ClinVar Miner

Variants from Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital with conflicting interpretations

Location: China  Primary collection method: research
Minimum review status of the submission from Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital: Collection method of the submission from Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital:
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
107 26 0 15 4 1 2 21

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
Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital pathogenic likely pathogenic uncertain significance likely benign benign affects
pathogenic 0 6 0 0 0 1
likely pathogenic 9 0 2 1 0 0
uncertain significance 0 0 0 4 1 0

Submitter to submitter summary #

Total submitters: 34
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 15 0 2 4 0 2 8
OMIM 0 12 0 4 0 0 0 4
Baylor Genetics 0 2 0 2 0 0 0 2
PreventionGenetics, part of Exact Sciences 0 0 0 0 2 0 0 2
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 0 0 2 0 0 0 2
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 0 0 2 0 0 0 2
Genome-Nilou Lab 0 4 0 2 0 0 0 2
Molecular Genetics, Centre for Human Genetics 0 1 0 2 0 0 0 2
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 2 0 2 0 0 0 2
Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand 0 1 0 2 0 0 0 2
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 4 0 1 0 0 0 1
Genetic Services Laboratory, University of Chicago 0 0 0 1 0 0 0 1
GeneDx 0 0 0 0 0 0 1 1
Eurofins Ntd Llc (ga) 0 0 0 0 0 0 1 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 6 0 1 0 0 0 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 6 0 1 0 0 0 1
Illumina Laboratory Services, Illumina 0 4 0 1 0 0 0 1
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 0 0 1 0 0 0 1
Department of Medical Genetics, Sanjay Gandhi Post Graduate Institute of Medical Sciences 0 1 0 1 0 0 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 2 0 1 0 0 0 1
Genetics and Molecular Pathology, SA Pathology 0 0 0 1 0 0 0 1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 0 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 0 0 1 0 0 0 1
Genomic Medicine Lab, University of California San Francisco 0 0 0 1 0 0 0 1
Genetic Testing Center for Deafness, Department of Otolaryngology Head & Neck Surgery, Institute of Otolaryngology, Chinese PLA General Hospital 0 0 0 1 0 0 0 1
Center of Excellence in Genomics and Precision Dentistry, Faculty of Dentistry, Chulalongkorn University 0 0 0 1 0 0 0 1
3billion 0 7 0 1 0 0 0 1
Pediatrics, All India Institute of Medical Sciences, New Delhi 0 0 0 0 0 1 0 1
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein 0 0 0 1 0 0 0 1
Department of Pediatrics, Taipei Veterans General Hospital 0 0 0 1 0 0 0 1
Provincial Medical Genetics Program of British Columbia, University of British Columbia 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 2 0 1 0 0 0 1
Institute Of Reproduction And Development, Obstetrics and Gynecology Hospital, Fudan University 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 21
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_004560.4(ROR2):c.1675G>A (p.Gly559Ser) rs117134265 0.00019
NM_000348.4(SRD5A2):c.680G>A (p.Arg227Gln) rs9332964 0.00016
NM_004560.4(ROR2):c.2117G>A (p.Arg706Gln) rs369717474 0.00013
NM_004560.4(ROR2):c.1930G>A (p.Asp644Asn) rs55798732 0.00011
NM_004560.4(ROR2):c.935G>A (p.Arg312His) rs188376581 0.00007
NM_004560.4(ROR2):c.2212C>T (p.Arg738Cys) rs56231927 0.00006
NM_002834.5(PTPN11):c.794G>A (p.Arg265Gln) rs376607329 0.00003
NM_000142.5(FGFR3):c.1612A>G (p.Ile538Val) rs80053154 0.00001
NM_000306.4(POU1F1):c.649C>T (p.Arg217Ter) rs761275346 0.00001
NM_000515.5(GH1):c.626G>A (p.Arg209His) rs137853223 0.00001
NM_002470.4(MYH3):c.4357-10G>A rs374066994 0.00001
NM_000202.8(IDS):c.1122C>T (p.Gly374=) rs113993948
NM_001042492.3(NF1):c.2329T>A (p.Trp777Arg) rs876658853
NM_001042492.3(NF1):c.6705-1G>A rs1060500356
NM_001370100.5(ZMYND11):c.1798C>T (p.Arg600Trp) rs797044854
NM_002834.5(PTPN11):c.1510A>G (p.Met504Val) rs397507547
NM_002834.5(PTPN11):c.182A>G (p.Asp61Gly) rs121918461
NM_002834.5(PTPN11):c.846C>G (p.Ile282Met) rs397507530
NM_002880.4(RAF1):c.1837C>G (p.Leu613Val) rs80338797
NM_006912.6(RIT1):c.270G>C (p.Met90Ile) rs483352822
NM_012448.4(STAT5B):c.1102del (p.Gln368fs) rs761761205

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