ClinVar Miner

Variants from Geisinger Autism and Developmental Medicine Institute, Geisinger Health System with conflicting interpretations

Location: United States  Primary collection method: provider interpretation
Minimum review status of the submission from Geisinger Autism and Developmental Medicine Institute, Geisinger Health System: Collection method of the submission from Geisinger Autism and Developmental Medicine Institute, Geisinger Health System:
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
102 35 0 9 3 2 10 19

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
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System pathogenic likely pathogenic uncertain significance likely benign benign protective risk factor other
pathogenic 0 7 3 1 1 1 1 1
likely pathogenic 3 0 1 1 1 1 0 1
uncertain significance 3 8 0 3 1 1 0 1
likely benign 1 1 1 0 1 1 0 1

Submitter to submitter summary #

Total submitters: 74
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 11 0 3 3 0 3 7
GeneDx 0 7 0 1 1 0 6 6
PreventionGenetics, part of Exact Sciences 0 0 0 0 2 0 1 2
MGZ Medical Genetics Center 0 2 0 2 0 0 0 2
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 1 0 2 0 0 0 2
Mayo Clinic Laboratories, Mayo Clinic 0 0 0 1 1 0 2 2
Illumina Laboratory Services, Illumina 0 7 0 1 1 0 2 2
Genome-Nilou Lab 0 7 0 2 0 0 0 2
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 2 0 2 0 0 1 2
OMIM 0 4 0 0 0 1 0 1
Baylor Genetics 0 5 0 1 0 0 1 1
Athena Diagnostics Inc 0 0 0 1 1 0 1 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 0 0 0 1 0 1 1
Ambry Genetics 0 2 0 0 1 0 1 1
Revvity Omics, Revvity 0 0 0 1 0 0 0 1
Elsea Laboratory, Baylor College of Medicine 0 0 0 1 0 0 1 1
Counsyl 0 3 0 1 0 0 0 1
Eurofins Ntd Llc (ga) 0 0 0 1 1 1 1 1
GeneReviews 0 0 0 0 0 0 1 1
Quest Diagnostics Nichols Institute San Juan Capistrano 0 0 0 1 1 0 1 1
Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre 0 0 0 1 0 0 1 1
Breast Cancer Information Core (BIC) (BRCA1) 0 0 0 0 0 0 1 1
Department of Psychiatry, Nagoya University 0 0 0 0 0 0 1 1
Department of Medical Genetics, Oslo University Hospital 0 1 0 1 0 0 0 1
Vavilov Institute of General Genetics RAS, Laboratory of Evolutional Genomics 0 0 0 0 0 1 0 1
University of Washington Center for Mendelian Genomics, University of Washington 0 0 0 1 0 0 1 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 1 0 1 0 0 0 1
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 0 0 0 1 1 0 1 1
Genome Sciences Centre, British Columbia Cancer Agency 0 0 0 1 0 0 1 1
CeGaT Center for Human Genetics Tuebingen 0 1 0 1 1 0 1 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 0 1 0 0 0 1
Pediatric Highly Intensive Care Unit, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico 0 0 0 1 0 0 1 1
Daryl Scott Lab, Baylor College of Medicine 0 1 0 1 0 0 1 1
Neurogenetics Laboratory - MEYER, AOU Meyer 0 0 0 1 0 0 1 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 0 0 1 0 0 1 1
Undiagnosed Diseases Network, NIH 0 0 0 1 1 0 1 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 1 0 1 1 0 1 1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 1 0 1 1 0 1 1
Institute of Human Genetics, University of Leipzig Medical Center 0 3 0 0 0 0 1 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine, Sinai Health System 0 0 0 0 1 0 1 1
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 0 0 0 0 0 1 1
Geisinger Autism and Developmental Medicine Institute, Geisinger Health System 155 0 0 1 1 0 1 1
Department of Obstetrics and Gynecology, Helsinki University Hospital 0 0 0 1 0 0 0 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 1 0 0 1 1
Flegel Lab, National Institutes of Health 0 0 0 1 0 0 1 1
Genetics Department, University Hospital of Toulouse 0 0 0 1 0 0 1 1
Laboratory of Diagnostic Genome Analysis, Leiden University Medical Center (LUMC) 0 0 0 0 1 0 1 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 1 0 0 1 0 1 1
Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital 0 0 0 1 0 0 1 1
Laboratoire de Genetique Moleculaire, Centre Hospitalier Universitaire de Bordeaux 0 0 0 0 1 0 1 1
Medical Genetics Lab, Policlinico S. Orsola.Malpighi 0 0 0 1 1 0 1 1
Génétique des Maladies du Développement, Hospices Civils de Lyon 0 1 0 1 0 0 1 1
Medical Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano 0 0 0 0 1 0 1 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 1 0 1 0 0 1 1
Molecular Pathology Diagnostics Labratory, University of Iowa Hospitals & Clinics 0 0 0 1 0 0 1 1
Institute of Human Genetics, Heidelberg University 0 0 0 0 0 0 1 1
Department of Genetics, Rouen University Hospital, Normandy Center for Genomic and Personalized Medicine 0 0 0 0 0 0 1 1
Biochemistry Laboratory of CDMU, Chengde Medical University 0 0 0 1 0 0 1 1
Myriad Genetics, Inc. 0 1 0 1 0 0 0 1
Rare Disease Group, University of Exeter 0 0 0 1 0 0 1 1
Molecular Genetics laboratory, Necker Hospital 0 0 0 0 0 0 1 1
Central Laboratory, The First Hospital of Lanzhou University 0 0 0 1 0 0 1 1
New York Genome Center 0 1 0 1 1 0 1 1
Genetics and Prenatal Diagnosis Center, The First Affiliated Hospital of Zhengzhou University 0 0 0 1 0 0 1 1
Lifecell International Pvt. Ltd 0 0 0 0 0 0 1 1
Genomic Medicine, Universita Cattolica del Sacro Cuore 0 0 0 1 0 0 1 1
Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli 0 0 0 0 0 0 1 1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 1 0 1 0 0 0 1
Genomics England Pilot Project, Genomics England 0 1 0 1 0 0 0 1
IU Genetic Testing Laboratories, Indiana University School of Medicine 0 0 0 1 0 0 1 1
Cytogenetics, Genetics Associates, Inc. 0 0 0 1 0 0 1 1
Chao Lab, Baylor College of Medicine, Texas Children's Hospital 0 0 0 1 0 0 1 1

