ClinVar Miner

Variants from Yale Center for Mendelian Genomics, Yale University with conflicting interpretations

Location: United States  Primary collection method: literature only
Minimum review status of the submission from Yale Center for Mendelian Genomics, Yale University: Collection method of the submission from Yale Center for Mendelian Genomics, Yale University:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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
642 66 0 128 1 2 35 157

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
Yale Center for Mendelian Genomics, Yale University pathogenic likely pathogenic uncertain significance likely benign benign drug response
pathogenic 0 24 4 0 0 0
likely pathogenic 106 0 29 3 2 1
uncertain significance 1 1 0 1 0 0
association 0 0 1 0 0 0

Submitter to submitter summary #

Total submitters: 75
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
Labcorp Genetics (formerly Invitae), Labcorp 0 16 0 56 1 1 9 67
GeneDx 0 19 0 25 0 0 7 32
Natera, Inc. 0 11 0 19 0 0 2 21
Ambry Genetics 0 6 0 20 0 0 0 20
CeGaT Center for Human Genetics Tuebingen 0 7 0 7 0 0 3 10
OMIM 0 22 0 10 0 0 0 10
Fulgent Genetics, Fulgent Genetics 0 7 0 6 0 0 3 9
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 6 0 6 0 0 0 6
PreventionGenetics, part of Exact Sciences 0 4 0 5 0 0 1 6
Baylor Genetics 0 7 0 3 0 0 2 5
Genetic Services Laboratory, University of Chicago 0 3 0 2 0 0 3 5
Sydney Genome Diagnostics, Children's Hospital Westmead 0 1 0 5 0 0 0 5
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill 0 3 0 4 0 0 1 5
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 1 0 2 0 0 2 4
Counsyl 0 1 0 3 0 0 1 4
Dasa 0 0 0 4 0 0 0 4
Department of Pathology and Laboratory Medicine, Sinai Health System 0 3 0 1 0 0 3 4
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 1 0 4 0 0 0 4
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 1 0 3 0 0 1 4
Revvity Omics, Revvity 0 5 0 2 0 0 2 4
CENTOGENE GmbH and LLC - Guiding Precision Medicine 0 2 0 3 0 0 0 3
Cambridge Genomics Laboratory, East Genomic Laboratory Hub, NHS Genomic Medicine Service 0 1 0 3 0 0 0 3
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 0 2 0 0 1 3
Mayo Clinic Laboratories, Mayo Clinic 0 0 0 3 0 0 0 3
3billion 0 7 0 1 0 0 1 2
Athena Diagnostics 0 0 0 2 0 0 0 2
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 0 1 0 2 0 0 0 2
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 2 0 0 0 2
Dubai Health Genomic Medicine Center, Dubai Health 0 1 0 2 0 0 0 2
Eurofins Ntd Llc (ga) 0 4 0 2 0 0 0 2
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 0 0 2 0 0 0 2
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia 0 0 0 2 0 0 0 2
Genomic Medicine Center of Excellence, King Faisal Specialist Hospital and Research Centre 0 4 0 2 0 0 0 2
Illumina Laboratory Services, Illumina 0 2 0 1 0 0 1 2
Institute Of Molecular Biology And Genetics, Federal Almazov National Medical Research Centre 0 0 0 2 0 0 0 2
Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital 0 0 0 2 0 0 0 2
