ClinVar Miner

Variants from Pathway Genomics with conflicting interpretations

Location: United States — Primary collection method: clinical testing
Minimum review status of the submission from Pathway Genomics: Collection method of the submission from Pathway Genomics:
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 Variants with at least 2 submissions 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 kind of conflict
26 63 37 117 77 9 18 149

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
Pathway Genomics pathogenic likely pathogenic uncertain significance likely benign benign drug response risk factor other
pathogenic 4 19 5 2 1 1 5 0
likely pathogenic 7 0 3 1 0 0 1 0
uncertain significance 3 2 4 16 6 1 0 0
likely benign 2 1 31 2 42 0 0 0
benign 1 1 28 49 27 0 0 1

Submitter to submitter summary #

Total submitters: 74
Download table as spreadsheet
Submitter Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
Invitae 0 133 0 47 12 0 3 62
Ambry Genetics 0 137 0 38 9 0 4 51
Color 0 112 0 34 13 0 1 48
Biesecker Lab/Clinical Genomics Section,National Institutes of Health 0 4 20 14 12 0 0 46
GeneDx 0 108 0 30 7 0 3 40
Illumina Clinical Services Laboratory,Illumina 0 36 0 36 3 0 0 39
Department of Pathology and Laboratory Medicine,Sinai Health System 0 66 0 28 5 0 2 35
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 66 0 28 4 0 0 32
Counsyl 0 75 0 30 2 0 0 32
Integrated Genetics/Laboratory Corporation of America 0 85 0 26 3 0 3 32
PreventionGenetics,PreventionGenetics 0 60 0 25 5 0 0 30
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) 0 14 21 6 0 0 1 28
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic 0 64 0 16 11 0 0 27
Mendelics 0 50 0 22 4 0 1 26
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 0 60 0 24 2 0 0 26
True Health Diagnostics 0 31 0 24 2 0 0 26
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) 0 37 0 23 0 0 2 25
Sharing Clinical Reports Project (SCRP) 0 37 0 21 2 0 0 23
Breast Cancer Information Core (BIC) (BRCA2) 0 16 0 6 16 0 0 22
Breast Cancer Information Core (BIC) (BRCA1) 0 18 0 2 15 0 1 18
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine 0 59 0 8 9 0 0 17
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia 0 13 0 10 7 0 0 17
Michigan Medical Genetics Laboratories,University of Michigan 0 20 0 17 0 0 0 17
Quest Diagnostics Nichols Institute San Juan Capistrano 0 56 0 14 3 0 0 17
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen 0 27 0 15 1 0 0 16
OMIM 0 20 0 2 3 6 4 14
Genome Diagnostics Laboratory,University Medical Center Utrecht 0 13 0 14 0 0 0 14
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center 0 31 0 14 0 0 0 14
Genetic Services Laboratory, University of Chicago 0 15 0 11 1 0 0 12
Vantari Genetics 0 15 0 10 2 0 0 12
