ClinVar Miner

Variants from deCODE genetics, Amgen with conflicting interpretations

Location: Iceland  Primary collection method: research
Minimum review status of the submission from deCODE genetics, Amgen: Collection method of the submission from deCODE genetics, Amgen:
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
96 31 1 57 0 2 8 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
deCODE genetics, Amgen pathogenic likely pathogenic uncertain significance likely benign benign drug response pathogenic, low penetrance
pathogenic 0 12 2 0 1 1 1
likely pathogenic 45 1 5 1 0 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 15 0 19 0 1 1 21
Myriad Genetics, Inc. 0 11 0 15 0 0 0 15
All of Us Research Program, National Institutes of Health 0 6 0 5 0 0 4 9
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) 0 5 0 7 0 0 1 8
Baylor Genetics 0 9 0 6 0 0 1 7
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge 0 5 0 6 0 0 0 6
Sharing Clinical Reports Project (SCRP) 0 3 0 5 0 0 0 5
Genome-Nilou Lab 0 0 0 5 0 0 0 5
OMIM 0 7 0 3 0 0 1 4
Breast Cancer Information Core (BIC) (BRCA2) 0 1 0 4 0 0 0 4
Center for Medical Genetics Ghent, University of Ghent 0 1 0 4 0 0 0 4
Institute of Human Genetics, University of Leipzig Medical Center 0 4 0 3 0 0 1 4
BRCAlab, Lund University 0 1 0 3 0 0 1 4
MGZ Medical Genetics Center 0 4 0 3 0 0 0 3
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 6 0 3 0 0 0 3
Department of Medical Genetics, Oslo University Hospital 0 1 0 2 0 0 1 3
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 2 0 3 0 0 0 3
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 2 0 3 0 0 0 3
Division of Genomic Medicine, Department of Advanced Medicine, Medical Research Institute, Kanazawa Medical University 0 0 0 3 0 0 0 3
Revvity Omics, Revvity 0 3 0 2 0 0 0 2
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 1 0 2 0 0 0 2
Counsyl 0 7 0 2 0 0 0 2
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 6 0 2 0 0 0 2
Mendelics 0 3 0 2 0 0 0 2
Fulgent Genetics, Fulgent Genetics 0 0 0 2 0 0 0 2
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 0 0 2 0 0 0 2
NIHR Bioresource Rare Diseases, University of Cambridge 0 0 0 2 0 0 0 2
Genetics and Molecular Pathology, SA Pathology 0 2 0 2 0 0 0 2
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 0 0 2 0 0 0 2
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 0 0 1 0 0 1 2
3billion 0 1 0 2 0 0 0 2
Greenwood Genetic Center Diagnostic Laboratories, Greenwood Genetic Center 0 0 0 1 0 0 0 1
Biesecker Lab/Clinical Genomics Section, National Institutes of Health 0 1 0 1 0 0 0 1
Genetic Services Laboratory, University of Chicago 0 2 0 1 0 0 0 1
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 5 0 1 0 0 0 1
GeneDx 0 1 0 1 0 0 0 1
PreventionGenetics, part of Exact Sciences 0 1 0 1 0 0 0 1
Michigan Medical Genetics Laboratories, University of Michigan 0 0 0 1 0 0 0 1
Cardiovascular Genetics Laboratory, PathWest Laboratory Medicine WA - Fiona Stanley Hospital 0 1 0 1 0 0 0 1
Institute of Human Genetics, Medical University Innsbruck 0 0 0 1 0 0 0 1
