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
76 76 0 70 47 0 7 86

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 0 7 1 0 1
likely pathogenic 3 0 2 0 0
uncertain significance 0 0 0 4 5
likely benign 2 0 23 0 36
benign 1 0 17 24 0

Submitter to submitter summary #

Total submitters: 32
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
Counsyl 0 53 0 27 2 0 0 29
Illumina Clinical Services Laboratory,Illumina 0 25 0 20 6 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
Mendelics 0 28 0 16 3 0 0 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 16 0 13 1 0 0 14
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center 0 23 0 14 0 0 0 14
Genome Diagnostics Laboratory,University Medical Center Utrecht 0 10 0 12 0 0 0 12
Invitae 0 34 0 6 5 0 0 11
Fulgent Genetics,Fulgent Genetics 0 4 0 8 0 0 0 8
Cancer Genetics Laboratory,Peter MacCallum Cancer Centre 0 0 0 5 3 0 0 8
Institute of Human Genetics, University of Leipzig Medical Center 0 5 0 1 5 0 2 8
Department of Pathology and Laboratory Medicine,Sinai Health System 0 11 0 4 0 0 0 4
OMIM 0 18 0 0 1 0 2 3
Center for Human Genetics, Inc,Center for Human Genetics, Inc 0 0 0 0 2 0 0 2
GeneReviews 0 3 0 0 0 0 2 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
Natera, Inc. 0 1 0 1 0 0 0 1
Human Genome Sequencing Center Clinical Lab, Baylor College of Medicine 0 12 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
Consortium of Investigators of Modifiers of BRCA1/2 (CIMBA), c/o University of Cambridge 0 20 0 1 0 0 0 1
IntelligeneCG 0 2 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
ClinGen CDH1 Variant Curation Expert Panel 0 5 0 1 0 0 0 1
Ding PR Lab,Sun Yat-sen University Cancer Center 0 0 0 1 0 0 0 1
Nilou-Genome Lab 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 86
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.3462AGA[2] (p.Glu1157del) rs386833391
NM_000038.6(APC):c.3927_3931del (p.Glu1309fs) rs121913224
NM_000038.6(APC):c.3949G>C (p.Glu1317Gln) rs1801166
NM_000038.6(APC):c.6473C>G (p.Pro2158Arg) rs587779804
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.2138A>T (p.Gln713Leu) rs55816687
NM_000059.3(BRCA2):c.2960A>T (p.Asn987Ile) rs2227944
NM_000059.3(BRCA2):c.4552del (p.Glu1518fs) rs398122783
NM_000059.3(BRCA2):c.7008-62A>G rs76584943
NM_000059.3(BRCA2):c.7052C>G (p.Ala2351Gly) rs80358932
NM_000059.4(BRCA2):c.10095delinsGAATTATATCT (p.Ser3366fs) rs276174803
NM_000059.4(BRCA2):c.10121C>T (p.Thr3374Ile) rs56309455
NM_000059.4(BRCA2):c.125A>G (p.Tyr42Cys) rs4987046
NM_000059.4(BRCA2):c.3869G>A (p.Cys1290Tyr) rs41293485
NM_000059.4(BRCA2):c.4187A>G (p.Gln1396Arg) rs55969723
NM_000059.4(BRCA2):c.4258G>T (p.Asp1420Tyr) rs28897727
NM_000059.4(BRCA2):c.4585G>A (p.Gly1529Arg) rs28897728
NM_000059.4(BRCA2):c.5744C>T (p.Thr1915Met) rs4987117
NM_000059.4(BRCA2):c.5785A>G (p.Ile1929Val) rs79538375
