ClinVar Miner

Variants from Elsea Laboratory, Baylor College of Medicine with conflicting interpretations

Location: United States  Primary collection method: clinical testing
Minimum review status of the submission from Elsea Laboratory, Baylor College of Medicine: Collection method of the submission from Elsea Laboratory, Baylor College of Medicine:
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
118 58 0 24 17 1 24 62

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
Elsea Laboratory, Baylor College of Medicine pathogenic likely pathogenic uncertain significance likely benign benign protective other
pathogenic 0 16 6 1 2 1 1
likely pathogenic 6 0 11 2 3 0 0
uncertain significance 5 4 0 10 9 0 0
likely benign 0 0 3 0 2 0 0

Submitter to submitter summary #

Total submitters: 80
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 43 0 8 15 0 15 38
Illumina Laboratory Services, Illumina 0 9 0 3 8 0 8 18
Natera, Inc. 0 4 0 3 8 0 1 12
OMIM 0 17 0 2 0 0 3 5
Revvity Omics, Revvity 0 11 0 2 0 0 3 5
Genome-Nilou Lab 0 7 0 2 1 0 2 5
Baylor Genetics 0 14 0 0 0 0 4 4
PreventionGenetics, part of Exact Sciences 0 0 0 1 0 0 3 4
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 12 0 2 0 0 2 4
New York Genome Center 0 5 0 1 0 0 4 4
Genetic Services Laboratory, University of Chicago 0 1 0 0 0 0 3 3
GeneDx 0 1 0 1 0 0 3 3
MGZ Medical Genetics Center 0 3 0 0 0 0 3 3
Counsyl 0 2 0 2 0 0 1 3
Mendelics 0 3 0 0 0 0 3 3
Eurofins Ntd Llc (ga) 0 0 0 1 0 1 3 3
Fulgent Genetics, Fulgent Genetics 0 18 0 1 0 0 2 3
CeGaT Center for Human Genetics Tuebingen 0 0 0 0 0 0 3 3
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 2 0 1 0 0 2 3
Athena Diagnostics Inc 0 0 0 1 0 0 2 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 5 0 0 0 0 2 2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 2 0 0 0 0 2 2
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 5 0 0 0 0 2 2
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 5 0 2 0 0 0 2
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 1 0 0 0 0 2 2
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 1 0 2 0 0 1 2
Genetics and Molecular Pathology, SA Pathology 0 0 0 0 0 0 2 2
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 2 0 0 0 0 2 2
Institute of Human Genetics, University of Leipzig Medical Center 0 2 0 1 0 0 1 2
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 0 1 0 0 1 2
Clinical Genomics Program, Stanford Medicine 0 1 0 0 0 0 2 2
Lifecell International Pvt. Ltd 0 0 0 1 0 0 1 2
3billion 0 6 0 0 0 0 2 2
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 2 0 1 0 0 1 2
Neuberg Supratech Reference Laboratories Pvt Ltd, Neuberg Centre for Genomic Medicine 0 0 0 1 0 0 1 2
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 1 0 0 0 0 1 1
Centogene AG - the Rare Disease Company 0 0 0 0 0 0 1 1
Mayo Clinic Laboratories, Mayo Clinic 0 0 0 1 0 0 1 1
Quest Diagnostics Nichols Institute San Juan Capistrano 0 0 0 0 0 0 1 1
Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre 0 0 0 1 0 0 0 1
UCLA Clinical Genomics Center, UCLA 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
