ClinVar Miner

Variants from GeneKor MSA with conflicting interpretations

Location: Greece — Primary collection method: clinical testing
Minimum review status of the submission from GeneKor MSA: Collection method of the submission from GeneKor MSA:
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
241 350 15 42 115 3 18 184

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
GeneKor MSA pathogenic likely pathogenic uncertain significance likely benign benign risk factor
pathogenic 2 6 8 0 1 2
likely pathogenic 26 0 5 0 0 0
uncertain significance 0 4 0 104 17 0
likely benign 0 0 1 0 5 0
benign 0 0 3 5 13 0
risk factor 1 1 0 0 0 0

Submitter to submitter summary #

Total submitters: 28
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
Ambry Genetics 0 259 0 19 87 1 3 110
Color Health, Inc 0 177 0 14 79 1 2 96
Biesecker Lab/Clinical Genomics Section,National Institutes of Health 0 0 13 0 0 0 0 13
True Health Diagnostics 0 14 0 3 5 0 1 9
Department of Pathology and Laboratory Medicine,Sinai Health System 0 46 0 1 2 0 5 8
GeneDx 0 64 0 7 0 0 0 7
Invitae 0 34 0 4 2 0 0 6
Mayo Clinic Laboratories, Mayo Clinic 0 27 0 3 0 0 1 4
Quest Diagnostics Nichols Institute San Juan Capistrano 0 44 0 4 0 0 0 4
University of Washington Department of Laboratory Medicine, University of Washington 0 7 0 4 0 0 0 4
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario 0 13 0 2 0 0 1 3
Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research 0 12 0 1 1 0 1 3
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 4 0 2 0 1 0 3
CeGaT Praxis fuer Humangenetik Tuebingen 0 11 0 3 0 0 0 3
Department of Pediatric Oncology, Hematology and Clinical Immunology,University Clinics Duesseldorf 0 2 0 0 0 0 3 3
OMIM 0 1 0 0 0 2 0 2
Integrated Genetics/Laboratory Corporation of America 0 13 0 2 0 0 0 2
GeneReviews 0 0 2 0 0 0 0 2
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 1 0 1 1 0 0 2
Illumina Clinical Services Laboratory,Illumina 0 3 0 1 1 0 0 2
Vantari Genetics 0 2 0 2 0 0 0 2
Institute for Biomarker Research,Medical Diagnostic Laboratories, L.L.C. 0 6 0 1 1 0 0 2
Leiden Open Variation Database 0 1 0 2 0 0 0 2
King Laboratory,University of Washington 0 0 0 0 0 0 1 1
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics 0 35 0 1 0 0 0 1
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 2 0 1 0 0 0 1
Research Molecular Genetics Laboratory,Women's College Hospital, University of Toronto 0 12 0 0 0 0 1 1
CZECANCA consortium 0 9 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 184
Download table as spreadsheet
HGVS dbSNP
NM_000038.6(APC):c.1589T>C (p.Val530Ala) rs202199891
NM_000038.6(APC):c.2593C>T (p.Pro865Ser) rs192620988
NM_000038.6(APC):c.3920T>A (p.Ile1307Lys) rs1801155
NM_000038.6(APC):c.6639G>A (p.Met2213Ile) rs35540155
NM_000038.6(APC):c.6857C>T (p.Ala2286Val) rs200587641
NM_000038.6(APC):c.7717A>G (p.Ile2573Val) rs145444830
NM_000051.3(ATM):c.1888G>A (p.Val630Met) rs148191382
NM_000051.3(ATM):c.2250G>A (p.Lys750=) rs1137887
NM_000051.3(ATM):c.2251-4A>G rs786202935
NM_000051.3(ATM):c.2396C>T (p.Ala799Val) rs199954262
