ClinVar Miner

Variants from Clinical Genetics Karolinska University Hospital,Karolinska University Hospital with conflicting interpretations

Location: Sweden — Primary collection method: clinical testing
Minimum review status of the submission from Clinical Genetics Karolinska University Hospital,Karolinska University Hospital: Collection method of the submission from Clinical Genetics Karolinska University Hospital,Karolinska University Hospital:
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
479 274 0 107 0 19 52 162

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
Clinical Genetics Karolinska University Hospital,Karolinska University Hospital pathogenic likely pathogenic uncertain significance likely benign benign confers sensitivity drug response risk factor other
pathogenic 0 38 24 4 4 1 5 8 5
likely pathogenic 69 0 23 4 3 0 1 0 0

Submitter to submitter summary #

Total submitters: 41
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
GeneDx 0 249 0 51 0 0 8 59
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics 0 88 0 25 0 0 10 35
CeGaT Praxis fuer Humangenetik Tuebingen 0 75 0 27 0 0 8 35
Invitae 0 27 0 16 0 0 6 22
Quest Diagnostics Nichols Institute San Juan Capistrano 0 124 0 11 0 0 8 19
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 118 0 10 0 0 8 18
OMIM 0 23 0 0 0 13 1 14
Department of Pathology and Laboratory Medicine,Sinai Health System 0 18 0 1 0 0 13 14
Integrated Genetics/Laboratory Corporation of America 0 13 0 0 0 0 13 13
Athena Diagnostics Inc 0 26 0 9 0 0 1 10
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 54 0 9 0 0 0 9
PreventionGenetics, PreventionGenetics 0 15 0 3 0 0 5 8
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 9 0 1 0 0 6 7
Fulgent Genetics,Fulgent Genetics 0 17 0 6 0 0 0 6
Mayo Clinic Laboratories, Mayo Clinic 0 33 0 3 0 0 2 5
Illumina Clinical Services Laboratory,Illumina 0 9 0 3 0 0 3 5
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 18 0 3 0 0 2 5
Ambry Genetics 0 13 0 2 0 0 2 4
PharmGKB 0 0 0 0 0 4 0 4
University of Washington Center for Mendelian Genomics, University of Washington 0 0 0 1 0 1 0 2
Laboratory of Molecular Genetics (Pr. Bezieau's lab), CHU de Nantes 0 5 0 2 0 0 0 2
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 9 0 2 0 0 0 2
Greenwood Genetic Center Diagnostic Laboratories,Greenwood Genetic Center 0 0 0 1 0 0 0 1
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario 0 18 0 0 0 0 1 1
Biesecker Lab/Clinical Genomics Section,National Institutes of Health 0 0 0 0 0 0 1 1
Genetic Services Laboratory, University of Chicago 0 5 0 0 0 0 1 1
Molecular Diagnostics Lab,Nemours Alfred I. duPont Hospital for Children 0 2 0 0 0 0 1 1
Counsyl 0 0 0 1 0 0 0 1
Foulkes Cancer Genetics LDI, Lady Davis Institute for Medical Research 0 19 0 0 0 0 1 1
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre 0 1 0 1 0 0 0 1
Wellcome Centre for Mitochondrial Research,Newcastle University 0 1 0 1 0 0 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 4 0 0 0 0 1 1
