ClinVar Miner

Variants from Gharavi Laboratory,Columbia University with conflicting interpretations

Location: United States — Primary collection method: research
Minimum review status of the submission from Gharavi Laboratory,Columbia University: Collection method of the submission from Gharavi Laboratory,Columbia University:
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 Variants with at least 2 submissions 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 kind of conflict
1329 112 7 59 14 8 48 119

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
Gharavi Laboratory,Columbia University pathogenic likely pathogenic uncertain significance likely benign benign drug response protective risk factor other
pathogenic 6 34 6 0 0 1 1 4 1
likely pathogenic 24 0 15 1 0 0 0 0 0
uncertain significance 10 13 1 8 1 2 0 1 0
likely benign 4 3 4 0 1 0 0 0 0
benign 0 0 1 0 0 0 0 0 0

Submitter to submitter summary #

Total submitters: 55
Download table as spreadsheet
Submitter Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
GeneDx 0 52 0 12 3 0 6 21
OMIM 0 26 0 5 0 6 8 19
Counsyl 0 24 0 9 1 0 9 19
Ambry Genetics 0 40 0 4 9 0 4 17
Invitae 0 68 0 4 4 0 6 14
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 0 17 0 4 3 0 6 13
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 20 0 4 3 0 3 10
ARUP Institute,ARUP Laboratories 0 9 3 7 0 0 0 10
Athena Diagnostics Inc 0 19 0 5 0 0 2 7
Integrated Genetics/Laboratory Corporation of America 0 22 0 3 2 0 2 7
GeneReviews 0 3 4 0 1 0 2 7
Fulgent Genetics 0 29 0 4 0 0 2 6
Genetic Services Laboratory, University of Chicago 0 3 0 2 1 0 1 4
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 10 0 2 0 0 2 4
Illumina Clinical Services Laboratory,Illumina 0 14 0 1 0 0 2 3
Laboratory of Genetics and Molecular Cardiology,University of São Paulo 0 1 0 3 0 0 0 3
SIB Swiss Institute of Bioinformatics 0 0 0 0 0 0 3 3
Center for Human Genetics, Inc 0 3 0 1 0 0 1 2
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic 0 3 0 2 0 0 0 2
Blueprint Genetics, 0 5 0 1 0 0 1 2
CSER_CC_NCGL; University of Washington Medical Center 0 5 0 1 1 0 0 2
Albrecht-Kossel-Institute,Medical University Rostock 0 0 0 0 0 2 1 2
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 4 0 0 0 0 2 2
Molecular Diagnostic Laboratory for Inherited Cardiovascular Disease,Montreal Heart Institute 0 0 0 2 0 0 0 2
Color 0 12 0 1 1 0 0 2
Database of Curated Mutations (DoCM) 0 1 0 0 0 0 2 2
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 5 0 2 0 0 0 2
Molecular Diagnostics Laboratory,M Health: University of Minnesota 0 1 0 2 0 0 0 2
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario 0 3 0 0 1 0 0 1
Biesecker Lab/Human Development Section,National Institutes of Health 0 1 1 0 0 0 0 1
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia 0 2 0 0 1 0 0 1
Sharing Clinical Reports Project (SCRP) 0 5 0 1 0 0 0 1
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre 0 0 0 1 0 0 0 1
Human Genome Sequencing Center Clinical Lab,Baylor College of Medicine 0 6 0 1 0 0 0 1
Institute of Human Genetics,Klinikum rechts der Isar 0 1 0 1 0 0 0 1
PharmGKB 0 0 0 0 0 1 0 1
