ClinVar Miner

Variants from Undiagnosed Diseases Network,NIH with conflicting interpretations

Location: United States — Primary collection method: clinical testing
Minimum review status of the submission from Undiagnosed Diseases Network,NIH: Collection method of the submission from Undiagnosed Diseases Network,NIH:
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
295 89 4 41 6 3 40 84

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
Undiagnosed Diseases Network,NIH pathogenic likely pathogenic uncertain significance likely benign benign drug response protective risk factor other
pathogenic 4 17 5 0 0 0 0 0 0
likely pathogenic 24 0 13 2 1 1 1 0 1
uncertain significance 16 7 0 5 1 1 1 2 1
likely benign 0 0 1 0 0 0 0 0 0

Submitter to submitter summary #

Total submitters: 79
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
OMIM 0 52 0 11 0 2 12 25
Invitae 0 24 0 3 1 0 8 11
University of Washington Center for Mendelian Genomics, University of Washington 0 0 0 0 0 0 7 7
GeneReviews 0 6 4 1 0 0 1 6
Baylor Genetics 0 22 0 3 0 0 3 5
Illumina Clinical Services Laboratory,Illumina 0 6 0 1 4 0 1 5
GeneDx 0 7 0 3 1 0 2 4
Broad Institute Rare Disease Group, Broad Institute 0 4 0 1 0 0 3 4
CeGaT Praxis fuer Humangenetik Tuebingen 0 5 0 1 2 0 2 3
Laboratory of Neurogenetics and Neuroinflammation,Institut Imagine 0 0 0 1 0 0 2 3
Counsyl 0 3 0 2 0 0 0 2
Mendelics 0 8 0 1 0 0 1 2
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics 0 1 0 1 1 1 2 2
Mayo Clinic Laboratories, Mayo Clinic 0 1 0 2 0 0 1 2
Fulgent Genetics,Fulgent Genetics 0 8 0 2 0 0 0 2
Institute of Human Genetics, Klinikum rechts der Isar 0 5 0 1 0 0 1 2
Center for Medical Genetics Ghent,University of Ghent 0 0 0 1 0 0 1 2
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 4 0 2 0 0 1 2
Gene Discovery Core-Manton Center,Boston Children's Hospital 0 0 0 1 0 0 1 2
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 0 0 0 1 0 1 2
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 1 0 2 0 0 1 2
Daryl Scott Lab,Baylor College of Medicine 0 0 0 2 0 0 1 2
NIHR Bioresource Rare Diseases, University of Cambridge 0 0 0 2 0 0 1 2
SIB Swiss Institute of Bioinformatics 0 0 0 2 0 0 0 2
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 2 0 1 0 0 1 2
Section for Clinical Neurogenetics,University of Tübingen 0 0 0 1 0 0 1 2
Athena Diagnostics Inc 0 2 0 0 1 0 1 1
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 0 0 0 0 0 1 1
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 0 0 0 0 0 1 1
Molecular Diagnostics Lab,Nemours Alfred I. duPont Hospital for Children 0 2 0 1 0 0 0 1
Elsea Laboratory,Baylor College of Medicine 0 0 0 1 0 0 1 1
Centogene AG - the Rare Disease Company 0 0 0 0 0 0 1 1
Centre for Inherited Metabolic Diseases, Karolinska University Hospital 0 0 0 0 0 0 1 1
MyeliNeuroGene Lab,McGill University Health Center Research Institute 0 0 0 0 0 0 1 1
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre 0 0 0 0 0 0 1 1
Department of Psychiatry,Nagoya University 0 0 0 1 0 0 1 1
CSER _CC_NCGL, University of Washington 0 0 0 1 0 0 0 1
Vavilov Institute of General Genetics RAS, Laboratory of Evolutional Genomics 0 0 0 0 0 1 0 1