Stanford Center for Inherited Cardiovascular Disease, Stanford University 0 1 0 1 0 0 0 1
NIHR Bioresource Rare Diseases, University of Cambridge 0 0 0 1 0 0 0 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 0 0 1 0 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
Rare Disease Group, Clinical Genetics,Karolinska Institutet 0 0 0 0 0 0 1 1
CIViC knowledgebase,Washington University School of Medicine 0 0 0 0 0 1 0 1
University of Washington Department of Laboratory Medicine, University of Washington 0 2 0 0 0 0 1 1
Genetics Laboratory, UDIAT-Centre Diagnòstic, Hospital Universitari Parc Tauli 0 2 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 162
Download table as spreadsheet
HGVS dbSNP
NM_000023.4(SGCA):c.739G>A (p.Val247Met) rs143570936
NM_000038.6(APC):c.2805C>A (p.Tyr935Ter) rs137854575
NM_000044.6(AR):c.1174C>T (p.Pro392Ser) rs201934623
NM_000059.4(BRCA2):c.1773_1776del (p.Ile591fs) rs80359304
NM_000059.4(BRCA2):c.5645C>A (p.Ser1882Ter) rs80358785
NM_000059.4(BRCA2):c.5946del (p.Ser1982fs) rs80359550
NM_000059.4(BRCA2):c.6275_6276del rs11571658
NM_000059.4(BRCA2):c.658_659del rs80359604
NM_000059.4(BRCA2):c.8351G>A (p.Arg2784Gln) rs80359076
NM_000059.4(BRCA2):c.9699_9702del rs80359775
NM_000061.3(BTK):c.1442G>C rs1057519825
NM_000070.3(CAPN3):c.1117T>C (p.Trp373Arg) rs775453643
NM_000083.3(CLCN1):c.2680C>T (p.Arg894Ter) rs55960271
NM_000090.4(COL3A1):c.3325C>T rs112371422
NM_000095.3(COMP):c.1153G>A (p.Asp385Asn)
NM_000127.3(EXT1):c.1018C>T rs119103290
NM_000138.5(FBN1):c.1583G>A rs794728170
NM_000138.5(FBN1):c.1948C>T rs193922185
NM_000138.5(FBN1):c.2645C>T rs794728195
NM_000138.5(FBN1):c.3712G>A rs794728208
NM_000138.5(FBN1):c.5959G>C (p.Gly1987Arg) rs727504642
NM_000138.5(FBN1):c.6453C>T rs794728251
NM_000138.5(FBN1):c.7379A>G (p.Lys2460Arg) rs144189837
NM_000138.5(FBN1):c.7754T>C (p.Ile2585Thr) rs727503054
NM_000231.2(SGCG):c.581T>C (p.Leu194Ser) rs547818652
NM_000232.5(SGCB):c.341C>T rs150518260
NM_000243.2(MEFV):c.1016C>T (p.Ser339Phe) rs104895157
NM_000243.2(MEFV):c.1437C>G (p.Phe479Leu) rs104895083
NM_000243.2(MEFV):c.1958G>A (p.Arg653His) rs104895085
NM_000243.2(MEFV):c.2084A>G rs104895094
NM_000243.2(MEFV):c.2230G>T rs61732874
NM_000243.2(MEFV):c.501G>C (p.Glu167Asp) rs104895079
NM_000243.3(MEFV):c.1105C>T rs11466023
NM_000243.3(MEFV):c.1223G>A rs11466024
NM_000243.3(MEFV):c.2076_2078del (p.Ile692del) rs104895093
NM_000243.3(MEFV):c.2282G>A (p.Arg761His) rs104895097
NM_000243.3(MEFV):c.329T>C rs11466018
NM_000243.3(MEFV):c.442G>C rs3743930
NM_000244.3(MEN1):c.65T>G (p.Leu22Arg) rs104894256
NM_000249.4(MLH1):c.793C>T (p.Arg265Cys) rs63751194
NM_000251.2(MSH2):c.2680dup (p.Met894fs) rs876658211
NM_000251.3(MSH2):c.1982_1985del rs587779120
NM_000251.3(MSH2):c.2038C>T (p.Arg680Ter) rs63749932
NM_000388.4(CASR):c.679C>T (p.Arg227Ter) rs1085307984
NM_000432.4(MYL2):c.401A>C (p.Glu134Ala) rs143139258
NM_000451.3(SHOX):c.-55C>T rs772910213
NM_000492.3(CFTR):c.1521_1523delCTT (p.Phe508delPhe) rs113993960