Agnes Ginges Centre for Molecular Cardiology,Centenary Institute 0 1 0 1 0 0 0 1
Stanford Center for Inherited Cardiovascular Disease,Stanford University 0 5 0 1 0 0 0 1
Division of Human Genetics,Children's Hospital of Philadelphia 0 5 0 1 0 0 0 1
HudsonAlpha Institute for Biotechnology 0 5 0 1 0 0 0 1
Endocrine Unit 2,University Hospital of Pisa 0 0 0 0 0 0 1 1
Lupski Lab, Baylor-Hopkins CMG,Baylor College of Medicine 0 1 0 1 0 0 0 1
Center of Genomic medicine, Geneva,University Hospital of Geneva 0 5 0 1 0 0 0 1
Clinical Genetics, Erasmus University Medical Center 0 0 0 0 0 0 1 1
Bioscientia Institut fuer Medizinische Diagnostik GmbH,Sonic Healthcare 0 7 0 1 0 0 0 1
Translational Genomics Laboratory,University of Maryland School of Medicine 0 0 0 1 0 0 0 1
CeGaT Praxis fuer Humangenetik Tuebingen 0 2 0 0 0 0 1 1
Robarts Research Institute,Western University 0 0 0 1 0 0 0 1
Equipe Genetique des Anomalies du Developpement,Université de Bourgogne 0 2 0 1 0 0 0 1
Department of Pathology and Laboratory Medicine,Sinai Health System 0 6 0 0 0 0 1 1
Section on Medical Neuroendocrinolgy,National Institutes of Health 0 0 0 0 0 0 1 1
CHLA Center for Personalized Medicine,Children's Hospital, Los Angeles 0 1 0 1 0 0 0 1
Broad Institute Rare Disease Group,Broad Institute 0 3 0 1 0 0 0 1
Department of Genetics,Sultan Qaboos University Hospital, Oman 0 1 0 1 0 0 0 1
Clinical Genomics Lab,St. Jude Children's Research Hospital 0 0 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 119
Download table as spreadsheet
HGVS dbSNP
NM_000059.3(BRCA2):c.5946delT (p.Ser1982Argfs) rs80359550
NM_000059.3(BRCA2):c.7024C>T (p.Gln2342Ter) rs80358928
NM_000059.3(BRCA2):c.8488-1G>A rs397507404
NM_000059.3(BRCA2):c.9253dupA (p.Thr3085Asnfs) rs80359752
NM_000091.4(COL4A3):c.172G>A (p.Gly58Ser) rs184730597
NM_000091.4(COL4A3):c.1927G>A (p.Gly643Ser) rs778034451
NM_000091.4(COL4A3):c.2452G>A (p.Gly818Arg) rs868002181
NM_000091.4(COL4A3):c.3499G>A (p.Gly1167Arg) rs267606745
NM_000091.4(COL4A3):c.352G>A (p.Gly118Arg) rs1293137291
NM_000091.4(COL4A3):c.3546_3548dup (p.Gly1183_Asn1184insGly) rs1175052474
NM_000091.4(COL4A3):c.4981C>T (p.Arg1661Cys) rs201697532
NM_000092.4(COL4A4):c.2279dup (p.Asp761Argfs) rs1553643669
NM_000092.4(COL4A4):c.5045G>A (p.Arg1682Gln) rs368404711
NM_000135.3(FANCA):c.863_866dup (p.Ser290Valfs) rs1348367722
NM_000168.5(GLI3):c.2119C>T (p.Pro707Ser) rs121917716
NM_000169.2(GLA):c.1088G>A (p.Arg363His) rs111422676
NM_000169.2(GLA):c.1196G>C (p.Trp399Ser) rs782449839
NM_000169.2(GLA):c.352C>T (p.Arg118Cys) rs148158093
NM_000169.2(GLA):c.376A>G (p.Ser126Gly) rs149391489
NM_000169.2(GLA):c.926C>T (p.Ala309Val) rs869312155
NM_000179.2(MSH6):c.1483C>T (p.Arg495Ter) rs587779212
NM_000179.2(MSH6):c.3716_3717delTA (p.Ile1239Lysfs) rs1064794384
NM_000218.2(KCNQ1):c.1265delA (p.Lys422Serfs) rs397508083
NM_000218.2(KCNQ1):c.797T>C (p.Leu266Pro) rs199473460
NM_000256.3(MYBPC3):c.1505G>A (p.Arg502Gln) rs397515907
NM_000256.3(MYBPC3):c.3286G>T (p.Glu1096Ter) rs121909377
NM_000256.3(MYBPC3):c.3815-1G>A rs397516044
NM_000257.3(MYH7):c.1816G>A (p.Val606Met) rs121913627
NM_000257.3(MYH7):c.2389G>A (p.Ala797Thr) rs3218716
