ClinVar Miner

Variants from Department of Genetics, Sultan Qaboos University Hospital with conflicting interpretations

Location: Oman  Primary collection method: curation
Minimum review status of the submission from Department of Genetics, Sultan Qaboos University Hospital: Collection method of the submission from Department of Genetics, Sultan Qaboos University Hospital:
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
139 109 0 75 7 0 29 102

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
Department of Genetics, Sultan Qaboos University Hospital pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 47 9 0 0
likely pathogenic 27 0 5 1 1
uncertain significance 8 7 0 3 1
benign 2 1 3 1 0

Submitter to submitter summary #

Total submitters: 82
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 48 0 12 0 0 5 17
Labcorp Genetics (formerly Invitae), Labcorp 0 86 0 7 4 0 4 15
3billion 0 34 0 6 0 0 3 9
Counsyl 0 14 0 6 2 0 1 9
Baylor Genetics 0 43 0 5 0 0 2 7
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 26 0 5 0 0 2 7
Natera, Inc. 0 25 0 7 0 0 0 7
Dubai Health Genomic Medicine Center, Dubai Health 0 18 0 5 0 0 1 6
Fulgent Genetics, Fulgent Genetics 0 23 0 5 0 0 1 6
Genome-Nilou Lab 0 33 0 6 0 0 0 6
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 24 0 4 0 0 2 6
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 9 0 3 0 0 1 4
Illumina Laboratory Services, Illumina 0 14 0 2 1 0 1 4
Institute of Human Genetics, University of Leipzig Medical Center 0 14 0 3 0 0 1 4
Neuberg Centre For Genomic Medicine, NCGM 0 18 0 3 0 0 1 4
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill 0 2 0 2 0 0 2 4
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 6 0 2 0 0 1 3
Mendelics 0 18 0 1 1 0 1 3
Revvity Omics, Revvity 0 15 0 1 1 0 1 3
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 19 0 2 0 0 1 3
Ambry Genetics 0 7 0 2 0 0 0 2
Bioscientia Institut fuer Medizinische Diagnostik GmbH, Sonic Healthcare 0 1 0 1 0 0 1 2
Department of Human Genetics, Hannover Medical School 0 6 0 2 0 0 0 2
Department of Molecular Genetics, Istishari Arab Hospital 0 2 0 1 0 0 1 2
Department of Pathology and Laboratory Medicine, Sinai Health System 0 7 0 1 0 0 1 2
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 4 0 1 0 0 1 2
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital 0 4 0 2 0 0 0 2
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 2 0 1 0 0 1 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 7 0 2 0 0 0 2
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 5 0 2 0 0 0 2
SIB Swiss Institute of Bioinformatics 0 0 0 2 0 0 0 2
Sharon lab, Hadassah-Hebrew University Medical Center 0 0 0 2 0 0 0 2
UCLA Clinical Genomics Center, UCLA 0 0 0 1 0 0 1 2
CENTOGENE GmbH and LLC - Guiding Precision Medicine 0 9 0 0 0 0 1 1
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 2 0 0 1 0 0 1
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 10 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 4 0 0 0 0 1 1
Centre for Translational Omics - GOSgene, University College London 0 0 0 1 0 0 0 1