Lyon Laboratory, Cold Spring Harbor Laboratory 0 0 0 0 0 0 1 1
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 4 0 1 0 0 0 1
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 0 0 0 1 0 0 1 1
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes 0 0 0 1 0 0 0 1
Genome Sciences Centre,British Columbia Cancer Agency 0 0 0 0 0 0 1 1
Laboratory of Molecular Genetics,CHU RENNES 0 0 0 0 0 0 1 1
Pediatric Highly Intensive Care Unit,Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico 0 0 0 1 0 0 1 1
Neurogenetics Laboratory - MEYER,AOU Meyer 0 1 0 1 0 0 1 1
Undiagnosed Diseases Network,NIH 467 0 0 0 0 0 1 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 5 0 1 0 0 1 1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 3 0 1 0 0 1 1
Institute of Human Genetics, University of Leipzig Medical Center 0 7 0 0 0 0 1 1
Department of Pathology and Laboratory Medicine,Sinai Health System 0 0 0 1 0 0 1 1
Geisinger Autism and Developmental Medicine Institute,Geisinger Health System 0 0 0 1 1 0 1 1
Rare Disease Group, Clinical Genetics,Karolinska Institutet 0 0 0 1 1 0 1 1
Institute of Cellular and Molecular Medicine,Copenhagen University 0 0 0 0 0 0 1 1
Flegel Lab,National Institutes of Health 0 0 0 1 0 0 1 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 2 0 1 0 0 0 1
Ocular Genomics Institute, Massachusetts Eye and Ear 0 1 0 1 0 0 0 1
Laboratoire de Genetique Moleculaire,Centre Hospitalier Universitaire de Bordeaux 0 0 0 0 0 0 1 1
Medical Genetics Lab,Policlinico S. Orsola.Malpighi 0 0 0 0 0 0 1 1
Génétique des Maladies du Développement, Hospices Civils de Lyon 0 3 0 1 0 0 0 1
Medical Cytogenetics and Molecular Genetics Laboratory,IRCCS Istituto Auxologico Italiano 0 0 0 0 1 0 1 1
Genomic Medicine Lab, University of California San Francisco 0 1 0 1 0 0 0 1
Michaelson Lab,University of Iowa 0 0 0 0 0 0 1 1
Molecular Pathology Diagnostics Labratory,University of Iowa Hospitals & Clinics 0 0 0 0 0 0 1 1
Children's Medical Research Institute,University of Sydney 0 0 0 1 0 0 0 1
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 0 1 0 1 0 0 0 1
Biochemistry Laboratory of CDMU,Chengde Medical University 0 0 0 1 0 0 1 1
UT Southwestern Medical Center, UT Southwestern Medical Center 0 0 0 0 0 1 0 1
Central Laboratory,The First Hospital of Lanzhou University 0 0 0 1 0 0 1 1
Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University 0 0 0 1 0 0 1 1
New York Genome Center 0 0 0 0 0 0 1 1
Genetics and Prenatal Diagnosis Center,The First Affiliated Hospital of Zhengzhou University 0 0 0 1 0 0 1 1
The William Harvey Research Institute,Queen Mary University 0 0 0 0 0 0 1 1
Department of Pediatrics, Salzburger Landeskliniken & Paracelsus Medical University 0 0 0 0 0 0 1 1
GenomeConnect - Simons Searchlight 0 0 0 1 0 0 0 1
Paris Brain Institute,Inserm - ICM 0 1 0 1 0 0 0 1
Dept. Genetics and Cancer, Menzies Institute for Medical Research,University of Tasmania 0 0 0 0 1 0 1 1
Massachusetts General Hospital Undiagnosed Diseases Network,Massachusetts General Hospital 0 1 0 1 0 0 0 1
Wilkie Group, Clinical Genetics Lab, WIMM,University of Oxford 0 0 0 1 0 0 1 1

