ClinVar Miner

Variants from Suma Genomics with conflicting interpretations

Location: India  Primary collection method: clinical testing
Minimum review status of the submission from Suma Genomics: Collection method of the submission from Suma Genomics:
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
180 67 1 54 1 2 23 73

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
Suma Genomics pathogenic likely pathogenic uncertain significance established risk allele risk factor
pathogenic 0 28 5 0 0
likely pathogenic 26 1 7 0 1
uncertain significance 6 11 0 1 1
likely benign 0 0 1 0 0

Submitter to submitter summary #

Total submitters: 76
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 34 0 11 1 0 7 19
Baylor Genetics 0 18 0 10 0 0 5 15
OMIM 0 33 0 8 0 1 3 12
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 16 0 5 0 0 4 9
Counsyl 0 6 0 5 0 0 3 8
Institute of Human Genetics, University of Leipzig Medical Center 0 15 0 3 0 0 3 6
Fulgent Genetics, Fulgent Genetics 0 10 0 4 0 0 1 5
3billion 0 18 0 3 0 0 2 5
Neuberg Centre For Genomic Medicine, NCGM 0 13 0 4 0 0 1 5
Natera, Inc. 0 6 0 1 0 0 3 4
Mendelics 0 9 0 0 0 0 4 4
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 13 0 3 0 0 1 4
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 5 0 3 0 0 1 4
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 10 0 2 0 0 2 4
Genome-Nilou Lab 0 13 0 1 0 0 3 4
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 8 0 1 0 0 3 4
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 8 0 2 0 0 1 3
Revvity Omics, Revvity 0 12 0 2 0 0 1 3
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 4 0 1 0 0 2 3
Lifecell International Pvt. Ltd 0 8 0 3 0 0 0 3
Genetic Services Laboratory, University of Chicago 0 9 0 0 0 0 2 2
Ambry Genetics 0 2 0 0 0 0 2 2
Illumina Laboratory Services, Illumina 0 7 0 1 0 0 1 2
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 2 0 0 0 0 2 2
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 3 0 1 0 0 1 2
Genetics and Molecular Pathology, SA Pathology 0 4 0 1 0 0 1 2
SIB Swiss Institute of Bioinformatics 0 1 0 2 0 0 0 2
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 2 0 0 0 0 2 2
Felix Claverie-Martin Laboratory, Hospital Universitario Nuestra Senora de Candelaria 0 0 0 2 0 0 0 2
New York Genome Center 0 2 0 1 0 0 1 2
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 5 0 0 0 0 2 2
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 4 0 0 0 0 1 1
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 4 0 0 0 0 1 1
Elsea Laboratory, Baylor College of Medicine 0 1 0 0 0 0 1 1
MGZ Medical Genetics Center 0 7 0 0 0 0 1 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 1 0 1 0 0 0 1
Centogene AG - the Rare Disease Company 0 7 0 0 0 0 1 1
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 0 0 1 0 0 0 0 1
LDLR-LOVD, British Heart Foundation 0 0 0 1 0 0 0 1
RettBASE 0 5 0 0 0 0 1 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 1 0 0 0 0 1 1
UCLA Clinical Genomics Center, UCLA 0 0 0 0 0 0 1 1
Center for Medical Genetics Ghent, University of Ghent 0 1 0 1 0 0 0 1
Division of Human Genetics, Children's Hospital of Philadelphia 0 4 0 0 0 0 1 1
Centre of Medical Genetics, University of Antwerp 0 0 0 1 0 0 0 1