CeGaT Praxis fuer Humangenetik Tuebingen 0 14 0 6 4 0 2 12
Cancer Genetics and Genomics Laboratory,British Columbia Cancer Agency 0 12 0 11 0 0 1 12
Fulgent Genetics,Fulgent Genetics 0 19 0 10 0 0 1 11
Institute for Biomarker Research,Medical Diagnostic Laboratories, L.L.C. 0 15 0 10 1 0 0 11
CSER _CC_NCGL, University of Washington 0 8 0 4 4 0 2 10
Database of Curated Mutations (DoCM) 0 1 0 8 0 0 1 9
Center for Human Genetics, Inc 0 5 0 1 7 0 0 8
Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research 0 6 0 3 4 0 1 8
GeneKor MSA 0 15 0 8 0 0 0 8
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 7 0 7 1 0 0 8
Cancer Genetics Laboratory,Peter MacCallum Cancer Centre 0 0 0 5 3 0 0 8
Baylor Genetics 0 13 0 7 0 0 0 7
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario 0 15 0 4 1 0 1 6
GeneReviews 0 6 4 0 0 0 2 6
Research Molecular Genetics Laboratory,Women's College Hospital, University of Toronto 0 20 0 4 1 0 1 6
German Consortium for Hereditary Breast and Ovarian Cancer Center Cologne,University Hospital Cologne 0 11 0 6 0 0 0 6
PALB2 database 0 5 0 2 1 0 1 4
A.C.Camargo Cancer Center / LGBM, A.C.Camargo Cancer Center 0 4 0 0 4 0 0 4
University of Washington Department of Laboratory Medicine, University of Washington 0 11 0 1 1 0 2 4
Department of Pathology and Molecular Medicine,Queen's University 0 6 0 3 0 0 0 3
Genome Diagnostics Laboratory,VU University Medical Center Amsterdam 0 9 0 2 1 0 0 3
Department of Medical Genetics,University Hospital of North Norway 0 2 0 2 0 0 0 2
Center of Medical Genetics and Primary Health Care 0 0 0 1 0 0 1 2
Science for Life laboratory, Karolinska Institutet 0 0 0 0 0 0 1 1
Systems Biology Platform Zhejiang California International NanoSystems Institute 0 0 0 0 0 1 0 1
Academic Department of Medical Genetics, University of Cambridge 0 3 0 1 0 0 0 1
Human Genome Sequencing Center Clinical Lab,Baylor College of Medicine 0 11 0 1 0 0 0 1
PharmGKB 0 0 0 0 0 1 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 1 0 1 0 0 0 1
Department of Medical Genetics,Oslo University Hospital 0 7 0 0 0 0 1 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 4 0 1 0 0 0 1
Dr. Peter K. Rogan Lab,Western University 0 0 0 0 1 0 0 1
Next Generation Diagnostics,Novartis Institutes for BioMedical Research, Inc. 0 0 0 0 1 0 0 1
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 2 0 0 0 0 1 1
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge 0 20 0 1 0 0 0 1
IntelligeneCG 0 3 0 0 1 0 0 1
Oxford Haemato-Oncology Service,Oxford University Hospitals NHS Foundation Trust 0 0 0 0 0 1 0 1
Endocrine oncology group,Uppsala University 0 0 0 1 0 0 0 1
Laboratory of Molecular Neuropathology,The University of Texas Health Science Center at Houston 0 0 0 0 0 0 1 1
Cancer Diagnostics Division,Gene Solutions 0 0 0 1 0 0 0 1