Division of Human Genetics, Children's Hospital of Philadelphia 0 0 0 0 0 0 1 1
University of Washington Center for Mendelian Genomics, University of Washington 0 0 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 Metabolic Disorders, Peking University First Hospital 0 2 0 1 0 0 0 1
Genome Sciences Centre, British Columbia Cancer Agency 0 0 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 0 0 0 0 1 1
Daryl Scott Lab, Baylor College of Medicine 0 1 0 0 0 0 1 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 0 0 1 0 0 0 1
Undiagnosed Diseases Network, NIH 0 1 0 1 0 0 1 1
SIB Swiss Institute of Bioinformatics 0 1 0 0 0 0 1 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 0 0 0 1 1
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System 0 0 0 1 0 0 1 1
Rare Disease Group, Clinical Genetics, Karolinska Institutet 0 0 0 1 0 0 1 1
Institute of Cellular and Molecular Medicine, Copenhagen University 0 0 0 1 0 0 0 1
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 1 0 0 0 0 1 1
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 0 0 0 0 0 1 1
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 3 0 0 0 0 1 1
Variantyx, Inc. 0 0 0 0 0 0 1 1
ClinGen PAH Variant Curation Expert Panel 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 1 0 0 1 1
Génétique des Maladies du Développement, Hospices Civils de Lyon 0 1 0 1 0 0 0 1
Medical Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano 0 0 0 0 0 0 1 1
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill 0 1 0 0 0 0 1 1
Kids Research, The Children's Hospital at Westmead 0 0 0 1 0 0 0 1
Molecular Pathology Diagnostics Labratory, University of Iowa Hospitals & Clinics 0 0 0 1 0 0 0 1
Biochemistry Laboratory of CDMU, Chengde Medical University 0 0 0 1 0 0 0 1
Al Jalila Children's Genomics Center, Al Jalila Childrens Speciality Hospital 0 0 0 0 0 0 1 1
Myriad Genetics, Inc. 0 3 0 0 0 0 1 1
Medical Genetics Laboratory, Tarbiat Modares University 0 0 0 1 0 0 0 1
Institute of Human Genetics, University Hospital Muenster 0 0 0 0 0 0 1 1
Rare Disease Group, University of Exeter 0 0 0 1 0 0 0 1
Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University 0 0 0 1 0 0 0 1
Suma Genomics 0 1 0 0 0 0 1 1
DASA 0 2 0 0 0 0 1 1
IU Genetic Testing Laboratories, Indiana University School of Medicine 0 0 0 1 0 0 0 1
ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel, ClinGen 0 0 0 0 0 0 1 1
Molecular Biology Laboratory, Department of Zoology, Quaid-i-azam University 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 62
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HGVS dbSNP gnomAD frequency
NM_001370658.1(BTD):c.1270G>C (p.Asp424His) rs13078881 0.03225
NM_153006.3(NAGS):c.182A>G (p.Glu61Gly) rs113134544 0.01375
NM_001370658.1(BTD):c.73G>A (p.Gly25Arg) rs34885143 0.01036
NM_000170.3(GLDC):c.319A>G (p.Met107Val) rs138454333 0.00707
NM_001127649.3(PEX26):c.130C>T (p.Leu44Phe) rs150895887 0.00683
NM_000170.3(GLDC):c.52G>T (p.Gly18Cys) rs535143891 0.00670
NM_000161.3(GCH1):c.68C>T (p.Pro23Leu) rs41298432 0.00389
NM_000156.6(GAMT):c.79T>C (p.Tyr27His) rs200833152 0.00345
