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 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
37 87 0 92 60 1 9 114

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 pathogenic, low penetrance
pathogenic 0 11 1 1 1 0
likely pathogenic 8 0 3 0 0 1
uncertain significance 1 1 0 9 8 0
likely benign 1 0 24 0 41 0
benign 1 0 23 32 0 0

Submitter to submitter summary #

Total submitters: 50
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
Illumina Laboratory Services, Illumina 0 38 0 26 11 0 0 37
Counsyl 0 66 0 29 2 0 0 31
Mendelics 0 37 0 23 2 0 1 26
Evidence-based Network for the Interpretation of Germline Mutant Alleles (ENIGMA) 0 34 0 22 0 0 2 24
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
KCCC/NGS Laboratory, Kuwait Cancer Control Center 0 33 0 20 0 0 0 20
Myriad Genetics, Inc. 0 48 0 9 9 0 1 19
Breast Cancer Information Core (BIC) (BRCA1) 0 18 0 2 15 0 1 18
Michigan Medical Genetics Laboratories, University of Michigan 0 20 0 17 0 0 0 17
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 27 0 14 1 0 0 15
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 13 0 14 0 0 0 14
Labcorp Genetics (formerly Invitae), Labcorp 0 44 0 5 7 1 0 13
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 31 0 13 0 0 0 13
Institute of Human Genetics, University of Leipzig Medical Center 0 17 0 3 5 0 1 9
BRCAlab, Lund University 0 21 0 8 0 0 1 9
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 2 0 1 7 0 0 8
Cancer Genetics Laboratory, Peter MacCallum Cancer Centre 0 0 0 5 3 0 0 8
All of Us Research Program, National Institutes of Health 0 12 0 6 2 0 0 8
Fulgent Genetics, Fulgent Genetics 0 5 0 6 0 0 0 6
Genome-Nilou Lab 0 5 0 3 3 0 0 6
OMIM 0 17 0 0 2 0 2 4
Department of Pathology and Laboratory Medicine, Sinai Health System 0 11 0 4 0 0 0 4
Baylor Genetics 0 33 0 1 0 0 2 3
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 3 0 1 0 0 1 2
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) 0 2 0 2 0 0 0 2
Department of Medical Genetics, University Hospital of North Norway 0 2 0 2 0 0 0 2
Genetics and Molecular Pathology, SA Pathology 0 7 0 2 0 0 0 2
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 9 0 2 0 0 0 2
St. Jude Molecular Pathology, St. Jude Children's Research Hospital 0 13 0 1 1 0 0 2
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet 0 10 0 1 0 0 0 1
Biesecker Lab/Clinical Genomics Section, National Institutes of Health 0 3 0 1 0 0 0 1
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 0 0 1 0 0 0 1
Natera, Inc. 0 4 0 1 0 0 0 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 4 0 0 0 0 1 1
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 15 0 1 0 0 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
CSER _CC_NCGL, University of Washington 0 1 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
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 0 0 1 0 0 0 1
Cancer Diagnostics Division, Gene Solutions 0 0 0 1 0 0 0 1
deCODE genetics, Amgen 0 0 0 1 0 0 0 1
Zotz-Klimas Genetics Lab, MVZ Zotz Klimas 0 1 0 1 0 0 0 1
Ding PR Lab, Sun Yat-sen University Cancer Center 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 4 0 0 0 0 1 1
Department of Medical and Surgical Sciences, University of Bologna 0 1 0 0 1 0 0 1
ClinGen InSiGHT Hereditary Colorectal Cancer/Polyposis Variant Curation Expert Panel 0 2 0 0 1 0 0 1
European Reference Network on Genetic Tumour Risk Syndromes (ERN-GENTURIS), i3s - Instituto de Investigação e Inovação em Saúde, University of Porto 0 4 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 114