Clinical Biochemistry Laboratory, Health Services Laboratory 0 1 0 1 0 0 0 1
Clinical Genetics Laboratory, Skane University Hospital Lund 0 0 0 1 0 0 0 1
Coban-Akdemir Lab, University of Texas Health Science Center 0 0 0 0 0 0 1 1
Constantin Polychronakos Laboratory, The Research Institute of the McGill University Health Centre 0 0 0 0 0 0 1 1
Daryl Scott Lab, Baylor College of Medicine 0 1 0 0 0 0 1 1
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet 0 0 0 1 0 0 0 1
Division of Human Genetics, Children's Hospital of Philadelphia 0 2 0 0 0 0 1 1
Dunham Lab, University of Washington 0 3 0 0 1 0 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 2 0 1 0 0 0 1
Genetic Diseases Diagnostic Center, Koc University Hospital 0 0 0 0 0 0 1 1
Genetics and Genomic Medicine Centre, NeuroGen Healthcare, NeuroGen Healthcare 0 1 0 1 0 0 0 1
Genetics and Molecular Pathology, SA Pathology 0 5 0 0 0 0 1 1
Genomic Medicine Lab, University of California San Francisco 0 0 0 0 0 0 1 1
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 6 0 0 0 0 1 1
Hadassah Hebrew University Medical Center 0 0 0 1 0 0 0 1
Houlden Lab, UCL Institute of Neurology 0 0 0 0 0 0 1 1
Immunogenetics and Transplant Biology Service, University Hospital "Città della Salute e della Scienza di Torino" 0 0 0 1 0 0 0 1
Inherited Neuropathy Consortium Ii, University Of Miami 0 0 0 0 0 0 1 1
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg 0 0 0 1 0 0 0 1
Institute of Human Genetics, University of Ulm 0 0 0 1 0 0 0 1
Johns Hopkins Genomics, Johns Hopkins University 0 4 0 0 0 0 1 1
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 0 0 0 1 0 0 0 1
Juno Genomics, Hangzhou Juno Genomics, Inc 0 11 0 1 0 0 0 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 4 0 0 0 0 1 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 3 0 1 0 0 0 1
Laboratory of Genetics in Ophthalmology, Institut Imagine 0 0 0 1 0 0 0 1
Laboratory of Human Genetics, Universidade de São Paulo 0 0 0 1 0 0 0 1
Laboratory of Molecular Genetics, Children's Memorial Health Institute 0 1 0 1 0 0 0 1
Lifecell International Pvt. Ltd 0 3 0 0 0 0 1 1
MGZ Medical Genetics Center 0 9 0 1 0 0 0 1
Medical Genetics, University of Parma 0 6 0 0 0 0 1 1
Molecular Biology Laboratory, Fundació Puigvert 0 0 0 1 0 0 0 1
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 0 0 1 0 0 0 1
Myriad Genetics, Inc. 0 12 0 1 0 0 0 1
National Institute of Allergy and Infectious Diseases - Centralized Sequencing Program, National Institutes of Health 0 0 0 1 0 0 0 1
New York Genome Center 0 4 0 0 0 0 1 1
OLLIN Analises Genomicas, OLLIN 0 1 0 1 0 0 0 1
Rare Pediatric Neurological Diseases Research Center, Mashhad University of Medical Sciences 0 0 0 0 0 0 1 1
Research Institute for Ophthalmology and Vision Science, Shahid Beheshti University of Medical Sciences 0 0 0 1 0 0 0 1
Service de Génétique Médicale, Centre Hospitalier Universitaire de Nice-Université Côte d'Azur 0 0 0 0 0 0 1 1
SingHealth Duke-NUS Institute of Precision Medicine 0 0 0 1 0 0 0 1
Undiagnosed Diseases Network, NIH 0 0 0 1 0 0 0 1