All variants with conflicting interpretations #

Total variants: 19
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001354604.2(MITF):c.1273G>A (p.Glu425Lys) rs149617956 0.00160
NM_024570.4(RNASEH2B):c.529G>A (p.Ala177Thr) rs75184679 0.00141
NM_004168.4(SDHA):c.91C>T (p.Arg31Ter) rs142441643 0.00025
NM_000199.5(SGSH):c.1063G>A (p.Glu355Lys) rs766938111 0.00004
NM_001205293.3(CACNA1E):c.4777A>G (p.Ile1593Val) rs1159957403 0.00001
NM_006245.4(PPP2R5D):c.758G>A (p.Arg253Gln) rs1131691266 0.00001
NM_006265.3(RAD21):c.1349G>A (p.Arg450His) rs1051321465 0.00001
NM_000199.5(SGSH):c.673T>C (p.Phe225Leu) rs1057521801
NM_000535.7(PMS2):c.1731_1732delinsAGT (p.Arg578fs) rs1057515572
NM_001130021.3(ATP6V0A1):c.2219G>A (p.Arg740Gln) rs1567871600
NM_002397.5(MEF2C):c.3G>C (p.Met1Ile) rs1554150607
NM_002880.4(RAF1):c.1871C>G (p.Ser624Cys) rs1057524239
NM_002941.4(ROBO1):c.3503_3505dup (p.Gly1168dup) rs148625921
NM_004572.3(PKP2):c.1677dup (p.Gly560Trpfs) rs1555144459
NM_006516.4(SLC2A1):c.1199G>A (p.Arg400His) rs776095655
NM_012199.5(AGO1):c.536TCT[1] (p.Phe180del) rs1553154062
NM_020719.3(PRR12):c.5187del (p.Glu1730fs) rs1568430264
NM_138576.4(BCL11B):c.1097G>A (p.Arg366Gln) rs1566794698
Single allele

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