Cancer Variant Interpretation Group UK,Institute of Cancer Research, London 0 0 0 0 0 0 1 1
Institute for Genomic Medicine (IGM) Clinical Laboratory,Nationwide Children's Hospital 0 0 0 1 0 0 0 1
ClinGen CDH1 Variant Curation Expert Panel 0 5 0 1 0 0 0 1
Xiao lab, Department of Pathology, Memorial Sloan Kettering Cancer Center 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 149
Download table as spreadsheet
HGVS dbSNP
NM_000038.6(APC):c.1240C>T (p.Arg414Cys) rs137854567
NM_000038.6(APC):c.1604C>T (p.Ser535Phe) rs75870842
NM_000038.6(APC):c.1744-2A>G rs587783035
NM_000038.6(APC):c.3462_3464AGA[2] (p.Glu1157del) rs386833391
NM_000038.6(APC):c.3922_3926AAAGA[1] (p.Glu1309fs) rs121913224
NM_000038.6(APC):c.3949G>C (p.Glu1317Gln) rs1801166
NM_000038.6(APC):c.5465T>A (p.Val1822Asp) rs459552
NM_000038.6(APC):c.8068G>A (p.Ala2690Thr) rs140868933
NM_000057.4(BLM):c.2119C>T (p.Pro707Ser) rs146077918
NM_000057.4(BLM):c.2603C>T (p.Pro868Leu) rs2227935
NM_000059.3(BRCA2):c.10095delinsGAATTATATCT (p.Ser3366fs) rs276174803
NM_000059.3(BRCA2):c.10121C>T (p.Thr3374Ile) rs56309455
NM_000059.3(BRCA2):c.125A>G (p.Tyr42Cys) rs4987046
NM_000059.3(BRCA2):c.2138A>T (p.Gln713Leu) rs55816687
NM_000059.3(BRCA2):c.2960A>T (p.Asn987Ile) rs2227944
NM_000059.3(BRCA2):c.3869G>A (p.Cys1290Tyr) rs41293485
NM_000059.3(BRCA2):c.4187A>G (p.Gln1396Arg) rs55969723
NM_000059.3(BRCA2):c.4258G>T (p.Asp1420Tyr) rs28897727
NM_000059.3(BRCA2):c.4436G>C (p.Ser1479Thr) rs80358678
NM_000059.3(BRCA2):c.4552del (p.Glu1518fs) rs398122783
NM_000059.3(BRCA2):c.4585G>A (p.Gly1529Arg) rs28897728
NM_000059.3(BRCA2):c.467A>G (p.Asp156Gly) rs68071147
NM_000059.3(BRCA2):c.5744C>T (p.Thr1915Met) rs4987117
NM_000059.3(BRCA2):c.5785A>G (p.Ile1929Val) rs79538375
NM_000059.3(BRCA2):c.5946del (p.Ser1982fs) rs80359550
NM_000059.3(BRCA2):c.6100C>T (p.Arg2034Cys) rs1799954
NM_000059.3(BRCA2):c.6275_6276del (p.Leu2092fs) rs11571658
NM_000059.3(BRCA2):c.6323G>A (p.Arg2108His) rs35029074
NM_000059.3(BRCA2):c.68-7T>A rs81002830
NM_000059.3(BRCA2):c.6853A>G (p.Ile2285Val) rs56272235
NM_000059.3(BRCA2):c.7008-62A>G rs76584943
NM_000059.3(BRCA2):c.7017G>C (p.Lys2339Asn) rs45574331
NM_000059.3(BRCA2):c.7052C>G (p.Ala2351Gly) rs80358932
NM_000059.3(BRCA2):c.7057G>C (p.Gly2353Arg) rs80358935
NM_000059.3(BRCA2):c.7150C>A (p.Gln2384Lys) rs55977008
NM_000059.3(BRCA2):c.7319A>G (p.His2440Arg) rs4986860
NM_000059.3(BRCA2):c.7469T>C (p.Ile2490Thr) rs11571707
NM_000059.3(BRCA2):c.8149G>T (p.Ala2717Ser) rs28897747
NM_000059.3(BRCA2):c.8182G>A (p.Val2728Ile) rs28897749
NM_000059.3(BRCA2):c.8503T>C (p.Ser2835Pro) rs11571746
NM_000059.3(BRCA2):c.8567A>C (p.Glu2856Ala) rs11571747
NM_000059.3(BRCA2):c.8830A>T (p.Ile2944Phe) rs4987047
NM_000059.3(BRCA2):c.8851G>A (p.Ala2951Thr) rs11571769
NM_000059.3(BRCA2):c.9976A>T (p.Lys3326Ter) rs11571833