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000546.6(TP53):c.215C>G (p.Pro72Arg) rs1042522 0.62654
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) rs1042821 0.18742
NM_000535.7(PMS2):c.59G>A (p.Arg20Gln) rs10254120 0.07445
NM_000057.4(BLM):c.2603C>T (p.Pro868Leu) rs2227935 0.06742
NM_000249.4(MLH1):c.1558+14G>A rs41562513 0.05554
NM_007294.4(BRCA1):c.1067A>G (p.Gln356Arg) rs1799950 0.04695
NM_000249.4(MLH1):c.2152C>T (p.His718Tyr) rs2020873 0.02345
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) rs17217772 0.02317
NM_024675.4(PALB2):c.2014G>C (p.Glu672Gln) rs45532440 0.02171
NM_024675.4(PALB2):c.629C>T (p.Pro210Leu) rs57605939 0.02101
NM_000059.4(BRCA2):c.5744C>T (p.Thr1915Met) rs4987117 0.01834
NM_024675.4(PALB2):c.2993G>A (p.Gly998Glu) rs45551636 0.01717
NM_000251.3(MSH2):c.965G>A (p.Gly322Asp) rs4987188 0.01714
NM_024675.4(PALB2):c.1010T>C (p.Leu337Ser) rs45494092 0.01508
NM_004360.5(CDH1):c.1849G>A (p.Ala617Thr) rs33935154 0.01412
NM_000059.4(BRCA2):c.8830A>T (p.Ile2944Phe) rs4987047 0.01281
NM_000249.4(MLH1):c.1039-8T>A rs193922367 0.01153
NM_007294.4(BRCA1):c.3119G>A (p.Ser1040Asn) rs4986852 0.01109
NM_000535.7(PMS2):c.1789A>T (p.Thr597Ser) rs1805318 0.01006
NM_000059.4(BRCA2):c.7319A>G (p.His2440Arg) rs4986860 0.00984
NM_007294.4(BRCA1):c.2458A>G (p.Lys820Glu) rs56082113 0.00964
NM_000249.4(MLH1):c.1959G>T (p.Leu653=) rs1800146 0.00913
NM_000059.4(BRCA2):c.7469T>C (p.Ile2490Thr) rs11571707 0.00868
NM_000535.7(PMS2):c.52A>G (p.Ile18Val) rs63750123 0.00861
NM_000059.4(BRCA2):c.8851G>A (p.Ala2951Thr) rs11571769 0.00809
NM_000059.4(BRCA2):c.7017G>C (p.Lys2339Asn) rs45574331 0.00792
NM_000059.4(BRCA2):c.4258G>T (p.Asp1420Tyr) rs28897727 0.00609
NM_000059.4(BRCA2):c.9976A>T (p.Lys3326Ter) rs11571833 0.00597
NM_000038.6(APC):c.3949G>C (p.Glu1317Gln) rs1801166 0.00570
NM_000179.3(MSH6):c.1186C>G (p.Leu396Val) rs2020908 0.00565
NM_024675.4(PALB2):c.53A>G (p.Lys18Arg) rs138789658 0.00530
NM_007294.4(BRCA1):c.5468-10C>A rs8176316 0.00464
NM_024675.4(PALB2):c.2794G>A (p.Val932Met) rs45624036 0.00449
NM_000059.4(BRCA2):c.7008-62A>G rs76584943 0.00439
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) rs17879961 0.00434
NM_007294.4(BRCA1):c.4039A>G (p.Arg1347Gly) rs28897689 0.00419
NM_000059.4(BRCA2):c.2960A>T (p.Asn987Ile) rs2227944 0.00356
NM_000455.5(STK11):c.1062C>G (p.Phe354Leu) rs59912467 0.00348
NM_004360.5(CDH1):c.1774G>A (p.Ala592Thr) rs35187787 0.00311
NM_000059.4(BRCA2):c.3869G>A (p.Cys1290Tyr) rs41293485 0.00307
NM_007294.4(BRCA1):c.557C>A (p.Ser186Tyr) rs55688530 0.00301
NM_024675.4(PALB2):c.2590C>T (p.Pro864Ser) rs45568339 0.00287
NM_000059.4(BRCA2):c.68-7T>A rs81002830 0.00277
NM_000059.4(BRCA2):c.6100C>T (p.Arg2034Cys) rs1799954 0.00268
NM_000059.4(BRCA2):c.6323G>A (p.Arg2108His) rs35029074 0.00260
NM_007294.4(BRCA1):c.4535G>T (p.Ser1512Ile) rs1800744 0.00240
NM_000059.4(BRCA2):c.8182G>A (p.Val2728Ile) rs28897749 0.00239
NM_000059.4(BRCA2):c.7150C>A (p.Gln2384Lys) rs55977008 0.00203
NM_000059.4(BRCA2):c.8503T>C (p.Ser2835Pro) rs11571746 0.00202
NM_000251.3(MSH2):c.23C>T (p.Thr8Met) rs17217716 0.00184
NM_000057.4(BLM):c.2119C>T (p.Pro707Ser) rs146077918 0.00172
NM_000059.4(BRCA2):c.4187A>G (p.Gln1396Arg) rs55969723 0.00168
NM_000059.4(BRCA2):c.125A>G (p.Tyr42Cys) rs4987046 0.00158
NM_000059.4(BRCA2):c.8567A>C (p.Glu2856Ala) rs11571747 0.00158
NM_007294.4(BRCA1):c.1137T>G (p.Ile379Met) rs56128296 0.00158
NM_001048174.2(MUTYH):c.1501C>A (p.Leu501Met) rs3219496 0.00154