All variants with conflicting interpretations #

Total variants: 84
Download table as spreadsheet
HGVS dbSNP
NM_000023.4(SGCA):c.92T>C (p.Leu31Pro) rs903823830
NM_000138.4(FBN1):c.871G>T (p.Glu291Ter) rs1232880706
NM_000263.4(NAGLU):c.1915G>T (p.Glu639Ter) rs555145190
NM_000264.5(PTCH1):c.395-1G>A rs368869806
NM_000304.4(PMP22):c.353C>T (p.Thr118Met) rs104894619
NM_000516.6(GNAS):c.344C>T (p.Pro115Leu) rs137854539
NM_001042681.2(RERE):c.4304A>G (p.His1435Arg) rs1553154130
NM_001077415.3(CRELD1):c.959del (p.Gln320fs) rs759473511
NM_001085411.3(NADK2):c.1A>G (p.Met1Val) rs1277388010
NM_001110792.2(MECP2):c.352C>T (p.Arg118Trp) rs28934907
NM_001134407.3(GRIN2A):c.2452G>A (p.Ala818Thr) rs1555483699
NM_001160036.2(RHOBTB2):c.1448G>A (p.Arg483His) rs1554504663
NM_001193416.3(DDX3X):c.1600C>T (p.Arg534Cys) rs1555954284
NM_001199758.1(MTHFS):c.263G>A (p.Arg88Gln) rs753635972
NM_001199758.1(MTHFS):c.313C>T (p.Gln105Ter) rs771379232
NM_001220.5(CAMK2B):c.416C>T (p.Pro139Leu) rs1554389088
NM_001267550.2(TTN):c.82402A>C (p.Lys27468Gln) rs201958805
NM_001303256.3(MORC2):c.394C>T (p.Arg132Cys) rs1064795559
NM_001330504.1(ALG1):c.854+3A>G rs369160589
NM_001348768.2(HECW2):c.4334A>G (p.Glu1445Gly) rs878854424
NM_001370466.1(NOD2):c.2023C>T (p.Arg675Trp) rs2066844
NM_001370466.1(NOD2):c.2717+158C>T rs5743289
NM_001606.5(ABCA2):c.1193C>A (p.Thr398Lys) rs143473036
NM_001792.5(CDH2):c.2027A>G (p.Tyr676Cys) rs199984052
NM_001958.4(EEF1A2):c.796C>T (p.Arg266Trp) rs1555883505
NM_002437.5(MPV17):c.376-9T>G rs368900406
NM_003119.2(SPG7):c.1529C>T rs61755320
NM_003119.4(SPG7):c.2271del (p.Met757fs) rs1217391623
NM_003632.3(CNTNAP1):c.1163G>C (p.Arg388Pro) rs779027563
NM_003709.4(KLF7):c.790G>A (p.Asp264Asn) rs1057518995
NM_003718.5(CDK13):c.2524A>G (p.Asn842Asp) rs1554333853
NM_004004.6(GJB2):c.269T>C (p.Leu90Pro) rs80338945
NM_004035.7(ACOX1):c.710A>G (p.Asn237Ser) rs1567876984
NM_004204.4(PIGQ):c.942+1G>A rs200661329
NM_004859.4(CLTC):c.2669C>T (p.Pro890Leu) rs1555606635
NM_004895.4(NLRP3):c.2182A>G (p.Ser728Gly) rs147946775
NM_004959.5(NR5A1):c.274C>T (p.Arg92Trp) rs886039769
NM_005186.4(CAPN1):c.1605+5G>A rs375817528
NM_005859.5(PURA):c.299T>C (p.Leu100Pro) rs587782995
NM_005859.5(PURA):c.493G>A (p.Gly165Ser) rs1561793272
NM_006180.4(NTRK2):c.1301A>G (p.Tyr434Cys) rs886041091
NM_006662.3(SRCAP):c.7303C>T (p.Arg2435Ter) rs199469465
NM_006767.4(LZTR1):c.1943-256C>T rs761685529
NM_006796.2(AFG3L2):c.2011G>A (p.Gly671Arg) rs151344517
NM_007055.4(POLR3A):c.1771-7C>G rs201314157
NM_013432.5(TONSL):c.1837G>T (p.Val613Leu) rs778625348
NM_013432.5(TONSL):c.329G>A (p.Trp110Ter) rs1002531030
NM_013432.5(TONSL):c.595G>A (p.Glu199Lys) rs1335783881
NM_013432.5(TONSL):c.866-1G>C rs1424148372
NM_015021.3(ZNF292):c.6578A>C (p.Tyr2193Ser) rs1554208945
NM_015711.3(BICRA):c.936del (p.Ala313fs)
NM_016373.4(WWOX):c.689A>C (p.Gln230Pro)
NM_016525.5(UBAP1):c.426_427del (p.Lys143fs) rs1563920252
NM_017534.6(MYH2):c.5673+1G>C rs1400481053
NM_018116.3(MSTO1):c.971C>T (p.Thr324Ile) rs622288
NM_020442.6(VARS2):c.1168G>A rs202201763
NM_020451.3(SELENON):c.943G>A (p.Gly315Ser) rs121908188
NM_022089.4(ATP13A2):c.3057del (p.Tyr1020fs) rs765632065
NM_022168.4(IFIH1):c.1879G>T (p.Glu627Ter) rs35744605
NM_022786.3(ARV1):c.674-2A>T rs1192627743
NM_024496.4(IRF2BPL):c.519C>G (p.Tyr173Ter) rs1555377415
NM_024818.4(UBA5):c.907T>C (p.Cys303Arg) rs1553770577
NM_025137.4(SPG11):c.642del (p.Phe214fs) rs312262717
NM_025144.4(ALPK1):c.710C>T (p.Thr237Met) rs1052954321
NM_030632.3(ASXL3):c.3039+1G>A rs1555743003
NM_030662.3(MAP2K2):c.395G>A (p.Gly132Asp) rs387906800
NM_032271.3(TRAF7):c.1964G>A (p.Arg655Gln) rs1331463984
NM_032536.4(NTNG2):c.858-13G>A
NM_052876.4(NACC1):c.892C>T (p.Arg298Trp) rs1060505041
NM_144991.3(TSPEAR):c.589C>T (p.Arg197Ter) rs139455627
NM_145059.3(FCSK):c.2047C>T (p.Arg683Cys) rs755169246
NM_145059.3(FCSK):c.667T>C (p.Ser223Pro) rs769009456
NM_145207.3(SPATA5):c.983CAA[2] (p.Thr330del) rs796052243
NM_152328.5(ADSS1):c.781G>A (p.Asp261Asn) rs140614802
NM_153033.4(KCTD7):c.456G>A (p.Val152=) rs796052686
NM_153033.5(KCTD7):c.280C>T rs387907260
NM_177972.3(TUB):c.1215+1G>A rs1589996458
NM_183065.4(TMEM107):c.*617C>T rs117735243
NM_183065.4(TMEM107):c.*634C>T rs545394298
NM_183065.4(TMEM107):c.*745C>G
NR_023343.1(RNU4ATAC):n.13C>T rs559979281
NR_023343.1(RNU4ATAC):n.48G>A rs863225422
Single allele
m.15923A>G rs1556424691

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