NM_000179.2(MSH6):c.116G>A (p.Gly39Glu) rs1042821
NM_000179.2(MSH6):c.1186C>G (p.Leu396Val) rs2020908
NM_000179.2(MSH6):c.1508C>G (p.Ser503Cys) rs63750897
NM_000179.2(MSH6):c.1526T>C (p.Val509Ala) rs63751005
NM_000179.2(MSH6):c.2384T>C (p.Ile795Thr) rs202127474
NM_000249.3(MLH1):c.1039-8T>A rs193922367
NM_000249.3(MLH1):c.1151T>A (p.Val384Asp) rs63750447
NM_000249.3(MLH1):c.1321G>A (p.Ala441Thr) rs63750365
NM_000249.3(MLH1):c.1327A>C (p.Lys443Gln) rs34213726
NM_000249.3(MLH1):c.1558+14G>A rs41562513
NM_000249.3(MLH1):c.1853A>C (p.Lys618Thr) rs63750449
NM_000249.3(MLH1):c.1959G>T (p.Leu653=) rs1800146
NM_000249.3(MLH1):c.2152C>T (p.His718Tyr) rs2020873
NM_000249.3(MLH1):c.655A>G (p.Ile219Val) rs1799977
NM_000249.3(MLH1):c.955G>A (p.Glu319Lys) rs63750796
NM_000249.3(MLH1):c.977T>C (p.Val326Ala) rs63751049
NM_000251.2(MSH2):c.1511-9A>T rs12998837
NM_000251.2(MSH2):c.1661+12G>A rs3732183
NM_000251.2(MSH2):c.2006-6T>C rs2303428
NM_000251.2(MSH2):c.211+9C>G rs2303426
NM_000251.2(MSH2):c.23C>T (p.Thr8Met) rs17217716
NM_000251.2(MSH2):c.2732T>G (p.Leu911Arg) rs41295182
NM_000251.2(MSH2):c.317G>A (p.Arg106Lys) rs41295286
NM_000251.2(MSH2):c.380A>G (p.Asn127Ser) rs17217772
NM_000251.2(MSH2):c.965G>A (p.Gly322Asp) rs4987188
NM_000314.7(PTEN):c.388C>T (p.Arg130Ter) rs121909224
NM_000314.7(PTEN):c.968dup (p.Asn323fs) rs121913291
NM_000455.4(STK11):c.1062C>G (p.Phe354Leu) rs59912467
NM_000455.4(STK11):c.465-4G>A rs587780009
NM_000535.7(PMS2):c.1408C>T (p.Pro470Ser) rs1805321
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu) rs63750668
NM_000535.7(PMS2):c.1789A>T (p.Thr597Ser) rs1805318
NM_000535.7(PMS2):c.1831dup (p.Ile611fs) rs63750250
NM_000535.7(PMS2):c.1A>G (p.Met1Val) rs587779333
NM_000535.7(PMS2):c.2007-4G>A rs1805326
NM_000535.7(PMS2):c.2012C>T (p.Thr671Met) rs587780046
NM_000535.7(PMS2):c.2113G>A (p.Glu705Lys) rs267608161
NM_000535.7(PMS2):c.2182A>G (p.Thr728Ala) rs141893001
NM_000535.7(PMS2):c.2184_2185TC[1] (p.Leu729fs) rs587779335
NM_000535.7(PMS2):c.2253T>C (p.Phe751=) rs1805325
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) rs17420802
NM_000535.7(PMS2):c.2570G>C (p.Gly857Ala) rs1802683
NM_000535.7(PMS2):c.52A>G (p.Ile18Val) rs63750123
NM_000535.7(PMS2):c.59G>A (p.Arg20Gln) rs10254120
NM_001048171.1(MUTYH):c.1145-2A>G rs587781628
NM_001048171.1(MUTYH):c.1378C>T (p.Arg460Cys) rs200229669
NM_001048171.1(MUTYH):c.697C>T (p.Arg233Ter) rs587782885
NM_001048171.1(MUTYH):c.972G>C (p.Gln324His) rs3219489
NM_001126112.2(TP53):c.139C>T (p.Pro47Ser) rs1800371
NM_001126112.2(TP53):c.215C>G (p.Pro72Arg) rs1042522
NM_001126112.2(TP53):c.524G>A (p.Arg175His) rs28934578
NM_001126112.2(TP53):c.566C>T (p.Ala189Val) rs121912665
NM_001126112.2(TP53):c.638G>A (p.Arg213Gln) rs587778720
NM_001126112.2(TP53):c.733G>A (p.Gly245Ser) rs28934575