NM_000492.4(CFTR):c.1367T>C rs193922500
NM_000492.4(CFTR):c.1517T>C rs397508224
NM_000492.4(CFTR):c.2834C>T (p.Ser945Leu) rs397508442
NM_000492.4(CFTR):c.3297C>A rs747754623
NM_000492.4(CFTR):c.3454G>C (p.Asp1152His) rs75541969
NM_000492.4(CFTR):c.4333G>A (p.Asp1445Asn) rs148783445
NM_000500.9(CYP21A2):c.844G>T (p.Val282Leu) rs6471
NM_000500.9(CYP21A2):c.874G>A (p.Gly292Ser) rs201552310
NM_000518.4(HBB):c.25A>G (p.Lys9Glu) rs33926764
NM_000518.4(HBB):c.364G>C (p.Glu122Gln) rs33946267
NM_000518.4(HBB):c.404T>C (p.Val135Ala) rs33966761
NM_000518.5(HBB):c.20A>T (p.Glu7Val) rs334
NM_000518.5(HBB):c.79G>A (p.Glu27Lys) rs33950507
NM_000535.7(PMS2):c.137G>T (p.Ser46Ile) rs121434629
NM_000535.7(PMS2):c.2113G>A (p.Glu705Lys) rs267608161
NM_000540.3(RYR1):c.11314C>T rs763112609
NM_000540.3(RYR1):c.14833C>T rs1432807966
NM_000540.3(RYR1):c.325C>T rs118192173
NM_000540.3(RYR1):c.3523G>A rs769744438
NM_000540.3(RYR1):c.7093G>A rs761224660
NM_000540.3(RYR1):c.7373G>A (p.Arg2458His) rs121918594
NM_000546.5(TP53):c.751A>C (p.Ile251Leu) rs730882007
NM_000546.6(TP53):c.638G>A (p.Arg213Gln) rs587778720
NM_000546.6(TP53):c.733G>A (p.Gly245Ser) rs28934575
NM_000546.6(TP53):c.743G>A (p.Arg248Gln) rs11540652
NM_000551.4(VHL):c.449del rs794727253
NM_000551.4(VHL):c.501_502insTTGTCCGT rs398123483
NM_000551.4(VHL):c.598C>T (p.Arg200Trp) rs28940298
NM_000827.4(GRIA1):c.1906G>A (p.Ala636Thr) rs587776937
NM_000834.4(GRIN2B):c.2539C>T (p.Arg847Ter) rs879253931
NM_000902.4(MME):c.467del (p.Pro156fs) rs749320057
NM_001015880.2(PAPSS2):c.712C>T (p.Arg238Ter)
NM_001015880.2(PAPSS2):c.809G>A (p.Gly270Asp) rs138943074
NM_001035.3(RYR2):c.1259G>A (p.Arg420Gln) rs794728721
NM_001048174.2(MUTYH):c.1103G>A (p.Gly368Asp) rs36053993
NM_001048174.2(MUTYH):c.637C>T (p.Arg213Trp) rs34126013
NM_001101.5(ACTB):c.1043C>T (p.Ser348Leu) rs886041309
NM_001110792.2(MECP2):c.433C>T (p.Arg145Cys) rs28934904
NM_001111125.3(IQSEC2):c.2984G>A (p.Arg995Gln) rs886041767
NM_001114748.2(TMEM240):c.509C>T (p.Pro170Leu) rs606231451
NM_001130987.2(DYSF):c.2864+1G>A rs199954546
NM_001143992.2(WRAP53):c.1192C>T (p.Arg398Trp) rs281865548
NM_001172509.2(SATB2):c.1165C>T (p.Arg389Cys)
NM_001205293.3(CACNA1E):c.2104G>A (p.Ala702Thr) rs12131800
NM_001267550.2(TTN):c.104399del (p.Arg34800fs) rs747662439
NM_001282386.1(IDH1):c.394C>T (p.Arg132Cys) rs121913499
NM_001349253.2(SCN11A):c.3473T>C (p.Leu1158Pro) rs141686175
NM_001374258.1(BRAF):c.1919T>A (p.Val640Glu) rs113488022
NM_001374828.1(ARID1B):c.5763_5766del (p.Phe1921fs) rs1554237269
NM_001376.5(DYNC1H1):c.917A>G (p.His306Arg) rs387906738
NM_001377.3(DYNC2H1):c.12581C>T (p.Ser4194Phe) rs886042136
NM_001377.3(DYNC2H1):c.1540C>T (p.Arg514Ter) rs1565317399
NM_001377.3(DYNC2H1):c.9044A>G (p.Asp3015Gly) rs137853027
NM_001415.4(EIF2S3):c.1394_1397del (p.Ile465fs) rs886040857
NM_001605.3(AARS1):c.986G>A (p.Arg329His) rs267606621
NM_001844.5(COL2A1):c.2059G>A (p.Gly687Ser)
NM_001844.5(COL2A1):c.2862C>T (p.Gly954=)
NM_001852.4(COL9A2):c.186G>A (p.Pro62=) rs1085307973