Scripps Translational Science Institute, Scripps Health and The Scripps Research Institute 0 0 0 1 0 0 0 1
Laboratory of Genetics and Molecular Cardiology, University of São Paulo 0 0 0 1 0 0 0 1
UW Hindbrain Malformation Research Program, University of Washington 0 0 0 1 0 0 0 1
Center of Genomic medicine, Geneva, University Hospital of Geneva 0 0 0 0 0 1 0 1
Center for Human Genetics, University of Leuven 0 0 0 1 0 0 0 1
Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare 0 2 0 1 0 0 0 1
Database of Curated Mutations (DoCM) 0 0 0 1 0 0 0 1
Cardiovascular Research Group, Instituto Nacional de Saude Doutor Ricardo Jorge 0 0 0 0 0 0 1 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 2 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 0 0 1 0 0 0 1
Molecular Genetics Laboratory, Centre for Cardiovascular Surgery and Transplantation 0 0 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 0 0 1 0 1
Fundacion Hipercolesterolemia Familiar 0 0 0 0 0 0 1 1
Iberoamerican FH Network 0 0 0 0 0 0 1 1
Department Of Genetics, Lifeline Super Speciality Hospital, Adoor. 0 0 0 1 0 0 0 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 1 0 0 0 1
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 8 0 0 0 0 1 1
Variantyx, Inc. 0 0 0 0 0 0 1 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 3 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 6 0 0 0 0 1 1
Cavalleri Lab, Royal College of Surgeons in Ireland 0 0 0 1 0 0 0 1
Genomics Facility, Ludwig-Maximilians-Universität München 0 0 0 1 0 0 0 1
Clinical Genomics Program, Stanford Medicine 0 2 0 0 0 0 1 1
Institute of Human Genetics, University Hospital Muenster 0 0 0 0 0 0 1 1
Allergy Immunology Laboratory, Postgraduate Institute of Medical Education and Research, Chandigarh 0 0 0 0 0 0 1 1
Bioinformatics Unit, Institut Pasteur de Montevideo 0 0 0 1 0 0 0 1
DASA 0 3 0 0 0 0 1 1
Laboratory of molecular diagnosis of dyslipidemias, Università egli studi di Napoli Federico II 0 0 0 1 0 0 0 1
Genomics England Pilot Project, Genomics England 0 1 0 1 0 0 0 1
Molecular Biology Laboratory, Department of Zoology, Quaid-i-azam University 0 0 0 0 0 0 1 1
All of Us Research Program, National Institutes of Health 0 2 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 73
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001370658.1(BTD):c.1270G>C (p.Asp424His) rs13078881 0.03225
NM_000492.4(CFTR):c.1210-11T>G rs73715573 0.00886
NM_012452.3(TNFRSF13B):c.310T>C (p.Cys104Arg) rs34557412 0.00403
NM_016038.4(SBDS):c.258+2T>C rs113993993 0.00323
NM_000155.4(GALT):c.563A>G (p.Gln188Arg) rs75391579 0.00192
NM_001111.5(ADAR):c.577C>G (p.Pro193Ala) rs145588689 0.00162
NM_000235.4(LIPA):c.894G>A (p.Gln298=) rs116928232 0.00075
NM_000018.4(ACADVL):c.520G>A (p.Val174Met) rs369560930 0.00009
NM_025114.4(CEP290):c.6645+1G>A rs201218801 0.00006
NM_138694.4(PKHD1):c.4870C>T (p.Arg1624Trp) rs200391019 0.00006
NM_000481.4(AMT):c.887G>A (p.Arg296His) rs386833690 0.00003
NM_001010867.4(IBA57):c.316A>G (p.Thr106Ala) rs1053773776 0.00003
NM_002354.3(EPCAM):c.556-14A>G rs376155665 0.00003
NM_013335.4(GMPPA):c.1096C>T (p.Arg366Ter) rs770582052 0.00003
NM_000018.4(ACADVL):c.1077G>A (p.Ala359=) rs779458466 0.00002
NM_000071.3(CBS):c.430G>A (p.Glu144Lys) rs121964966 0.00002
