ClinVar Miner

Variants from Laan Lab, Human Genetics Research Group, University of Tartu with conflicting interpretations

Location: Estonia  Primary collection method: research
Minimum review status of the submission from Laan Lab, Human Genetics Research Group, University of Tartu: Collection method of the submission from Laan Lab, Human Genetics Research Group, University of Tartu:
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
66 16 0 18 0 0 18 32

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
Laan Lab, Human Genetics Research Group, University of Tartu pathogenic likely pathogenic uncertain significance likely benign
pathogenic 0 11 5 2
likely pathogenic 7 0 11 2

Submitter to submitter summary #

Total submitters: 41
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 9 0 4 0 0 6 10
PreventionGenetics, part of Exact Sciences 0 5 0 3 0 0 3 6
Invitae 0 10 0 2 0 0 4 6
OMIM 0 4 0 3 0 0 0 3
Revvity Omics, Revvity 0 6 0 3 0 0 0 3
Eurofins Ntd Llc (ga) 0 3 0 1 0 0 2 3
CeGaT Center for Human Genetics Tuebingen 0 4 0 0 0 0 3 3
Baylor Genetics 0 4 0 2 0 0 0 2
Ambry Genetics 0 4 0 1 0 0 1 2
Blueprint Genetics 0 1 0 2 0 0 0 2
LDLR-LOVD, British Heart Foundation 0 0 0 2 0 0 0 2
Laboratory of Genetics and Molecular Cardiology, University of São Paulo 0 1 0 2 0 0 0 2
Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge 0 0 0 2 0 0 0 2
Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix 0 0 0 2 0 0 0 2
Institute of Human Genetics, University of Leipzig Medical Center 0 3 0 2 0 0 0 2
Fundacion Hipercolesterolemia Familiar 0 0 0 2 0 0 0 2
Iberoamerican FH Network 0 0 0 2 0 0 0 2
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 2 0 1 0 0 1 2
All of Us Research Program, National Institutes of Health 0 6 0 0 0 0 2 2
Athena Diagnostics Inc 0 2 0 0 0 0 1 1
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia 0 0 0 0 0 0 1 1
MGZ Medical Genetics Center 0 3 0 1 0 0 0 1
Clinical Genetics, Academic Medical Center 0 0 0 1 0 0 0 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 3 0 0 0 0 1 1
Sharing Clinical Reports Project (SCRP) 0 4 0 1 0 0 0 1
Fulgent Genetics, Fulgent Genetics 0 4 0 1 0 0 0 1
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 4 0 1 0 0 0 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 1 0 1 0 0 0 1
Illumina Laboratory Services, Illumina 0 1 0 0 0 0 1 1
Institute for Integrative and Experimental Genomics, University of Luebeck 0 0 0 1 0 0 0 1
Center for Individualized Medicine, Mayo Clinic 0 0 0 1 0 0 0 1
Center of Genomic medicine, Geneva, University Hospital of Geneva 0 0 0 1 0 0 0 1
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden 0 1 0 0 0 0 1 1
Robarts Research Institute, Western University 0 0 0 1 0 0 0 1
Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation 0 0 0 1 0 0 0 1
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 1 0 0 0 0 1 1
St. Jude Molecular Pathology, St. Jude Children's Research Hospital 0 1 0 1 0 0 0 1
Myriad Genetics, Inc. 0 0 0 1 0 0 0 1
Laboratory of Molecular Genetics, National Medical Research Center for Therapy and Preventive Medicine 0 0 0 1 0 0 0 1
Clinical Cancer Genomics Laboratory, City of Hope Comprehensive Cancer Center 0 0 0 1 0 0 0 1
Laboratory of molecular diagnosis of dyslipidemias, Università egli studi di Napoli Federico II 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 32
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001048174.2(MUTYH):c.1103G>A (p.Gly368Asp) rs36053993 0.00341
NM_138289.4(ACTRT1):c.547dup (p.Met183fs) rs771087307 0.00191
NM_031272.5(TEX14):c.1003C>T (p.Arg335Ter) rs141801212 0.00112
NM_020937.4(FANCM):c.5101C>T (p.Gln1701Ter) rs147021911 0.00104
NM_000535.7(PMS2):c.137G>T (p.Ser46Ile) rs121434629 0.00018
NM_021728.4(OTX2):c.425C>G (p.Pro142Arg) rs199761861 0.00016
NM_003865.3(HESX1):c.326G>A (p.Arg109Gln) rs768165720 0.00011
NM_170707.4(LMNA):c.1718C>T (p.Ser573Leu) rs60890628 0.00011
NM_144773.4(PROKR2):c.868C>T (p.Pro290Ser) rs149992595 0.00010
NM_020937.4(FANCM):c.1491dup (p.Gln498fs) rs797045116 0.00005
NM_000256.3(MYBPC3):c.1484G>A (p.Arg495Gln) rs200411226 0.00004
NM_000335.5(SCN5A):c.4874G>A (p.Arg1625His) rs199473283 0.00004
NM_001308093.3(GATA4):c.487C>T (p.Pro163Ser) rs387906769 0.00004
NM_000044.6(AR):c.1723C>G (p.Leu575Val) rs376443652 0.00003
NM_000257.4(MYH7):c.2167C>T (p.Arg723Cys) rs121913630 0.00002
NM_000138.5(FBN1):c.287G>C (p.Arg96Thr) rs794728291 0.00001
NM_000363.5(TNNI3):c.586G>A (p.Asp196Asn) rs104894727 0.00001
NM_006767.4(LZTR1):c.509G>A (p.Arg170Gln) rs781431741 0.00001
NM_006767.4(LZTR1):c.848G>A (p.Arg283Gln) rs1223430276 0.00001
NM_017780.4(CHD7):c.6194G>A (p.Arg2065His) rs1197494895 0.00001
NM_000059.4(BRCA2):c.1796_1800del (p.Thr598_Ser599insTer) rs276174813
NM_000059.4(BRCA2):c.8488-1G>A rs397507404
NM_000527.5(LDLR):c.1216C>T (p.Arg406Trp)
NM_000527.5(LDLR):c.1775G>A (p.Gly592Glu)
NM_000540.3(RYR1):c.10347+1G>A rs111436401
NM_000540.3(RYR1):c.12319del (p.Ile4107fs) rs754572007
NM_001042492.3(NF1):c.4348G>T (p.Ala1450Ser)
NM_005633.4(SOS1):c.1310T>C (p.Ile437Thr) rs397517150
NM_006080.3(SEMA3A):c.1450C>T (p.Arg484Trp)
NM_130768.3(ASZ1):c.460A>G (p.Met154Val)
NM_144773.4(PROKR2):c.253C>T (p.Arg85Cys) rs141090506
NM_144773.4(PROKR2):c.254G>A (p.Arg85His) rs74315418

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