NM_002381.5(MATN3):c.359C>T (p.Thr120Met) rs397515546
NM_002693.3(POLG):c.2243G>C rs113994097
NM_003119.2(SPG7):c.1529C>T rs61755320
NM_003165.6(STXBP1):c.875G>A rs796053361
NM_003242.6(TGFBR2):c.569G>A (p.Arg190His) rs780542125
NM_003482.4(KMT2D):c.15088C>T rs1555185875
NM_004004.6(GJB2):c.101T>C (p.Met34Thr) rs35887622
NM_004004.6(GJB2):c.109G>A (p.Val37Ile) rs72474224
NM_004168.4(SDHA):c.223C>T (p.Arg75Ter) rs781764920
NM_004329.3(BMPR1A):c.1330T>C rs774061725
NM_004369.4(COL6A3):c.7447A>G rs139260335
NM_004369.4(COL6A3):c.761del rs780921503
NM_005199.5(CHRNG):c.256C>T (p.Arg86Cys) rs777219451
NM_005359.6(SMAD4):c.1486C>T (p.Arg496Cys) rs397518413
NM_005609.4(PYGM):c.1726C>T (p.Arg576Ter) rs119103255
NM_006086.4(TUBB3):c.785G>A (p.Arg262His) rs864321716
NM_006087.4(TUBB4A):c.745G>A (p.Asp249Asn) rs483352809
NM_006118.4(HAX1):c.91del rs764082747
NM_006796.3(AFG3L2):c.2105G>A rs151344523
NM_006912.6(RIT1):c.270G>C (p.Met90Ile) rs483352822
NM_007194.4(CHEK2):c.1100del (p.Thr367fs) rs555607708
NM_007194.4(CHEK2):c.1427C>T (p.Thr476Met) rs142763740
NM_007194.4(CHEK2):c.629_632del (p.Ser210fs) rs756131136
NM_007254.4(PNKP):c.1385G>C (p.Arg462Pro) rs376854895
NM_007294.3(BRCA1):c.5266dupC (p.Gln1756Profs) rs80357906
NM_007294.4(BRCA1):c.122A>G (p.His41Arg) rs80357276
NM_007294.4(BRCA1):c.1881_1884del (p.Ser628fs) rs80357567
NM_007294.4(BRCA1):c.4675G>A (p.Glu1559Lys) rs80356988
NM_007294.4(BRCA1):c.4689C>G (p.Tyr1563Ter) rs80357433
NM_007294.4(BRCA1):c.5096G>A (p.Arg1699Gln) rs41293459
NM_007294.4(BRCA1):c.68_69del (p.Glu23fs) rs80357914
NM_012222.2(MUTYH):c.875C>T (p.Pro292Leu) rs374950566
NM_013275.6(ANKRD11):c.3770_3771del (p.Lys1257fs) rs886039477
NM_014140.4(SMARCAL1):c.2459G>A (p.Arg820His) rs200666300
NM_014363.6(SACS):c.7394C>T (p.Ser2465Leu)
NM_014363.6(SACS):c.8393C>A (p.Pro2798Gln) rs140551762
NM_018075.5(ANO10):c.132dup (p.Asp45fs) rs540331226
NM_018418.5(SPATA7):c.288T>A (p.Cys96Ter) rs767745816
NM_018480.5(TMEM126B):c.635G>T (p.Gly212Val) rs141542003
NM_018972.4(GDAP1):c.368A>G (p.His123Arg) rs397515442
NM_019040.5(ELP4):c.*6411T>A rs121907922
NM_020732.3(ARID1B):c.5267_5270del (p.Glu1756fs) rs1583513256
NM_020987.5(ANK3):c.2902G>C (p.Asp968His) rs730882195
NM_021070.4(LTBP3):c.132del (p.Pro45fs) rs1286042594
NM_024301.5(FKRP):c.826C>A (p.Leu276Ile) rs28937900
NM_024577.4(SH3TC2):c.2860C>T (p.Arg954Ter) rs80338933
NM_024675.3(PALB2):c.1592del (p.Leu531fs) rs180177102
NM_024675.3(PALB2):c.2368C>T (p.Gln790Ter) rs886039480
NM_024675.4(PALB2):c.172_175del (p.Gln60fs) rs180177143
NM_030632.3(ASXL3):c.3106C>T (p.Arg1036Ter)
NM_058216.3(RAD51C):c.774del (p.Thr259fs) rs754367349
NM_133433.4(NIPBL):c.6893G>A (p.Arg2298His) rs587784024
NM_152743.4(BRAT1):c.294dup (p.Leu99fs) rs776913277
NM_170707.4(LMNA):c.1357C>T (p.Arg453Trp) rs58932704
NM_170707.4(LMNA):c.746G>A (p.Arg249Gln) rs59332535
NM_177559.3(CSNK2A1):c.593A>G (p.Lys198Arg) rs869312840
NM_183075.3(CYP2U1):c.947A>T (p.Asp316Val) rs397514513

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