ClinVar Miner

Variants from NeuroMeGen, Hospital Clinico Santiago de Compostela with conflicting interpretations

Location: Spain  Primary collection method: clinical testing
Minimum review status of the submission from NeuroMeGen, Hospital Clinico Santiago de Compostela: Collection method of the submission from NeuroMeGen, Hospital Clinico Santiago de Compostela:
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
94 12 0 33 0 0 13 43

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
NeuroMeGen, Hospital Clinico Santiago de Compostela pathogenic uncertain significance likely benign benign
pathogenic 0 1 0 0
likely pathogenic 33 8 3 3

Submitter to submitter summary #

Total submitters: 65
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
Labcorp Genetics (formerly Invitae), Labcorp 0 1 0 7 0 0 9 16
3billion 0 3 0 10 0 0 0 10
OMIM 0 1 0 10 0 0 0 10
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 1 0 8 0 0 0 8
Baylor Genetics 0 1 0 4 0 0 1 5
Institute of Human Genetics, University of Leipzig Medical Center 0 0 0 5 0 0 0 5
RettBASE 0 0 0 5 0 0 0 5
Center for Bioinformatics, Peking University 0 0 0 4 0 0 0 4
Institute of Human Genetics Munich, TUM University Hospital 0 1 0 4 0 0 0 4
Neuberg Centre For Genomic Medicine, NCGM 0 6 0 4 0 0 0 4
Revvity Omics, Revvity 0 0 0 2 0 0 2 4
CENTOGENE GmbH and LLC - Guiding Precision Medicine 0 0 0 2 0 0 1 3
Genetic Services Laboratory, University of Chicago 0 0 0 3 0 0 0 3
Mendelics 0 1 0 3 0 0 0 3
Centre for Population Genomics, CPG 0 0 0 2 0 0 0 2
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein 0 1 0 2 0 0 0 2
First Genomix Gene Laboratory, Genetic Diagnostics Department 0 0 0 2 0 0 0 2
Fulgent Genetics, Fulgent Genetics 0 1 0 2 0 0 0 2
Genetics and Molecular Pathology, SA Pathology 0 0 0 2 0 0 0 2
Genomics England Pilot Project, Genomics England 0 0 0 2 0 0 0 2
Institute of Immunology and Genetics Kaiserslautern 0 0 0 2 0 0 0 2
MGZ Medical Genetics Center 0 2 0 2 0 0 0 2
Medical and Scientific Branch, Hong Kong Genome Institute 0 0 0 2 0 0 0 2
Variantyx, Inc. 0 0 0 2 0 0 0 2
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 0 0 2 0 0 0 2
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 0 0 1 0 0 0 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 0 0 1 0 0 0 1
Center of Human Genetics, Hôpital Erasme 0 0 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 0 0 1 0 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 0 1 0 0 0 1
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital 0 0 0 1 0 0 0 1
Daryl Scott Lab, Baylor College of Medicine 0 0 0 1 0 0 0 1
Department of Human Genetics, Hannover Medical School 0 0 0 1 0 0 0 1
GeneDx 0 0 0 1 0 0 0 1
Genesolutions, Medical Genetics Institutes, Ho Chi Minh City, Vietnam 0 0 0 1 0 0 0 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 0 0 1 0 0 0 1
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 1 0 0 0 0 1 1
Génétique des Maladies du Développement, Hospices Civils de Lyon 0 1 0 1 0 0 0 1
Illumina Laboratory Services, Illumina 0 0 0 0 0 0 1 1
Imagene.me medical diagnostic laboratory, IMAGENE.ME SA 0 0 0 1 0 0 0 1
Institute for Genomic Medicine (IGM) Clinical Laboratory, Nationwide Children's Hospital 0 0 0 1 0 0 0 1
Institute of Human Genetics, Heidelberg University 0 0 0 1 0 0 0 1
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 1 0 1 0 0 0 1
Juno Genomics, Hangzhou Juno Genomics, Inc 0 0 0 1 0 0 0 1
Kariminejad - Najmabadi Pathology & Genetics Center 0 2 0 1 0 0 0 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 0 0 1 0 0 0 1
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 0 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 0 0 1 0 0 0 1