Eurofins Ntd Llc (ga) 0 0 0 1 0 0 0 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 2 0 1 0 0 0 1
Familial Cancer Clinic, Veneto Institute of Oncology 0 0 1 0 0 0 0 1
PharmGKB 0 0 0 0 0 1 0 1
Breast Cancer Information Core (BIC) (BRCA1) 0 3 0 0 0 0 1 1
Illumina Laboratory Services, Illumina 0 2 0 1 0 0 0 1
Pathway Genomics 0 0 0 1 0 0 0 1
Genologica Medica 0 0 0 1 0 0 0 1
CSER _CC_NCGL, University of Washington 0 0 0 0 0 0 1 1
Centre of Medical Genetics, University of Antwerp 0 1 0 1 0 0 0 1
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 0 0 0 1 0 0 0 1
Cancer Genetics Laboratory, Peter MacCallum Cancer Centre 0 0 0 1 0 0 0 1
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease, Montreal Heart Institute 0 1 0 1 0 0 0 1
U4M - Lille University & CHRU Lille, Université de Lille - CHRU de Lille 0 2 0 1 0 0 0 1
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 0 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 2 0 1 0 0 0 1
Robarts Research Institute, Western University 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
Centre de Génétique Moléculaire et Chromosomique, Unité de génétique de l'Obésité et des Dyslipidémies, APHP, GH Hôpitaux Universitaires Pitié-Salpêtrière / Charles-Foix 0 6 0 1 0 0 0 1
Clinical Genetics Laboratory, Region Ostergotland 0 0 0 1 0 0 0 1
Laboratorium voor Moleculaire Diagnostiek Experimentele Vasculaire Geneeskunde, Academisch Medisch Centrum 0 0 0 1 0 0 0 1
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 0 0 1 0 0 0 1
Department of Molecular Diagnostics, Institute of Oncology Ljubljana 0 2 0 1 0 0 0 1
St. Jude Molecular Pathology, St. Jude Children's Research Hospital 0 2 0 1 0 0 0 1
Genomic Medicine Lab, University of California San Francisco 0 1 0 1 0 0 0 1
University of Washington Department of Laboratory Medicine, University of Washington 0 1 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
Brunham Lab, Centre for Heart and Lung Innovation, University of British Columbia 0 0 0 1 0 0 0 1
Division of Medical Genetics, University of Washington 0 1 0 1 0 0 0 1
Cardiology unit, Meyer University Hospital 0 0 0 1 0 0 0 1
Institute of Human Genetics, University Hospital Muenster 0 0 0 1 0 0 0 1
AiLife Diagnostics, AiLife Diagnostics 0 0 0 1 0 0 0 1
ClinGen Familial Hypercholesterolemia Variant Curation Expert Panel 0 0 0 1 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 0 0 1 0 0 0 1
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein 0 1 0 1 0 0 0 1
Molecular Genetics, Royal Melbourne Hospital 0 2 0 1 0 0 0 1
ClinGen FBN1 Variant Curation Expert Panel, ClinGen 0 1 0 1 0 0 0 1
Geisinger Clinic, Geisinger Health System 0 0 0 1 0 0 0 1
Department of Medical and Surgical Sciences, University of Bologna 0 0 0 1 0 0 0 1
Genomics And Bioinformatics Analysis Resource, Columbia University 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 62
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000410.4(HFE):c.845G>A (p.Cys282Tyr) rs1800562 0.03880
NM_001048174.2(MUTYH):c.452A>G (p.Tyr151Cys) rs34612342 0.00168
NM_000540.3(RYR1):c.6721C>T (p.Arg2241Ter) rs200563280 0.00013
NM_000257.4(MYH7):c.2606G>A (p.Arg869His) rs202141173 0.00009