NM_000059.4(BRCA2):c.6100C>T (p.Arg2034Cys) rs1799954
NM_000059.4(BRCA2):c.6323G>A (p.Arg2108His) rs35029074
NM_000059.4(BRCA2):c.68-7T>A rs81002830
NM_000059.4(BRCA2):c.6853A>G (p.Ile2285Val) rs56272235
NM_000059.4(BRCA2):c.7017G>C (p.Lys2339Asn) rs45574331
NM_000059.4(BRCA2):c.7057G>C (p.Gly2353Arg) rs80358935
NM_000059.4(BRCA2):c.7150C>A (p.Gln2384Lys) rs55977008
NM_000059.4(BRCA2):c.7319A>G (p.His2440Arg) rs4986860
NM_000059.4(BRCA2):c.7469T>C (p.Ile2490Thr) rs11571707
NM_000059.4(BRCA2):c.8149G>T (p.Ala2717Ser) rs28897747
NM_000059.4(BRCA2):c.8182G>A (p.Val2728Ile) rs28897749
NM_000059.4(BRCA2):c.8503T>C (p.Ser2835Pro) rs11571746
NM_000059.4(BRCA2):c.8567A>C (p.Glu2856Ala) rs11571747
NM_000059.4(BRCA2):c.8830A>T (p.Ile2944Phe) rs4987047
NM_000059.4(BRCA2):c.8851G>A (p.Ala2951Thr) rs11571769
NM_000059.4(BRCA2):c.9976A>T (p.Lys3326Ter) rs11571833
NM_000249.4(MLH1):c.350C>T (p.Thr117Met) rs63750781
NM_000251.2(MSH2):c.23C>T (p.Thr8Met) rs17217716
NM_000251.2(MSH2):c.965G>A (p.Gly322Asp) rs4987188
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) rs17217772
NM_000455.5(STK11):c.1062C>G (p.Phe354Leu) rs59912467
NM_000455.5(STK11):c.465-4G>A rs587780009
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.52A>G (p.Ile18Val) rs63750123
NM_000546.6(TP53):c.215C>G (p.Pro72Arg) rs1042522
NM_000546.6(TP53):c.743G>A (p.Arg248Gln) rs11540652
NM_000546.6(TP53):c.818G>A (p.Arg273His) rs28934576
NM_001048171.1(MUTYH):c.697C>T (p.Arg233Ter) rs587782885
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.4096+3A>G rs80358015
NM_007294.4(BRCA1):c.1067A>G (p.Gln356Arg) rs1799950
NM_007294.4(BRCA1):c.1137T>G (p.Ile379Met) rs56128296
NM_007294.4(BRCA1):c.1487G>A (p.Arg496His) rs28897677
NM_007294.4(BRCA1):c.1789G>A (p.Glu597Lys) rs55650082
NM_007294.4(BRCA1):c.2428A>T (p.Asn810Tyr) rs28897682
NM_007294.4(BRCA1):c.2458A>G (p.Lys820Glu) rs56082113
NM_007294.4(BRCA1):c.2998_3003del (p.Glu1000_Glu1001del) rs80358333
NM_007294.4(BRCA1):c.3024G>A (p.Met1008Ile) rs1800704
NM_007294.4(BRCA1):c.3119G>A (p.Ser1040Asn) rs4986852
NM_007294.4(BRCA1):c.3608G>A (p.Arg1203Gln) rs55930959
NM_007294.4(BRCA1):c.4039A>G (p.Arg1347Gly) rs28897689
NM_007294.4(BRCA1):c.4535G>T (p.Ser1512Ile) rs1800744
NM_007294.4(BRCA1):c.5117G>C (p.Gly1706Ala) rs80356860
NM_007294.4(BRCA1):c.5348T>C (p.Met1783Thr) rs55808233
NM_007294.4(BRCA1):c.5468-10C>A rs8176316
NM_007294.4(BRCA1):c.557C>A (p.Ser186Tyr) rs55688530
NM_007294.4(BRCA1):c.571G>A (p.Val191Ile) rs80357090
NM_007294.4(BRCA1):c.594-2A>C rs80358033
NM_007294.4(BRCA1):c.823G>A (p.Gly275Ser) rs8176153
NM_007299.4(BRCA1):c.1675-1G>A rs730881495
NM_012222.2(MUTYH):c.1576C>A (p.Leu526Met) rs3219496
NM_024675.3(PALB2):c.1010T>C (p.Leu337Ser) rs45494092
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
NM_024675.4(PALB2):c.2014G>C (p.Glu672Gln) rs45532440

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