Laboratory of Medical Genetics, University of Torino 0 0 0 1 0 0 0 1
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes 0 0 0 1 0 0 0 1
Medical Genetic Department, The Affiliated Hospital of Qingdao University 0 0 0 1 0 0 0 1
Myriad Genetics, Inc. 0 0 0 1 0 0 0 1
Natera, Inc. 0 0 0 1 0 0 0 1
Neurology Department, Shenzhen Children's Hospital 0 0 0 1 0 0 0 1
Neuromuscular Department, Shariati Hospital, Tehran University of Medical Sciences 0 0 0 0 0 0 1 1
New York Genome Center 0 0 0 1 0 0 0 1
Next Generation Genetic Polyclinic 0 0 0 1 0 0 0 1
Pediatric Department, Xiangya Hospital, Central South University 0 0 0 1 0 0 0 1
Pediatric Genetics Clinic, Sheba Medical Center 0 0 0 1 0 0 0 1
Pediatrics, Sichuan Provincial Hospital For Women And Children 0 0 0 1 0 0 0 1
Service de Génétique Moléculaire, Hôpital Robert Debré 0 0 0 0 0 0 1 1
UCLA Clinical Genomics Center, UCLA 0 0 0 1 0 0 0 1
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan 0 1 0 1 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 43
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001849.4(COL6A2):c.1466G>A (p.Arg489Gln) rs61735828 0.00627
NM_017534.6(MYH2):c.4774C>A (p.Leu1592Met) rs138393827 0.00107
NM_213599.3(ANO5):c.692G>T (p.Gly231Val) rs137854523 0.00098
NM_024577.4(SH3TC2):c.2860C>T (p.Arg954Ter) rs80338933 0.00067
NM_021942.6(TRAPPC11):c.2147C>G (p.Ala716Gly) rs143990563 0.00064
NM_006950.3(SYN1):c.1297C>T (p.His433Tyr) rs41298474 0.00038
NM_000070.3(CAPN3):c.2120A>G (p.Asp707Gly) rs200379491 0.00005
NM_001101362.3(KBTBD13):c.290T>C (p.Leu97Pro) rs767384093 0.00005
NM_001069.3(TUBB2A):c.743C>T (p.Ala248Val) rs2808001 0.00003
NM_001195553.2(DCX):c.-22-364C>T rs761786389 0.00003
NM_001199107.2(TBC1D24):c.724C>T (p.Arg242Cys) rs398122965 0.00003
NM_017534.6(MYH2):c.3460G>A (p.Glu1154Lys) rs376357016 0.00002
NM_207346.3(TSEN54):c.371G>T (p.Gly124Val) rs774157225 0.00002
NM_002180.3(IGHMBP2):c.1327C>T (p.Arg443Cys) rs751549678 0.00001
NM_024577.4(SH3TC2):c.3511C>T (p.Arg1171Cys) rs759785462 0.00001
NM_000070.3(CAPN3):c.1963del (p.Arg655fs) rs1566984441
NM_000166.6(GJB1):c.547C>T (p.Arg183Cys) rs863224471
NM_001005361.3(DNM2):c.1856C>T (p.Ser619Leu) rs121909095
NM_001032221.6(STXBP1):c.416C>T (p.Pro139Leu) rs796053353
NM_001040142.2(SCN2A):c.2995G>A (p.Glu999Lys) rs796053126
NM_001040142.2(SCN2A):c.4303C>T (p.Arg1435Ter) rs796053138
NM_001101362.3(KBTBD13):c.244G>A (p.Val82Met) rs1303411209
NM_001110792.2(MECP2):c.953G>A (p.Arg318His) rs61751443
NM_001134407.3(GRIN2A):c.2069C>T (p.Thr690Met) rs1445802934
NM_001165963.4(SCN1A):c.4822G>T (p.Asp1608Tyr) rs121917915
NM_001165963.4(SCN1A):c.4973C>T (p.Thr1658Met) rs121917922
NM_001165963.4(SCN1A):c.4997C>T (p.Ser1666Phe) rs794726760
NM_001165963.4(SCN1A):c.664C>T (p.Arg222Ter) rs121918624
NM_001267550.2(TTN):c.38661_38665del (p.Lys12887fs) rs1553775212
NM_001323289.2(CDKL5):c.163_166del (p.Glu55fs) rs267608433
NM_001323289.2(CDKL5):c.2413C>T (p.Gln805Ter) rs267608659
NM_001323289.2(CDKL5):c.2635_2636del (p.Leu879fs) rs61753251
NM_001323289.2(CDKL5):c.455G>A (p.Cys152Tyr) rs122460157
NM_001323289.2(CDKL5):c.616G>T (p.Asp206Tyr) rs1555950468
NM_001330260.2(SCN8A):c.2620G>A (p.Ala874Thr) rs1057524820
NM_001378969.1(KCND3):c.1111G>A (p.Gly371Arg) rs1057521793
NM_005027.4(PIK3R2):c.1117G>A (p.Gly373Arg) rs587776934
NM_005249.5(FOXG1):c.256C>T (p.Gln86Ter) rs398124202
NM_021072.4(HCN1):c.1172G>A (p.Gly391Asp) rs1057519547
NM_145239.3(PRRT2):c.649dup (p.Arg217fs) rs587778771
NM_172107.4(KCNQ2):c.1588G>A (p.Glu530Lys) rs897976020
NM_172107.4(KCNQ2):c.833T>C (p.Ile278Thr) rs1057523728
NM_213599.3(ANO5):c.191dup (p.Asn64fs) rs137854521

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