NM_000051.3(ATM):c.2873A>G (p.Glu958Gly) rs587778069
NM_000051.3(ATM):c.3016A>G (p.Met1006Val) rs139893395
NM_000051.3(ATM):c.3614G>A (p.Arg1205His) rs769106895
NM_000051.3(ATM):c.4703A>G (p.His1568Arg) rs368830730
NM_000051.3(ATM):c.4910A>G (p.Asp1637Gly) rs763457172
NM_000051.3(ATM):c.8988-1G>C rs730881386
NM_000051.4(ATM):c.1444A>C (p.Lys482Gln) rs202173660
NM_000051.4(ATM):c.146C>G rs1800054
NM_000051.4(ATM):c.2021A>G (p.His674Arg) rs201762714
NM_000051.4(ATM):c.2289T>A (p.Phe763Leu) rs34231402
NM_000051.4(ATM):c.2932T>C (p.Ser978Pro) rs139552233
NM_000051.4(ATM):c.3299C>T (p.Thr1100Met) rs189445371
NM_000051.4(ATM):c.5975A>C (p.Lys1992Thr) rs150757822
NM_000051.4(ATM):c.6067G>A (p.Gly2023Arg) rs11212587
NM_000051.4(ATM):c.7187C>G (p.Thr2396Ser) rs370559102
NM_000051.4(ATM):c.749G>A (p.Arg250Gln) rs56123940
NM_000051.4(ATM):c.7740A>C (p.Arg2580Ser) rs199915459
NM_000057.4(BLM):c.191A>T (p.Asp64Val) rs140382474
NM_000057.4(BLM):c.3879A>G (p.Glu1293=) rs28377085
NM_000059.3(BRCA2):c.-175C>T rs55880202
NM_000059.3(BRCA2):c.10089A>G (p.Ile3363Met) rs80358390
NM_000059.3(BRCA2):c.2944A>C (p.Ile982Leu) rs28897717
NM_000059.3(BRCA2):c.3032C>G (p.Thr1011Arg) rs80358548
NM_000059.3(BRCA2):c.3562A>G (p.Ile1188Val) rs202230438
NM_000059.3(BRCA2):c.5704G>A (p.Asp1902Asn) rs4987048
NM_000059.3(BRCA2):c.5921C>T (p.Thr1974Ile) rs55730620
NM_000059.3(BRCA2):c.6613G>A (p.Val2205Met) rs80358889
NM_000059.3(BRCA2):c.7985C>T (p.Thr2662Met) rs431825362
NM_000059.3(BRCA2):c.8023A>G (p.Ile2675Val) rs397507954
NM_000059.4(BRCA2):c.1114A>C (p.Asn372His) rs144848
NM_000059.4(BRCA2):c.2971A>G (p.Asn991Asp) rs1799944
NM_000059.4(BRCA2):c.3861TAA[1] (p.Asn1288del) rs276174837
NM_000059.4(BRCA2):c.5946del (p.Ser1982fs) rs80359550
NM_000059.4(BRCA2):c.771_775del rs80359671
NM_000059.4(BRCA2):c.7879A>T (p.Ile2627Phe) rs80359014
NM_000059.4(BRCA2):c.8377G>A (p.Gly2793Arg) rs80359082
NM_000059.4(BRCA2):c.865A>C (p.Asn289His) rs766173
NM_000059.4(BRCA2):c.9472A>G (p.Thr3158Ala) rs786204284
NM_000059.4(BRCA2):c.9976A>T (p.Lys3326Ter) rs11571833
NM_000179.2(MSH6):c.3727A>T (p.Thr1243Ser) rs147453999
NM_000179.3(MSH6):c.1615CTT[1] (p.Leu540del) rs1064793600
NM_000179.3(MSH6):c.2398G>C (p.Val800Leu) rs61748083
NM_000179.3(MSH6):c.4002-4T>C rs370428032
NM_000179.3(MSH6):c.663A>C (p.Glu221Asp) rs41557217
NM_000244.3(MEN1):c.1449C>T (p.Gly483=) rs200280309
NM_000249.3(MLH1):c.1409+1G>A rs267607825
NM_000249.3(MLH1):c.1964T>C (p.Ile655Thr) rs63751225
NM_000249.3(MLH1):c.2041G>A (p.Ala681Thr) rs63750217
NM_000249.3(MLH1):c.2174G>A (p.Arg725His) rs566928243
NM_000249.3(MLH1):c.479C>T (p.Ala160Val) rs63749924
NM_000249.4(MLH1):c.1360G>C (p.Gly454Arg) rs63750527
NM_000249.4(MLH1):c.199G>A (p.Gly67Arg) rs63750206
NM_000249.4(MLH1):c.677G>T (p.Arg226Leu) rs63751711
NM_000251.2(MSH2):c.1462T>G (p.Leu488Val) rs587781314
NM_000251.2(MSH2):c.1748A>G (p.Asn583Ser) rs201118107
NM_000251.2(MSH2):c.182A>C (p.Gln61Pro) rs587779113
NM_000251.2(MSH2):c.499G>C (p.Asp167His) rs63750255
NM_000251.2(MSH2):c.557A>G (p.Asn186Ser) rs151129360
NM_000251.3(MSH2):c.1787A>G (p.Asn596Ser) rs41295288