NM_000666.3(ACY1):c.1057C>T (p.Arg353Cys) rs121912698 0.00260
NM_000170.3(GLDC):c.2683A>G (p.Met895Val) rs141152043 0.00200
NM_000155.4(GALT):c.563A>G (p.Gln188Arg) rs75391579 0.00192
NM_153006.3(NAGS):c.374C>A (p.Thr125Lys) rs185863881 0.00187
NM_016327.3(UPB1):c.917-1G>A rs143493067 0.00169
NM_001698.3(AUH):c.381A>G (p.Ile127Met) rs146227896 0.00125
NM_001127649.3(PEX26):c.911G>A (p.Arg304His) rs17851387 0.00121
NM_013391.3(DMGDH):c.972G>A (p.Trp324Ter) rs139044238 0.00088
NM_016327.3(UPB1):c.358G>T (p.Ala120Ser) rs138872001 0.00084
NM_003849.4(SUCLG1):c.202-4T>C rs141973418 0.00063
NM_001378120.1(MBD5):c.236G>A (p.Gly79Glu) rs34995577 0.00061
NM_022132.5(MCCC2):c.1015G>A (p.Val339Met) rs150591260 0.00057
NM_001378120.1(MBD5):c.3842C>T (p.Thr1281Ile) rs145475623 0.00034
NM_000532.5(PCCB):c.180G>A (p.Lys60=) rs140636870 0.00031
NM_015506.3(MMACHC):c.19G>A (p.Glu7Lys) rs377405910 0.00030
NM_000161.3(GCH1):c.507G>A (p.Ala169=) rs150158277 0.00029
NM_001182.5(ALDH7A1):c.1279G>C (p.Glu427Gln) rs121912707 0.00024
NM_001370658.1(BTD):c.-148C>T rs774964227 0.00022
NM_001875.5(CPS1):c.3626T>C (p.Met1209Thr) rs200569046 0.00018
NM_016327.3(UPB1):c.105-2A>G rs138081800 0.00010
NM_001080.3(ALDH5A1):c.764A>G (p.Asn255Ser) rs145087265 0.00007
NM_000277.3(PAH):c.842+1G>A rs5030852 0.00004
NM_001080.3(ALDH5A1):c.589G>A (p.Val197Met) rs768219929 0.00004
NM_001182.5(ALDH7A1):c.834G>A (p.Val278=) rs201948406 0.00004
NM_004092.4(ECHS1):c.538A>G (p.Thr180Ala) rs557128093 0.00004
NM_001082971.2(DDC):c.260C>T (p.Pro87Leu) rs746244631 0.00002
NM_014362.4(HIBCH):c.353T>C (p.Phe118Ser) rs758938066 0.00002
NM_000016.6(ACADM):c.320T>C (p.Leu107Ser) rs746136472 0.00001
NM_001080.3(ALDH5A1):c.1226G>A (p.Gly409Asp) rs118203984 0.00001
NM_001080.3(ALDH5A1):c.1478A>G (p.Asn493Ser) rs776978579 0.00001
NM_001080.3(ALDH5A1):c.1592G>A (p.Cys531Tyr) rs953870735 0.00001
NM_001080.3(ALDH5A1):c.515G>A (p.Arg172His) rs773814880 0.00001
NM_001080.3(ALDH5A1):c.608C>T (p.Pro203Leu) rs906284769 0.00001
NM_014362.4(HIBCH):c.365A>G (p.Tyr122Cys) rs121918329 0.00001
NM_018706.7(DHTKD1):c.1118C>T (p.Pro373Leu) rs556384043 0.00001
NM_145199.3(LIPT1):c.212C>T (p.Ser71Phe) rs767568897 0.00001
NM_000045.4(ARG1):c.745G>C (p.Val249Leu) rs182650447
NM_000235.4(LIPA):c.539-5C>A rs2297472
NM_000277.3(PAH):c.805A>C (p.Ile269Leu) rs62508692
NM_001080.3(ALDH5A1):c.1014+723_1173+796del
NM_001080.3(ALDH5A1):c.1015-3C>G rs2127387935
NM_001080.3(ALDH5A1):c.1267A>G (p.Thr423Ala)
NM_001080.3(ALDH5A1):c.1274T>C (p.Leu425Pro)
NM_001080.3(ALDH5A1):c.1324C>T (p.Pro442Ser) rs750638943
NM_001080.3(ALDH5A1):c.1402+1G>T rs762290992
NM_001080.3(ALDH5A1):c.1498G>C (p.Val500Leu) rs999671766
NM_001080.3(ALDH5A1):c.1529C>T (p.Ser510Phe) rs578023593
NM_001080.3(ALDH5A1):c.587G>A (p.Gly196Asp)
NM_001080.3(ALDH5A1):c.667T>C (p.Cys223Arg)
NM_001378414.1(HDAC4):c.731C>A (p.Thr244Lys) rs2042442594
NM_003849.4(SUCLG1):c.242A>C (p.Lys81Thr) rs564792232
NM_020686.6(ABAT):c.631C>T (p.Leu211Phe) rs724159990
NM_183050.4(BCKDHB):c.885del (p.Gly296fs) rs398124599
Single allele

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