NM_001126112.2(TP53):c.743G>A (p.Arg248Gln) rs11540652
NM_001126112.2(TP53):c.766A>G (p.Thr256Ala) rs587781433
NM_001126112.2(TP53):c.817C>T (p.Arg273Cys) rs121913343
NM_001126112.2(TP53):c.818G>A (p.Arg273His) rs28934576
NM_001126112.2(TP53):c.844C>T (p.Arg282Trp) rs28934574
NM_001354630.1(MLH1):c.1732-878_1732-877delinsGC rs35502531
NM_004360.5(CDH1):c.1137G>A (p.Thr379=) rs587783050
NM_004360.5(CDH1):c.1774G>A (p.Ala592Thr) rs35187787
NM_004360.5(CDH1):c.1849G>A (p.Ala617Thr) rs33935154
NM_007194.4(CHEK2):c.1100del (p.Thr367fs) rs555607708
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) rs17879961
NM_007294.3(BRCA1):c.1067A>G (p.Gln356Arg) rs1799950
NM_007294.3(BRCA1):c.1137T>G (p.Ile379Met) rs56128296
NM_007294.3(BRCA1):c.144G>A (p.Met48Ile) rs587783040
NM_007294.3(BRCA1):c.1487G>A (p.Arg496His) rs28897677
NM_007294.3(BRCA1):c.1789G>A (p.Glu597Lys) rs55650082
NM_007294.3(BRCA1):c.1912G>A (p.Glu638Lys) rs80357005
NM_007294.3(BRCA1):c.2428A>T (p.Asn810Tyr) rs28897682
NM_007294.3(BRCA1):c.2458A>G (p.Lys820Glu) rs56082113
NM_007294.3(BRCA1):c.2998_3003del (p.Glu1000_Glu1001del) rs80358333
NM_007294.3(BRCA1):c.3119G>A (p.Ser1040Asn) rs4986852
NM_007294.3(BRCA1):c.4039A>G (p.Arg1347Gly) rs28897689
NM_007294.3(BRCA1):c.4096+3A>G rs80358015
NM_007294.3(BRCA1):c.4535G>T (p.Ser1512Ile) rs1800744
NM_007294.3(BRCA1):c.5117G>C (p.Gly1706Ala) rs80356860
NM_007294.3(BRCA1):c.5266dupC (p.Gln1756Profs) rs80357906
NM_007294.3(BRCA1):c.5348T>C (p.Met1783Thr) rs55808233
NM_007294.3(BRCA1):c.5468-10C>A rs8176316
NM_007294.3(BRCA1):c.594-2A>C rs80358033
NM_007294.3(BRCA1):c.66_67AG[1] (p.Glu23fs) rs80357914
NM_007294.3(BRCA1):c.694G>A (p.Asp232Asn) rs55975699
NM_007294.3(BRCA1):c.823G>A (p.Gly275Ser) rs8176153
NM_007299.4(BRCA1):c.1675-1G>A rs730881495
NM_007299.4(BRCA1):c.557C>A (p.Ser186Tyr) rs55688530
NM_007299.4(BRCA1):c.571G>A (p.Val191Ile) rs80357090
NM_007300.4(BRCA1):c.3024G>A (p.Met1008Ile) rs1800704
NM_007300.4(BRCA1):c.3608G>A (p.Arg1203Gln) rs55930959
NM_012222.2(MUTYH):c.1138del (p.Ala382fs) rs587778536
NM_012222.2(MUTYH):c.1178G>A (p.Gly393Asp) rs36053993
NM_012222.2(MUTYH):c.1218_1219dup (p.Glu407fs) rs587780078
NM_012222.2(MUTYH):c.1267C>T (p.Arg423Cys) rs150792276
NM_012222.2(MUTYH):c.1576C>A (p.Leu526Met) rs3219496
NM_012222.2(MUTYH):c.527A>G (p.Tyr176Cys) rs34612342
NM_024675.3(PALB2):c.1010T>C (p.Leu337Ser) rs45494092
NM_024675.3(PALB2):c.2014G>C (p.Glu672Gln) rs45532440
NM_024675.3(PALB2):c.2590C>T (p.Pro864Ser) rs45568339
NM_024675.3(PALB2):c.2794G>A (p.Val932Met) rs45624036
NM_024675.3(PALB2):c.2993G>A (p.Gly998Glu) rs45551636
NM_024675.3(PALB2):c.3113G>A (p.Trp1038Ter) rs180177132
NM_024675.3(PALB2):c.53A>G (p.Lys18Arg) rs138789658
NM_024675.3(PALB2):c.629C>T (p.Pro210Leu) rs57605939

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