Yale Center for Mendelian Genomics, Yale University 859 4 0 2 0 0 0 2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 2 0 1 0 0 0 1
All of Us Research Program, National Institutes of Health 0 0 0 0 0 0 1 1
Blueprint Genetics 0 0 0 0 0 0 1 1
Centre for Genomic and Experimental Medicine, University of Edinburgh 0 0 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 0 1 0 0 0 1
Clinical Genetics Laboratory, Skane University Hospital Lund 0 1 0 1 0 0 0 1
Department of Genetics, Sultan Qaboos University Hospital 0 1 0 1 0 0 0 1
Department of Neurology and Geriatrics, Kagoshima University Graduate School of Medical and Dental Sciences 0 0 0 1 0 0 0 1
Department of Pediatrics, Gifu University 0 0 0 1 0 0 0 1
GenePathDx, GenePath diagnostics 0 0 0 1 0 0 0 1
Genetics Laboratory, Great Ormond Street Hospital NHS Foundation Trust, North Thames Genomic Laboratory Hub 0 1 0 1 0 0 0 1
Genetics and Genomic Medicine Centre, NeuroGen Healthcare, NeuroGen Healthcare 0 0 0 1 0 0 0 1
Genomenon, Inc, Genomenon, Inc 0 1 0 1 0 0 0 1
Génétique des Maladies du Développement, Hospices Civils de Lyon 0 0 0 1 0 0 0 1
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden 0 0 0 1 0 0 0 1
Institute of Human Genetics Munich, TUM University Hospital 0 2 0 1 0 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 1 0 0 0 0 1 1
Institute of Medical and Molecular Genetics, Hospital Universitario La Paz 0 0 0 1 0 0 0 1
Juno Genomics, Hangzhou Juno Genomics, Inc 0 2 0 1 0 0 0 1
Kariminejad - Najmabadi Pathology & Genetics Center 0 0 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 3 0 1 0 0 0 1
MGZ Medical Genetics Center 0 1 0 1 0 0 0 1
Mendelics 0 1 0 1 0 0 0 1
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals 0 0 0 1 0 0 0 1
Molecular Genetics, Royal Melbourne Hospital 0 1 0 1 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 4 0 0 0 0 1 1
Neurogenetics Laboratory - MEYER, AOU Meyer 0 0 0 1 0 0 0 1
New York Genome Center 0 1 0 1 0 0 0 1
Oxford Haemato-Oncology Service, Oxford University Hospitals NHS Foundation Trust 0 0 0 0 0 1 0 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1
Service de Génétique Moléculaire, Hôpital Robert Debré 0 0 0 1 0 0 0 1
Solve-RD Consortium 0 0 0 1 0 0 0 1
UCLA Clinical Genomics Center, UCLA 0 0 0 1 0 0 0 1
University Health Network, Princess Margaret Cancer Centre 0 0 0 1 0 0 0 1
University of Washington Center for Mendelian Genomics, University of Washington 0 0 0 1 0 0 0 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 8 0 1 0 0 0 1
Wangler Lab, Baylor College of Medicine 0 0 0 0 0 0 1 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 2 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 157
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000098.3(CPT2):c.338C>T (p.Ser113Leu) rs74315294 0.00131
NM_213607.3(DNAAF19):c.461A>C (p.His154Pro) rs145457535 0.00123
NM_000030.3(AGXT):c.508G>A (p.Gly170Arg) rs121908529 0.00067
NM_002470.4(MYH3):c.875C>G (p.Ser292Cys) rs139480342 0.00064