NM_000059.4(BRCA2):c.2138A>T (p.Gln713Leu) rs55816687 0.00138
NM_000059.4(BRCA2):c.8149G>T (p.Ala2717Ser) rs28897747 0.00127
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) rs63750447 0.00077
NM_000038.6(APC):c.1604C>T (p.Ser535Phe) rs75870842 0.00071
NM_000179.3(MSH6):c.1526T>C (p.Val509Ala) rs63751005 0.00067
NM_007294.4(BRCA1):c.3024G>A (p.Met1008Ile) rs1800704 0.00065
NM_007294.4(BRCA1):c.1487G>A (p.Arg496His) rs28897677 0.00060
NM_000059.4(BRCA2):c.10121C>T (p.Thr3374Ile) rs56309455 0.00059
NM_007294.4(BRCA1):c.5348T>C (p.Met1783Thr) rs55808233 0.00058
NM_000038.6(APC):c.1240C>T (p.Arg414Cys) rs137854567 0.00053
NM_000059.4(BRCA2):c.4585G>A (p.Gly1529Arg) rs28897728 0.00044
NM_000249.4(MLH1):c.977T>C (p.Val326Ala) rs63751049 0.00037
NM_000249.4(MLH1):c.1321G>A (p.Ala441Thr) rs63750365 0.00034
NM_000059.4(BRCA2):c.5785A>G (p.Ile1929Val) rs79538375 0.00031
NM_000059.4(BRCA2):c.6853A>G (p.Ile2285Val) rs56272235 0.00026
NM_007294.4(BRCA1):c.571G>A (p.Val191Ile) rs80357090 0.00021
NM_007294.4(BRCA1):c.1789G>A (p.Glu597Lys) rs55650082 0.00019
NM_000535.7(PMS2):c.2253T>C (p.Phe751=) rs1805325 0.00018
NM_000535.7(PMS2):c.857A>G (p.Asp286Gly) rs116788608 0.00011
NM_000038.6(APC):c.6473C>G (p.Pro2158Arg) rs587779804 0.00007
NM_000179.3(MSH6):c.2384T>C (p.Ile795Thr) rs202127474 0.00007
NM_000251.3(MSH2):c.2732T>G (p.Leu911Arg) rs41295182 0.00007
NM_000059.4(BRCA2):c.7057G>C (p.Gly2353Arg) rs80358935 0.00006
NM_000249.4(MLH1):c.955G>A (p.Glu319Lys) rs63750796 0.00006
NM_007294.4(BRCA1):c.2428A>T (p.Asn810Tyr) rs28897682 0.00006
NM_007294.4(BRCA1):c.3608G>A (p.Arg1203Gln) rs55930959 0.00006
NM_000059.4(BRCA2):c.7052C>G (p.Ala2351Gly) rs80358932 0.00005
NM_007294.4(BRCA1):c.5117G>C (p.Gly1706Ala) rs80356860 0.00005
NM_000535.7(PMS2):c.1A>G (p.Met1Val) rs587779333 0.00004
NM_000535.7(PMS2):c.2113G>A (p.Glu705Lys) rs267608161 0.00003
NM_007294.4(BRCA1):c.594-2A>C rs80358033 0.00003
NM_000038.6(APC):c.1685C>T (p.Thr562Met) rs587783034 0.00002
NM_000546.6(TP53):c.743G>A (p.Arg248Gln) rs11540652 0.00002
NM_001048174.2(MUTYH):c.655C>T (p.Arg219Ter) rs587782885 0.00002
NM_024675.4(PALB2):c.3113G>A (p.Trp1038Ter) rs180177132 0.00002
NM_000059.4(BRCA2):c.4552del (p.Glu1518fs) rs398122783 0.00001
NM_000546.6(TP53):c.817C>T (p.Arg273Cys) rs121913343 0.00001
NM_000546.6(TP53):c.844C>T (p.Arg282Trp) rs28934574 0.00001
NM_000038.6(APC):c.3462AGA[2] (p.Glu1157del) rs386833391
NM_000038.6(APC):c.3927_3931del (p.Glu1309fs) rs121913224
NM_000059.4(BRCA2):c.10095delinsGAATTATATCT (p.Ser3366fs) rs276174803
NM_000249.4(MLH1):c.1852_1853delinsGC (p.Lys618Ala) rs35502531
NM_000249.4(MLH1):c.1853A>C (p.Lys618Thr) rs63750449
NM_000249.4(MLH1):c.350C>T (p.Thr117Met) rs63750781
NM_000314.8(PTEN):c.697C>T (p.Arg233Ter) rs121909219
NM_000314.8(PTEN):c.968dup (p.Asn323fs) rs121913291
NM_000455.5(STK11):c.465-4G>A rs587780009
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu) rs63750668
NM_000535.7(PMS2):c.1831dup (p.Ile611fs) rs63750250
NM_000535.7(PMS2):c.2186_2187del (p.Leu729fs) rs587779335
NM_000546.6(TP53):c.267del (p.Ser90fs) rs587783062
NM_000546.6(TP53):c.818G>A (p.Arg273His) rs28934576
NM_004360.5(CDH1):c.1137G>A (p.Thr379=) rs587783050
NM_007294.4(BRCA1):c.1912G>A (p.Glu638Lys) rs80357005
NM_007294.4(BRCA1):c.2998_3003del (p.Glu1000_Glu1001del) rs80358333
NM_007294.4(BRCA1):c.4096+3A>G rs80358015
NM_007294.4(BRCA1):c.4987-1G>A rs730881495
NM_007294.4(BRCA1):c.823G>A (p.Gly275Ser) rs8176153

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.