NM_000152.5(GAA):c.971C>T (p.Pro324Leu) rs750030887 0.00002
NM_000159.4(GCDH):c.938G>A (p.Arg313Gln) rs746220312 0.00002
NM_001739.2(CA5A):c.721G>A (p.Glu241Lys) rs563971993 0.00002
NM_024120.5(NDUFAF5):c.686T>C (p.Leu229Pro) rs118203929 0.00002
NM_000048.4(ASL):c.978G>C (p.Gln326His) rs764356037 0.00001
NM_000051.4(ATM):c.3965T>C (p.Leu1322Pro) rs786203306 0.00001
NM_000138.5(FBN1):c.5788+5G>A rs193922219 0.00001
NM_000492.4(CFTR):c.2210C>T (p.Ser737Phe) rs186089140 0.00001
NM_001061.7(TBXAS1):c.1235G>A (p.Arg412Gln) rs199422117 0.00001
NM_001370658.1(BTD):c.176G>A (p.Arg59His) rs397514343 0.00001
NM_004870.4(MPDU1):c.218G>A (p.Gly73Glu) rs104894586 0.00001
NM_006267.5(RANBP2):c.1754C>T (p.Thr585Met) rs121434502 0.00001
NM_012203.2(GRHPR):c.494G>A (p.Gly165Asp) rs180177314 0.00001
NM_000051.4(ATM):c.3137T>C (p.Leu1046Pro) rs568461905
NM_000053.4(ATP7B):c.3971A>G (p.Asn1324Ser) rs760285767
NM_000142.5(FGFR3):c.749C>G (p.Pro250Arg) rs4647924
NM_000152.5(GAA):c.794G>A (p.Ser265Asn) rs772002851
NM_000155.4(GALT):c.904+1G>T rs367543271
NM_000310.4(PPT1):c.713C>T (p.Pro238Leu) rs878853322
NM_000391.4(TPP1):c.380+5G>A rs1564855725
NM_000487.6(ARSA):c.1492dup (p.Arg498fs) rs774153480
NM_000487.6(ARSA):c.739G>A (p.Gly247Arg) rs74315471
NM_000492.4(CFTR):c.3944_3951del (p.Ile1315fs) rs754392413
NM_000527.5(LDLR):c.2389G>A (p.Val797Met)
NM_001040142.2(SCN2A):c.1561G>C (p.Asp521His) rs1574572514
NM_001042492.3(NF1):c.2540T>C (p.Leu847Pro) rs199474747
NM_001065.4(TNFRSF1A):c.295T>C (p.Cys99Arg) rs104895228
NM_001110792.2(MECP2):c.916C>T (p.Arg306Ter) rs61751362
NM_001110792.2(MECP2):c.941C>G (p.Pro314Arg) rs61749723
NM_001110792.2(MECP2):c.961C>T (p.Arg321Trp) rs61751444
NM_001134831.2(AHI1):c.1799_1802del (p.Lys600fs) rs1786504555
NM_001197104.2(KMT2A):c.6445C>T (p.Arg2149Ter) rs781843315
NM_001286704.2(UFM1):c.-273_-271del rs747359907
NM_001367721.1(CASK):c.617G>A (p.Gly206Asp) rs587783367
NM_001370658.1(BTD):c.38_44delinsTCC (p.Cys13fs) rs80338684
NM_001370658.1(BTD):c.416G>A (p.Ser139Asn) rs144717999
NM_001375380.1(EBF3):c.422A>G (p.Tyr141Cys) rs1057519519
NM_001378452.1(ITPR1):c.805C>T (p.Arg269Trp) rs886039392
NM_001378615.1(CC2D2A):c.4226T>C (p.Ile1409Thr) rs863225176
NM_001844.5(COL2A1):c.2965C>T (p.Arg989Cys) rs121912874
NM_003676.4(DEGS1):c.565A>G (p.Asn189Asp) rs771864122
NM_004629.2(FANCG):c.619del (p.Leu207fs)
NM_005271.5(GLUD1):c.1519C>T (p.His507Tyr) rs121909730
NM_006009.4(TUBA1A):c.1204C>T (p.Arg402Cys) rs587784483
NM_006580.4(CLDN16):c.103G>A (p.Asp35Asn) rs2108658339
NM_006580.4(CLDN16):c.137T>C (p.Leu46Pro) rs2108670592
NM_007118.4(TRIO):c.4382C>G (p.Pro1461Arg) rs1747667518
NM_020297.4(ABCC9):c.3460C>T (p.Arg1154Trp) rs387907208
NM_020533.3(MCOLN1):c.571+2T>C rs1555741822
NM_020975.6(RET):c.1901G>A (p.Cys634Tyr) rs75996173
NM_021095.4(SLC5A6):c.1285A>G (p.Ser429Gly) rs2147992303
NM_021830.5(TWNK):c.1075G>A (p.Ala359Thr) rs111033573
NM_021939.4(FKBP10):c.831dup (p.Gly278fs) rs137853883
NM_022336.4(EDAR):c.292C>T (p.Arg98Trp) rs557166582
NM_033629.6(TREX1):c.868_885del (p.Pro290_Ala295del) rs79318303
NM_138615.3(DHX30):c.2353C>T (p.Arg785Cys) rs1085307451
NM_198239.2(CCN6):c.1010G>A (p.Cys337Tyr) rs781986930

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