NM_014625.4(NPHS2):c.413G>A (p.Arg138Gln) rs74315342 0.00054
NM_138694.4(PKHD1):c.107C>T (p.Thr36Met) rs137852944 0.00048
NM_181426.2(CCDC39):c.1167+1261A>G rs577069249 0.00048
NM_012144.4(DNAI1):c.48+2dup rs397515363 0.00045
NM_032551.5(KISS1R):c.890G>T (p.Arg297Leu) rs144670595 0.00043
NM_017950.4(CCDC40):c.248del (p.Ala83fs) rs397515393 0.00029
NM_002386.4(MC1R):c.515G>T (p.Ser172Ile) rs376670171 0.00023
NM_004722.4(AP4M1):c.1100G>A (p.Arg367Gln) rs139861201 0.00021
NM_001369.3(DNAH5):c.10815del (p.Pro3606fs) rs397515540 0.00019
NM_001369.3(DNAH5):c.7502G>C (p.Arg2501Pro) rs78853309 0.00011
NM_024753.5(TTC21B):c.626C>T (p.Pro209Leu) rs140511594 0.00011
NM_000341.4(SLC3A1):c.1799G>A (p.Gly600Glu) rs141944551 0.00009
NM_001128126.3(AP4S1):c.289C>T (p.Arg97Ter) rs200440467 0.00009
NM_001253852.3(AP4B1):c.577G>A (p.Val193Ile) rs376478015 0.00009
NM_181426.2(CCDC39):c.610-2A>G rs756235547 0.00009
NM_004722.4(AP4M1):c.920G>C (p.Gly307Ala) rs542768500 0.00008
NM_014714.4(IFT140):c.634G>A (p.Gly212Arg) rs201188361 0.00008
NM_001127898.4(CLCN5):c.925C>T (p.Arg309Cys) rs782056386 0.00006
NM_001277115.2(DNAH11):c.6244C>T (p.Arg2082Ter) rs200693106 0.00006
NM_001369.3(DNAH5):c.13486C>T (p.Arg4496Ter) rs200901816 0.00006
NM_033380.3(COL4A5):c.899C>T (p.Pro300Leu) rs375377003 0.00006
NM_000486.6(AQP2):c.782C>T (p.Ser261Leu) rs376000406 0.00005
NM_001369.3(DNAH5):c.6249G>A (p.Met2083Ile) rs753614861 0.00005
NM_001128126.3(AP4S1):c.43C>T (p.Arg15Ter) rs754944359 0.00004
NM_001253852.3(AP4B1):c.1557T>A (p.Tyr519Ter) rs529495094 0.00004
NM_001845.6(COL4A1):c.2351C>T (p.Pro784Leu) rs372750171 0.00004
NM_004722.4(AP4M1):c.1012C>T (p.Arg338Ter) rs146262009 0.00004
NM_004722.4(AP4M1):c.916C>T (p.Arg306Ter) rs369459721 0.00004
NM_001277115.2(DNAH11):c.6130C>T (p.Arg2044Ter) rs767595964 0.00003
NM_001369.3(DNAH5):c.3905del (p.Leu1302fs) rs754698253 0.00003
NM_001369.3(DNAH5):c.5710-2A>G rs548521732 0.00003
NM_130810.4(DNAAF4):c.988C>T (p.Arg330Trp) rs201173498 0.00003
NM_000030.3(AGXT):c.245G>A (p.Gly82Glu) rs121908522 0.00002
NM_001128126.3(AP4S1):c.295-3C>A rs185246578 0.00002
NM_001142966.3(GREB1L):c.5651G>A (p.Arg1884His) rs1372640211 0.00002
NM_001253852.3(AP4B1):c.617G>A (p.Arg206Gln) rs149705131 0.00002
NM_001369.3(DNAH5):c.12617G>A (p.Trp4206Ter) rs372118787 0.00002
NM_001369.3(DNAH5):c.1432C>T (p.Arg478Ter) rs747900131 0.00002
NM_014967.5(FAN1):c.2774_2775del (p.Leu925fs) rs765970053 0.00002
NM_000019.4(ACAT1):c.1160T>C (p.Ile387Thr) rs748303093 0.00001
NM_000204.5(CFI):c.1A>G (p.Met1Val) rs770655669 0.00001
NM_001113378.2(FANCI):c.217A>T (p.Ile73Phe) rs138808921 0.00001
NM_001128126.3(AP4S1):c.294+1G>T rs886041127 0.00001
NM_001253852.3(AP4B1):c.1115-2A>G rs1210851910 0.00001
NM_001253852.3(AP4B1):c.1216C>T (p.Arg406Ter) rs776976178 0.00001
NM_001253852.3(AP4B1):c.304C>T (p.Arg102Ter) rs777248758 0.00001
NM_001364171.2(ODAD1):c.448C>T (p.Arg150Ter) rs752269093 0.00001
NM_001369.3(DNAH5):c.12009G>A (p.Trp4003Ter) rs2126564103 0.00001