Yale Center for Mendelian Genomics, Yale University 0 1 0 1 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 4 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 102
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000402.4(G6PD):c.466A>G (p.Asn156Asp) rs1050829 0.08672
NM_000402.4(G6PD):c.292G>A (p.Val98Met) rs1050828 0.03616
NM_001065.4(TNFRSF1A):c.362G>A (p.Arg121Gln) rs4149584 0.01206
NM_000350.3(ABCA4):c.5882G>A (p.Gly1961Glu) rs1800553 0.00269
NM_000104.4(CYP1B1):c.1103G>A (p.Arg368His) rs79204362 0.00125
NM_000155.4(GALT):c.404C>T (p.Ser135Leu) rs111033690 0.00094
NM_005732.4(RAD50):c.3036+5G>A rs181016343 0.00078
NM_000265.7(NCF1):c.579G>A (p.Trp193Ter) rs145360423 0.00054
NM_138694.4(PKHD1):c.107C>T (p.Thr36Met) rs137852944 0.00048
NM_014249.4(NR2E3):c.932G>A (p.Arg311Gln) rs28937873 0.00032
NM_001298.3(CNGA3):c.967G>C (p.Ala323Pro) rs146195955 0.00030
NM_000402.4(G6PD):c.653C>T (p.Ser218Phe) rs5030868 0.00028
NM_000137.4(FAH):c.1062+5G>A rs80338901 0.00027
NM_020975.6(RET):c.785T>C (p.Val262Ala) rs139790943 0.00025
NM_001014437.3(CARS1):c.1955T>A (p.Phe652Tyr) rs781761299 0.00019
NM_000104.4(CYP1B1):c.182G>A (p.Gly61Glu) rs28936700 0.00017
NM_024422.6(DSC2):c.2471C>T (p.Ser824Leu) rs143413607 0.00017
NM_001277115.2(DNAH11):c.6506C>T (p.Ser2169Leu) rs373946181 0.00016
NM_025132.4(WDR19):c.3533G>A (p.Arg1178Gln) rs79436363 0.00015
NM_002225.5(IVD):c.358G>A (p.Gly120Arg) rs142761835 0.00013
NM_005629.4(SLC6A8):c.92C>T (p.Pro31Leu) rs868950793 0.00011
NM_003742.4(ABCB11):c.1460G>A (p.Arg487His) rs188824058 0.00009
NM_015087.5(SPART):c.364_365del (p.Met122fs) rs775736341 0.00009
NM_033419.5(PGAP3):c.558-10G>A rs200598755 0.00009
NM_003560.4(PLA2G6):c.2370T>G (p.Tyr790Ter) rs121908680 0.00006
NM_017671.5(FERMT1):c.811C>T (p.Arg271Ter) rs121918293 0.00006
NM_138694.4(PKHD1):c.4870C>T (p.Arg1624Trp) rs200391019 0.00006
NM_000260.4(MYO7A):c.5648G>A (p.Arg1883Gln) rs111033215 0.00004
NM_000320.3(QDPR):c.49G>C (p.Gly17Arg) rs757483045 0.00003
NM_000402.4(G6PD):c.1093G>A (p.Ala365Thr) rs5030869 0.00003
NM_001673.5(ASNS):c.146G>A (p.Arg49Gln) rs769236847 0.00003
NM_002225.5(IVD):c.1175G>A (p.Arg392His) rs982218848 0.00003
NM_006759.4(UGP2):c.34A>G (p.Met12Val) rs768305634 0.00003
NM_013328.4(PYCR2):c.355C>T (p.Arg119Cys) rs372781135 0.00003
NM_000030.3(AGXT):c.346G>A (p.Gly116Arg) rs180177207 0.00002
NM_000359.3(TGM1):c.832G>A (p.Gly278Arg) rs121918725 0.00002
NM_001042492.3(NF1):c.4330A>G (p.Lys1444Glu) rs137854550 0.00002
NM_000016.6(ACADM):c.362C>T (p.Thr121Ile) rs121434283 0.00001
NM_000143.4(FH):c.1048C>T (p.Arg350Trp) rs755436052 0.00001
NM_000159.4(GCDH):c.416C>T (p.Ser139Leu) rs139851890 0.00001
NM_000196.4(HSD11B2):c.622C>T (p.Arg208Cys) rs121917780 0.00001
NM_000263.4(NAGLU):c.1597C>T (p.Arg533Ter) rs1244655820 0.00001
NM_000294.3(PHKG2):c.469G>A (p.Glu157Lys) rs752961445 0.00001
NM_000391.4(TPP1):c.1525C>T (p.Gln509Ter) rs1184563885 0.00001
NM_000521.4(HEXB):c.841C>T (p.Arg281Ter) rs138914144 0.00001
NM_001182.5(ALDH7A1):c.1556G>A (p.Arg519Lys) rs561343926 0.00001
NM_001369.3(DNAH5):c.3013A>T (p.Asn1005Tyr) rs770975422 0.00001