NM_000251.3(MSH2):c.435T>G (p.Ile145Met) rs63750124
NM_000267.3(NF1):c.1166A>G (p.His389Arg) rs149739570
NM_000314.8(PTEN):c.235G>A (p.Ala79Thr) rs202004587
NM_000314.8(PTEN):c.389G>T rs121909229
NM_000455.4(STK11):c.580G>A (p.Asp194Asn) rs121913315
NM_000455.5(STK11):c.1225C>T (p.Arg409Trp) rs368466538
NM_000465.4(BARD1):c.1127C>T (p.Ser376Leu) rs587782333
NM_000465.4(BARD1):c.1448A>G (p.His483Arg) rs587781874
NM_000465.4(BARD1):c.160A>G (p.Thr54Ala) rs200254470
NM_000465.4(BARD1):c.2282G>A (p.Ser761Asn) rs142155101
NM_000465.4(BARD1):c.716T>A (p.Leu239Gln) rs200359745
NM_000535.7(PMS2):c.1490G>A (p.Gly497Asp) rs199739859
NM_000535.7(PMS2):c.1567T>A (p.Ser523Thr) rs63751132
NM_000535.7(PMS2):c.1717A>T (p.Thr573Ser) rs63751211
NM_000535.7(PMS2):c.2012C>T (p.Thr671Met) rs587780046
NM_000535.7(PMS2):c.2149G>A (p.Val717Met) rs201671325
NM_000535.7(PMS2):c.2356C>A (p.Leu786Met) rs576055272
NM_000535.7(PMS2):c.52A>G (p.Ile18Val) rs63750123
NM_000535.7(PMS2):c.620G>A (p.Gly207Glu) rs374704824
NM_000535.7(PMS2):c.852A>G (p.Ser284=) rs766177007
NM_000546.5(TP53):c.665C>T (p.Pro222Leu) rs146340390
NM_000546.6(TP53):c.743G>A (p.Arg248Gln) rs11540652
NM_000546.6(TP53):c.818G>A (p.Arg273His) rs28934576
NM_000546.6(TP53):c.844C>T (p.Arg282Trp) rs28934574
NM_000546.6(TP53):c.847C>T (p.Arg283Cys) rs149633775
NM_001042492.3(NF1):c.3436G>A (p.Val1146Ile) rs201047812
NM_001042492.3(NF1):c.3883A>G (p.Thr1295Ala) rs143836226
NM_001048171.1(MUTYH):c.530G>A (p.Arg177Gln) rs369677603
NM_001048174.2(MUTYH):c.1103G>A (p.Gly368Asp) rs36053993
NM_001048174.2(MUTYH):c.1192C>T (p.Arg398Cys) rs150792276
NM_001048174.2(MUTYH):c.841C>T (p.Arg281Cys) rs138089183
NM_001126112.2(TP53):c.376-2dup rs751253294
NM_001167617.2(MLH1):c.-426_-425delinsTG rs63749994
NM_002485.4(NBN):c.278C>T (p.Ser93Leu) rs12721593
NM_002485.4(NBN):c.37+1G>A rs574673404
NM_002485.5(NBN):c.511A>G (p.Ile171Val) rs61754966
NM_002485.5(NBN):c.643C>T (p.Arg215Trp) rs34767364
NM_002485.5(NBN):c.657_661del (p.Lys219fs) rs587776650
NM_002878.3(RAD51D):c.394G>A (p.Val132Ile) rs201141245
NM_002878.3(RAD51D):c.413A>G (p.Asn138Ser) rs201676898
NM_002878.3(RAD51D):c.620C>G (p.Ser207Trp) rs370228071
NM_002878.3(RAD51D):c.932T>A (p.Ile311Asn) rs145309168
NM_004329.2(BMPR1A):c.499A>G (p.Met167Val) rs200951235
NM_004360.5(CDH1):c.1223C>T (p.Ala408Val) rs138135866
NM_004360.5(CDH1):c.214G>A (p.Asp72Asn) rs35606263
NM_004360.5(CDH1):c.2387G>A (p.Arg796Gln) rs587782549
NM_004360.5(CDH1):c.2494G>A (p.Val832Met) rs35572355
NM_004360.5(CDH1):c.2512A>G (p.Ser838Gly) rs121964872
NM_004360.5(CDH1):c.344C>T (p.Thr115Met) rs370973869
NM_004360.5(CDH1):c.546A>C (p.Lys182Asn) rs201141645
NM_005359.6(SMAD4):c.424+5G>A rs200772603
NM_005431.2(XRCC2):c.190C>T (p.Arg64Ter) rs151110146
NM_005591.3(MRE11):c.1462C>T (p.Arg488Cys) rs375261439
NM_005591.3(MRE11):c.1727G>A (p.Arg576Gln) rs139461096
NM_005732.4(RAD50):c.1094G>A (p.Arg365Gln) rs146370443
NM_005732.4(RAD50):c.2177G>A (p.Arg726His) rs28903092
NM_005732.4(RAD50):c.2288G>A (p.Arg763His) rs141989813
NM_005732.4(RAD50):c.3036+5G>A rs181016343
