 2 0 0 0 2
LDLR-LOVD, British Heart Foundation 0 0 0 2 0 0 0 2
Robarts Research Institute, Western University 0 0 0 2 0 0 0 2
Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital 0 1 0 2 0 0 0 2
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 7 0 1 0 0 1 2
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 12 0 1 0 0 0 1
GeneDx 0 5 0 1 0 0 0 1
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 1 0 1 0 0 0 1
Counsyl 0 2 0 1 0 0 0 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 11 0 0 0 0 1 1
Fulgent Genetics, Fulgent Genetics 0 8 0 1 0 0 0 1
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 0 0 0 1 0 0 0 1
RettBASE 0 1 0 1 0 0 0 1
UCLA Clinical Genomics Center, UCLA 0 1 0 1 0 0 0 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 1 0 1 0 0 0 1
Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare 0 2 0 1 0 0 0 1
CeGaT Center for Human Genetics Tuebingen 0 3 0 0 0 0 1 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 1 0 1 0 0 0 1
Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix 0 1 0 1 0 0 0 1
Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation 0 0 0 1 0 0 0 1
Kariminejad - Najmabadi Pathology & Genetics Center 0 0 0 1 0 0 0 1
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 1 0 1 0 0 0 1
CFTR-France 0 1 0 1 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 9 0 0 0 0 1 1
Centre for Population Genomics, CPG 0 1 0 1 0 0 0 1
All of Us Research Program, National Institutes of Health 0 3 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 30
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_145064.3(STAC3):c.851G>C (p.Trp284Ser) rs140291094 0.00039
NM_000359.3(TGM1):c.944G>T (p.Arg315Leu) rs143473912 0.00021
NM_000540.3(RYR1):c.14524G>A (p.Val4842Met) rs193922879 0.00011
NM_000540.3(RYR1):c.10348-6C>G rs193922837 0.00010
NM_000396.4(CTSK):c.953G>A (p.Cys318Tyr) rs762780994 0.00008
NM_004646.4(NPHS1):c.1379G>A (p.Arg460Gln) rs386833880 0.00002
NM_002834.5(PTPN11):c.188A>G (p.Tyr63Cys) rs121918459 0.00001
NM_007373.4(SHOC2):c.4A>G (p.Ser2Gly) rs267607048 0.00001
NM_000138.5(FBN1):c.2638G>A (p.Gly880Ser) rs794728194
NM_000138.5(FBN1):c.3037G>A (p.Gly1013Arg) rs140593
NM_000138.5(FBN1):c.5726T>C (p.Ile1909Thr) rs794728333
NM_000138.5(FBN1):c.640G>A (p.Gly214Ser) rs794728162
NM_000492.4(CFTR):c.3064_3117del (p.Val1022_Gln1039del) rs1554392027
NM_000492.4(CFTR):c.614C>G (p.Pro205Arg) rs397508769
NM_000527.5(LDLR):c.2054C>T (p.Pro685Leu)
NM_000527.5(LDLR):c.681C>G (p.Asp227Glu) rs121908028
NM_000548.5(TSC2):c.4628A>G (p.His1543Arg) rs2090628516
NM_000548.5(TSC2):c.5238_5255del (p.His1746_Arg1751del) rs137854218
NM_001042492.3(NF1):c.1885G>C (p.Gly629Arg) rs199474738
NM_001042492.3(NF1):c.2540T>C (p.Leu847Pro) rs199474747
NM_001042492.3(NF1):c.2681T>C (p.Phe894Ser) rs1282493551
NM_001042492.3(NF1):c.3113+5G>C rs1555614549
NM_001042492.3(NF1):c.5991G>A (p.Trp1997Ter) rs876660696
NM_001110792.2(MECP2):c.789dup (p.Gly264fs) rs61749751
NM_001844.5(COL2A1):c.905C>T (p.Ala302Val) rs1555168505
NM_002397.5(MEF2C):c.565C>T (p.Arg189Ter) rs587783747
NM_002834.5(PTPN11):c.1510A>G (p.Met504Val) rs397507547
NM_002834.5(PTPN11):c.182A>G (p.Asp61Gly) rs121918461
NM_002834.5(PTPN11):c.215C>G (p.Ala72Gly) rs121918454
NM_003722.5(TP63):c.1028G>A (p.Arg343Gln) rs121908841

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