NM_001918.5(DBT):c.1281+1G>T rs1557943881 0.00001
NM_002225.5(IVD):c.1184G>A (p.Arg395Gln) rs1477527791 0.00001
NM_003850.3(SUCLA2):c.920C>T (p.Ala307Val) rs1011464708 0.00001
NM_014254.3(RXYLT1):c.914+6T>G rs748809209 0.00001
NM_022041.4(GAN):c.601C>T (p.Arg201Ter) rs119485090 0.00001
NM_024306.5(FA2H):c.703C>T (p.Arg235Cys) rs387907039 0.00001
NM_025150.5(TARS2):c.326G>A (p.Arg109Gln) rs760526545 0.00001
NM_000044.6(AR):c.1846C>T (p.Arg616Cys) rs1555990485
NM_000071.3(CBS):c.969G>A (p.Trp323Ter) rs863223432
NM_000104.4(CYP1B1):c.1120G>A (p.Asp374Asn) rs104893622
NM_000180.4(GUCY2D):c.1956+2T>A rs61749758
NM_000342.4(SLC4A1):c.2573C>A (p.Ala858Asp) rs121912751
NM_000359.3(TGM1):c.1187G>A (p.Arg396His) rs121918721
NM_000369.5(TSHR):c.484C>T (p.Pro162Ser) rs121908863
NM_000383.4(AIRE):c.1637G>C (p.Ter546Ser) rs1568932096
NM_000426.4(LAMA2):c.7888C>T (p.Arg2630Ter) rs727502851
NM_000481.4(AMT):c.982dup (p.Ala328fs) rs1553638266
NM_000492.3(CFTR):c.1521_1523del (p.Phe508del) rs113993960
NM_000492.4(CFTR):c.1175T>G (p.Val392Gly) rs397508170
NM_000528.4(MAN2B1):c.1203C>G (p.Tyr401Ter) rs781291011
NM_000533.5(PLP1):c.634T>C (p.Trp212Arg) rs2147766937
NM_000642.3(AGL):c.772T>C (p.Ser258Pro) rs886039873
NM_001009944.3(PKD1):c.8896G>T (p.Glu2966Ter) rs773129632
NM_001032386.2(SUOX):c.1388C>T (p.Ser463Phe) rs1565799921
NM_001042492.3(NF1):c.1833del (p.Asn614fs) rs2508126744
NM_001042492.3(NF1):c.2540T>C (p.Leu847Pro) rs199474747
NM_001042492.3(NF1):c.3113+1G>T rs267606599
NM_001042492.3(NF1):c.3113+2T>G rs876658997
NM_001042492.3(NF1):c.3113+5G>T rs1555614549
NM_001042492.3(NF1):c.4341G>C (p.Gln1447His) rs876660206
NM_001042492.3(NF1):c.4577+1G>C rs1279529138
NM_001042492.3(NF1):c.6428-3C>G rs374014162
NM_001042492.3(NF1):c.755TGG[1] (p.Val253del) rs1060500323
NM_001042492.3(NF1):c.943C>T (p.Gln315Ter) rs766011053
NM_001354768.3(NRL):c.339C>G (p.Tyr113Ter) rs1566560531
NM_001370595.2(COA8):c.314T>C (p.Phe105Ser) rs587777786
NM_003193.5(TBCE):c.155_166del (p.Ser52_Gly55del) rs767004810
NM_003906.5(MCM3AP):c.2861T>C (p.Ile954Thr) rs2517390727
NM_004273.5(CHST3):c.911G>A (p.Arg304Gln) rs28937593
NM_004897.5(MINPP1):c.992T>G (p.Ile331Ser) rs749643952
NM_005687.5(FARSB):c.853G>A (p.Glu285Lys) rs767956337
NM_005984.5(SLC25A1):c.205G>T (p.Asp69Tyr) rs2083996886
NM_012472.6(DNAAF11):c.354_355del (p.Phe119fs) rs1821475039
NM_014625.4(NPHS2):c.467dup (p.Leu156fs) rs528833893
NM_015488.5(PNKD):c.20C>T (p.Ala7Val) rs121434512
NM_016464.5(TMEM138):c.389A>G (p.Tyr130Cys) rs387907135
NM_020964.3(EPG5):c.6084G>A (p.Trp2028Ter) rs1568107449
NM_021008.4(DEAF1):c.997+4A>C rs886040972
NM_133443.4(GPT2):c.815C>T (p.Pro272Leu) rs886038199
NM_152281.2(GORAB):c.-1_1delGAinsCT (p.Met(?_1)_Met1(?)) rs1557999318
NM_152564.5(VPS13B):c.7859G>A (p.Gly2620Asp) rs120074153
NM_152732.5(RSPH9):c.801GAA[1] (p.Lys268del) rs397515340
NM_153033.5(KCTD7):c.335G>A (p.Arg112His) rs774026720
NM_153704.6(TMEM67):c.383_384del (p.His128fs) rs386834200
NM_177400.3(NKX6-2):c.487C>G (p.Leu163Val) rs1131692048

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