NM_005732.4(RAD50):c.980G>A (p.Arg327His) rs28903091
NM_007194.4(CHEK2):c.1232G>A (p.Trp411Ter) rs371418985
NM_007194.4(CHEK2):c.1283C>T (p.Ser428Phe) rs137853011
NM_007194.4(CHEK2):c.1312G>T (p.Asp438Tyr) rs200050883
NM_007194.4(CHEK2):c.1427C>T (p.Thr476Met) rs142763740
NM_007194.4(CHEK2):c.1568G>A (p.Arg523His) rs948928965
NM_007194.4(CHEK2):c.190G>A (p.Glu64Lys) rs141568342
NM_007194.4(CHEK2):c.231CCAAGAACCTGAGGA[1] (p.77DQEPE[1]) rs587780181
NM_007194.4(CHEK2):c.444+1G>A rs121908698
NM_007194.4(CHEK2):c.470T>C (p.Ile157Thr) rs17879961
NM_007194.4(CHEK2):c.539G>A (p.Arg180His) rs137853009
NM_007194.4(CHEK2):c.793-1G>A rs730881687
NM_007194.4(CHEK2):c.902del (p.Leu301fs) rs748005072
NM_007294.3(BRCA1):c.4484+1del rs397509181
NM_007294.3(BRCA1):c.4485-63C>G rs273900734
NM_007294.3(BRCA1):c.66dupA (p.Glu23Argfs) rs80357783
NM_007294.4(BRCA1):c.1067A>G (p.Gln356Arg) rs1799950
NM_007294.4(BRCA1):c.1961del (p.Lys654fs) rs80357522
NM_007294.4(BRCA1):c.2077G>A (p.Asp693Asn) rs4986850
NM_007294.4(BRCA1):c.2458A>G (p.Lys820Glu) rs56082113
NM_007294.4(BRCA1):c.2612C>T (p.Pro871Leu) rs799917
NM_007294.4(BRCA1):c.2662C>T (p.His888Tyr) rs80357480
NM_007294.4(BRCA1):c.2722G>T (p.Glu908Ter) rs80356978
NM_007294.4(BRCA1):c.3113A>G (p.Glu1038Gly) rs16941
NM_007294.4(BRCA1):c.3119G>A (p.Ser1040Asn) rs4986852
NM_007294.4(BRCA1):c.3548A>G (p.Lys1183Arg) rs16942
NM_007294.4(BRCA1):c.4524G>A (p.Trp1508Ter) rs80356885
NM_007294.4(BRCA1):c.4689C>G (p.Tyr1563Ter) rs80357433
NM_007294.4(BRCA1):c.4837A>G (p.Ser1613Gly) rs1799966
NM_007294.4(BRCA1):c.4956G>A (p.Met1652Ile) rs1799967
NM_007294.4(BRCA1):c.4986+6T>C rs80358086
NM_007294.4(BRCA1):c.4993G>A (p.Val1665Met) rs80357169
NM_007294.4(BRCA1):c.5035del (p.Asn1678_Leu1679insTer) rs80357896
NM_007294.4(BRCA1):c.5074G>C (p.Asp1692His) rs80187739
NM_007294.4(BRCA1):c.5096G>A (p.Arg1699Gln) rs41293459
NM_007294.4(BRCA1):c.5497G>A (p.Val1833Met) rs80357268
NM_007294.4(BRCA1):c.68_69del (p.Glu23fs) rs80357914
NM_007297.4(BRCA1):c.407-58del rs8176144
NM_012222.2(MUTYH):c.725G>A (p.Arg242His) rs140342925
NM_012222.2(MUTYH):c.875C>T (p.Pro292Leu) rs374950566
NM_020975.6(RET):c.1894G>A (p.Glu632Lys) rs377767407
NM_020975.6(RET):c.1946C>T (p.Ser649Leu) rs148935214
NM_020975.6(RET):c.2410G>A (p.Val804Met) rs79658334
NM_020975.6(RET):c.785T>C (p.Val262Ala) rs139790943
NM_024675.3(PALB2):c.2747_2748+4del rs786203892
NM_024675.3(PALB2):c.292A>G (p.Ile98Val) rs587782831
NM_024675.3(PALB2):c.3054G>C (p.Glu1018Asp) rs183489969
NM_024675.3(PALB2):c.3508C>T (p.His1170Tyr) rs200283306
NM_024675.3(PALB2):c.3549C>G (p.Tyr1183Ter) rs118203998
NM_024675.4(PALB2):c.1544A>G (p.Lys515Arg) rs515726072
NM_032043.2(BRIP1):c.10A>G (p.Met4Val) rs45512093
NM_032043.2(BRIP1):c.2947del (p.Ile983fs) rs774684620
NM_032043.3(BRIP1):c.139C>G (p.Pro47Ala) rs28903098
NM_032043.3(BRIP1):c.2220G>T (p.Gln740His) rs45589637
NM_032043.3(BRIP1):c.2440C>T (p.Arg814Cys) rs201869624
NM_058216.3(RAD51C):c.790G>A (p.Gly264Ser) rs147241704
NM_058216.3(RAD51C):c.904+5G>T rs587782702

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