NM_001369.3(DNAH5):c.12107G>A (p.Trp4036Ter) rs760104757 0.00001
NM_001369.3(DNAH5):c.4117-2A>G rs1467301649 0.00001
NM_001369.3(DNAH5):c.4348C>T (p.Gln1450Ter) rs771663107 0.00001
NM_001369.3(DNAH5):c.5983C>T (p.Arg1995Ter) rs773711154 0.00001
NM_001369.3(DNAH5):c.6335_6336insT (p.Gln2112fs) rs779506456 0.00001
NM_001369.3(DNAH5):c.7096C>T (p.Arg2366Trp) rs868151020 0.00001
NM_001369.3(DNAH5):c.7915C>T (p.Arg2639Ter) rs375053470 0.00001
NM_001369.3(DNAH5):c.8010+3A>G rs748171209 0.00001
NM_001369.3(DNAH5):c.832del (p.Ala278fs) rs727502977 0.00001
NM_001369.3(DNAH5):c.8383C>T (p.Arg2795Ter) rs560398270 0.00001
NM_001369.3(DNAH5):c.9637del (p.Ala3213fs) rs1305797678 0.00001
NM_001377.3(DYNC2H1):c.9638A>G (p.Tyr3213Cys) rs923729821 0.00001
NM_003285.3(TNR):c.3574C>T (p.Arg1192Trp) rs1571308125 0.00001
NM_004525.3(LRP2):c.2639+1G>A rs746752313 0.00001
NM_004646.4(NPHS1):c.3478C>T (p.Arg1160Ter) rs267606919 0.00001
NM_004722.4(AP4M1):c.1137+1G>T rs770705832 0.00001
NM_004722.4(AP4M1):c.1321C>T (p.Arg441Ter) rs886041126 0.00001
NM_004722.4(AP4M1):c.955T>C (p.Cys319Arg) rs754498075 0.00001
NM_004985.5(KRAS):c.35G>A (p.Gly12Asp) rs121913529 0.00001
NM_030954.4(RNF170):c.396+3A>G rs1159600703 0.00001
NM_032756.4(HPDL):c.149G>A (p.Gly50Asp) rs1391712320 0.00001
NM_138694.4(PKHD1):c.5221G>A (p.Val1741Met) rs137852946 0.00001
NM_181426.2(CCDC39):c.1356C>A (p.Tyr452Ter) rs375839864 0.00001
NM_181426.2(CCDC39):c.1665+1G>A rs753580394 0.00001
NM_213607.3(DNAAF19):c.144-1G>A rs747091524 0.00001
NM_000030.3(AGXT):c.473C>T (p.Ser158Leu) rs180177225
NM_000038.6(APC):c.4127_4128del (p.Tyr1376fs) rs1554085533
NM_000069.3(CACNA1S):c.1678G>T (p.Ala560Ser) rs763794604
NM_000334.4(SCN4A):c.4343G>A (p.Arg1448His) rs121908545
NM_000458.4(HNF1B):c.1024T>C (p.Ser342Pro) rs1282596664
NM_000458.4(HNF1B):c.494G>A (p.Arg165His) rs121918675
NM_000458.4(HNF1B):c.857T>C (p.Leu286Pro) rs2147545592
NM_001040142.2(SCN2A):c.5645G>A (p.Arg1882Gln) rs794727444
NM_001099922.3(ALG13):c.2915G>T (p.Gly972Val) rs2148407095
NM_001128126.3(AP4S1):c.124C>T (p.Arg42Ter) rs387906970
NM_001174147.2(LMX1B):c.737G>A (p.Arg246Gln) rs1191455921
NM_001253852.3(AP4B1):c.114-2A>C rs879255396
NM_001253852.3(AP4B1):c.1160_1161del (p.Thr387fs) rs587779388
NM_001253852.3(AP4B1):c.311_312delinsC (p.Leu104fs) rs797045244
NM_001253852.3(AP4B1):c.530_531insA (p.Asn178fs) rs879255397
NM_001253852.3(AP4B1):c.664del (p.Leu222fs) rs1571563769
NM_001366385.1(CARD14):c.467T>C (p.Leu156Pro) rs387907240
NM_001369.3(DNAH5):c.13760A>G (p.Tyr4587Cys) rs1320036244
NM_001369.3(DNAH5):c.2772del (p.Thr924_Leu925insTer) rs1554090622
NM_001369.3(DNAH5):c.3037_3040del (p.Val1014fs) rs1580731750
NM_001369.3(DNAH5):c.3598+2T>C rs981267400
NM_001369.3(DNAH5):c.5147G>C (p.Arg1716Pro) rs74799487
NM_001369.3(DNAH5):c.5588del (p.Phe1863fs) rs2151860332
NM_001369.3(DNAH5):c.6037C>T (p.Arg2013Ter) rs1273352530
NM_001369.3(DNAH5):c.6932_6935del (p.Asp2311fs) rs1554062097
NM_001369.3(DNAH5):c.6988+2T>C rs2151806960
NM_001369.3(DNAH5):c.8147T>C (p.Ile2716Thr) rs746501395