NM_024675.4(PALB2):c.3256C>T (p.Arg1086Ter) rs587776527 0.00002
NM_000138.5(FBN1):c.5788+5G>A rs193922219 0.00001
NM_000535.7(PMS2):c.709C>T (p.Gln237Ter) rs1458321358 0.00001
NM_000540.3(RYR1):c.3686_3699del (p.Met1229fs) rs774319202 0.00001
NM_000540.3(RYR1):c.7361G>A (p.Arg2454His) rs118192122 0.00001
NM_000038.6(APC):c.2803dup (p.Tyr935fs)
NM_000038.6(APC):c.3340C>T (p.Arg1114Ter) rs121913331
NM_000038.6(APC):c.3724C>T (p.Gln1242Ter) rs1460397656
NM_000038.6(APC):c.6474del (p.Phe2159fs)
NM_000038.6(APC):c.7511G>A (p.Trp2504Ter) rs755046558
NM_000038.6(APC):c.7927_7928del (p.Leu2643fs) rs1766600757
NM_000059.3(BRCA2):c.2808_2811del (p.Ala938Profs) rs80359351
NM_000059.4(BRCA2):c.1599_1600del (p.Glu534fs) rs80359293
NM_000059.4(BRCA2):c.2918C>A (p.Ser973Ter) rs397507296
NM_000059.4(BRCA2):c.4037_4038del (p.Thr1346fs) rs80359421
NM_000059.4(BRCA2):c.5281G>T (p.Gly1761Ter) rs886038122
NM_000059.4(BRCA2):c.7033C>T (p.Gln2345Ter) rs886040685
NM_000059.4(BRCA2):c.9253dup (p.Thr3085fs) rs80359752
NM_000138.5(FBN1):c.1850G>A (p.Cys617Tyr) rs1555399836
NM_000138.5(FBN1):c.2860C>T (p.Arg954Cys) rs1555398835
NM_000138.5(FBN1):c.3290G>A (p.Cys1097Tyr) rs1555398627
NM_000138.5(FBN1):c.8038C>T (p.Arg2680Cys) rs794728283
NM_000138.5(FBN1):c.8149G>T (p.Glu2717Ter) rs187553035
NM_000169.3(GLA):c.966C>A (p.Asp322Glu) rs398123226
NM_000179.3(MSH6):c.3013C>T (p.Arg1005Ter) rs63750563
NM_000179.3(MSH6):c.3261dup (p.Phe1088fs) rs267608078
NM_000179.3(MSH6):c.843_844insAC (p.Val282fs)
NM_000218.3(KCNQ1):c.1780C>T (p.Arg594Ter) rs794728537
NM_000251.3(MSH2):c.1613dup (p.Asn538fs)
NM_000251.3(MSH2):c.2027C>A (p.Ser676Ter)
NM_000256.3(MYBPC3):c.506-1G>A rs397516056
NM_000368.5(TSC1):c.1525C>T (p.Arg509Ter) rs118203542
NM_000384.3(APOB):c.10580G>A (p.Arg3527Gln)
NM_000527.4(LDLR):c.694+2T>C rs200238879
NM_000527.5(LDLR):c.1424C>T (p.Ala475Val) rs879254897
NM_000527.5(LDLR):c.1618G>A (p.Ala540Thr)
NM_000527.5(LDLR):c.693C>A (p.Cys231Ter)
NM_000527.5(LDLR):c.919G>A (p.Asp307Asn) rs879254719
NM_000535.7(PMS2):c.211_214del (p.Asn71fs)
NM_000535.7(PMS2):c.2T>A (p.Met1Lys) rs587780059
NM_000545.8(HNF1A):c.475C>T (p.Arg159Trp) rs765432081
NM_000546.6(TP53):c.148dup (p.Ile50fs) rs1567556956
NM_000546.6(TP53):c.430C>T (p.Gln144Ter) rs757274881
NM_000546.6(TP53):c.437G>A (p.Trp146Ter) rs1206165503
NM_000548.5(TSC2):c.1096G>T (p.Glu366Ter) rs45517148
NM_000548.5(TSC2):c.1513C>T (p.Arg505Ter) rs45517179
NM_000548.5(TSC2):c.268C>T (p.Gln90Ter) rs45517099
NM_000548.5(TSC2):c.577G>T (p.Glu193Ter) rs45517112
NM_001114753.3(ENG):c.1513G>T (p.Glu505Ter) rs1830383454
NM_001114753.3(ENG):c.277C>T (p.Arg93Ter) rs886039506
NM_001458.5(FLNC):c.4021C>T (p.Arg1341Ter) rs1562998062
NM_005359.6(SMAD4):c.1245_1248del (p.Asp415Glufs) rs80338965
NM_007294.4(BRCA1):c.4096+3A>G rs80358015
NM_007294.4(BRCA1):c.5074G>A (p.Asp1692Asn) rs80187739
NM_017849.4(TMEM127):c.409+1G>T rs121908825
NM_024675.4(PALB2):c.373C>T (p.Gln125Ter)
NM_024675.4(PALB2):c.778C>T (p.Gln260Ter) rs1555461627
NM_174936.4(PCSK9):c.385G>A (p.Asp129Asn)

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