NM_001369.3(DNAH5):c.9799C>T (p.Gln3267Ter) rs923842695
NM_001371986.1(UNC80):c.8256+2T>G rs1575179679
NM_001376.5(DYNC1H1):c.10030C>T (p.Arg3344Trp) rs2048519381
NM_001395656.1(ROBO2):c.292G>T (p.Gly98Trp) rs2071367863
NM_001904.4(CTNNB1):c.160G>T (p.Glu54Ter) rs2078133150
NM_002067.5(GNA11):c.547C>T (p.Arg183Cys) rs1555702147
NM_002524.5(NRAS):c.181C>A (p.Gln61Lys) rs121913254
NM_003285.3(TNR):c.2713C>T (p.Arg905Ter) rs1287757170
NM_003285.3(TNR):c.2744_2745del (p.Val915fs) rs1571339601
NM_003361.4(UMOD):c.317G>A (p.Cys106Tyr) rs398123697
NM_003611.3(OFD1):c.2789_2793del (p.Ile930fs) rs797044945
NM_003611.3(OFD1):c.2862dup (p.Glu955Ter) rs2147086302
NM_004004.6(GJB2):c.35del (p.Gly12fs) rs80338939
NM_004040.4(RHOB):c.218C>T (p.Ser73Phe) rs550750241
NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) rs113488022
NM_004525.3(LRP2):c.13139dup (p.Cys4381fs) rs80338754
NM_004525.3(LRP2):c.7564T>C (p.Tyr2522His) rs80338747
NM_004621.6(TRPC6):c.523C>T (p.Arg175Trp) rs869025541
NM_004646.4(NPHS1):c.139del (p.Ala47fs) rs386833882
NM_004646.4(NPHS1):c.3250dup (p.Val1084fs) rs386833935
NM_004722.4(AP4M1):c.218dup (p.Asn73fs) rs1321353475
NM_004722.4(AP4M1):c.330C>G (p.Tyr110Ter) rs752598529
NM_004722.4(AP4M1):c.544-8_544-3del rs1064794383
NM_004722.4(AP4M1):c.694dup (p.Glu232fs) rs1584514057
NM_004722.4(AP4M1):c.952C>T (p.Arg318Ter) rs730882249
NM_005027.4(PIK3R2):c.1669G>T (p.Asp557Tyr) rs372272045
NM_005343.4(HRAS):c.37G>C (p.Gly13Arg) rs104894228
NM_006218.4(PIK3CA):c.2740G>A (p.Gly914Arg) rs587776932
NM_006939.4(SOS2):c.791C>A (p.Thr264Lys) rs1595001710
NM_007317.3(KIF22):c.443C>T (p.Pro148Leu) rs193922921
NM_007325.5(GRIA3):c.1888G>A (p.Gly630Arg) rs587777361
NM_012144.4(DNAI1):c.1463del (p.Pro488fs) rs2132081705
NM_012144.4(DNAI1):c.1612G>A (p.Ala538Thr) rs368248592
NM_014967.5(FAN1):c.2590C>T (p.Gln864Ter) rs767651793
NM_016580.4(PCDH12):c.2765_2766del (p.Pro922fs) rs1596646165
NM_017950.4(CCDC40):c.3358C>T (p.Gln1120Ter) rs2143789412
NM_021147.5(CCNO):c.248_252dup (p.Gly85fs) rs587777498
NM_021147.5(CCNO):c.258_262dup (p.Gln88fs) rs587777499
NM_032756.4(HPDL):c.569C>T (p.Pro190Leu) rs368625962
NM_032756.4(HPDL):c.816_817del (p.Val273fs) rs2149082140
NM_052867.4(NALCN):c.537del (p.Ile178_Trp179insTer) rs1594759803
NM_138694.4(PKHD1):c.10452dup (p.Leu3485fs) rs771623148
NM_138694.4(PKHD1):c.11452G>T (p.Val3818Phe) rs1385935333
NM_177400.3(NKX6-2):c.121A>T (p.Lys41Ter) rs1131692047
NM_177400.3(NKX6-2):c.196del (p.Arg66fs) rs1554961118
NM_177400.3(NKX6-2):c.487C>G (p.Leu163Val) rs1131692048
NM_177400.3(NKX6-2):c.599G>A (p.Arg200Gln) rs1008088032
NM_177400.3(NKX6-2):c.608G>A (p.Trp203Ter) rs1565019928
NM_178452.6(DNAAF1):c.778C>T (p.Gln260Ter) rs2087613070
NM_181426.2(CCDC39):c.1045del (p.Thr349fs) rs747980515
NM_181426.2(CCDC39):c.1484_1485del (p.Lys495fs) rs751239231
NM_181426.2(CCDC39):c.436del (p.Trp146fs) rs2108429507
NM_181426.2(CCDC39):c.830_831del (p.Thr277fs) rs773801386

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