NM_000267.3(NF1):c.2339C>G (p.Thr780Arg) rs199474746
NM_000296.3(PKD1):c.12688C>T (p.Gln4230Ter)
NM_000296.3(PKD1):c.2180T>C (p.Leu727Pro)
NM_000296.3(PKD1):c.3496G>A (p.Gly1166Ser) rs573566419
NM_000296.3(PKD1):c.7546C>T (p.Arg2516Cys) rs797044902
NM_000296.3(PKD1):c.8218G>T (p.Gly2740Ter) rs1555451368
NM_000297.3(PKD2):c.2240+1G>A rs1553927783
NM_000297.3:c.2208_2213delAAACTT
NM_000339.2(SLC12A3):c.1928C>T (p.Pro643Leu) rs140012781
NM_000339.2(SLC12A3):c.2191G>A (p.Gly731Arg)
NM_000339.2(SLC12A3):c.2221G>A (p.Gly741Arg) rs138977195
NM_000339.2(SLC12A3):c.2891G>A (p.Arg964Gln) rs202114767
NM_000339.2(SLC12A3):c.363G>C (p.Glu121Asp) rs146632606
NM_000368.4(TSC1):c.397G>A (p.Val133Ile) rs118203381
NM_000388.3(CASR):c.1189G>A (p.Gly397Arg) rs1064794291
NM_000435.2(NOTCH3):c.2182C>T (p.Arg728Cys) rs1057519101
NM_000458.3(HNF1B):c.1006C>G (p.His336Asp)
NM_000495.4(COL4A5):c.1276G>A (p.Gly426Arg) rs104886111
NM_000495.4(COL4A5):c.1607G>A (p.Gly536Asp) rs104886125
NM_000495.4(COL4A5):c.1871G>A (p.Gly624Asp) rs104886142
NM_000495.4(COL4A5):c.2332G>A (p.Gly778Ser) rs104886174
NM_000495.4(COL4A5):c.2804G>A (p.Gly935Asp) rs104886195
NM_000495.4(COL4A5):c.2821G>T (p.Gly941Cys) rs104886196
NM_000495.4(COL4A5):c.2959_2976del18 (p.Asp989_Gly994del) rs104886374
NM_000495.4(COL4A5):c.3685G>A (p.Gly1229Ser)
NM_000495.4(COL4A5):c.5030G>A (p.Arg1677Gln) rs104886308
NM_000518.5(HBB):c.20A>T (p.Glu7Val) rs334
NM_000527.4(LDLR):c.2043C>A (p.Cys681Ter) rs121908031
NM_000540.2(RYR1):c.7300G>A (p.Gly2434Arg) rs121918593
NM_000546.5(TP53):c.833C>G (p.Pro278Arg) rs876659802
NM_000551.3(VHL):c.241C>T (p.Pro81Ser) rs104893829
NM_001009944.2(PKD1):c.10420C>T (p.Gln3474Ter) rs1064794206
NM_001009944.2(PKD1):c.7327G>T (p.Gly2443Ter)
NM_001009944.2(PKD1):c.9829C>T (p.Arg3277Cys) rs148812376
NM_001042492.2(NF1):c.4252A>G (p.Ile1418Val) rs369345045
NM_001177317.1(SLC34A3):c.575C>T (p.Ser192Leu) rs199690076
NM_001360.2(DHCR7):c.199G>A (p.Ala67Thr) rs143999854
NM_001360.2(DHCR7):c.452G>A (p.Trp151Ter) rs11555217
NM_001360.2(DHCR7):c.91C>T (p.Arg31Cys) rs367585401
NM_001360.2(DHCR7):c.964-1G>C rs138659167
NM_001456.3(FLNA):c.2609A>G (p.His870Arg)
NM_002834.4(PTPN11):c.922A>G (p.Asn308Asp) rs28933386
NM_002968.2(SALL1):c.466_477dup (p.Ser159_Gly160insSerSerSerSer)
NM_003000.2(SDHB):c.136C>T (p.Arg46Ter) rs74315370
NM_003000.2(SDHB):c.269G>A (p.Arg90Gln) rs570278423
NM_003001.3(SDHC):c.405+1G>T rs587776653
NM_003361.3(UMOD):c.317G>T (p.Cys106Phe) rs398123697
NM_004064.4(CDKN1B):c.-80C>T rs551236750
NM_004380.2(CREBBP):c.5837delC (p.Pro1946Hisfs) rs587783507
NM_004572.3(PKP2):c.1440_1444delTCCCA (p.Asn480Lysfs) rs775995156
NM_004572.3(PKP2):c.1613G>A (p.Trp538Ter) rs193922672
NM_004572.3(PKP2):c.837_838delCG (p.Val280Hisfs) rs772220644
NM_004621.5(TRPC6):c.428A>G (p.Asn143Ser) rs121434391
NM_004646.3(NPHS1):c.2335-1G>A rs150038620
NM_004985.4(KRAS):c.108A>G (p.Ile36Met) rs727503109
NM_005912.2(MC4R):c.466C>T (p.Gln156Ter) rs369841551
NM_006218.3(PIK3CA):c.1145G>A (p.Arg382Lys) rs587777794
NM_012203.1(GRHPR):c.598+1G>T rs111256477
NM_014625.3(NPHS2):c.451+2T>A rs786204708
NM_014625.3(NPHS2):c.538G>A (p.Val180Met) rs74315347
NM_014625.3(NPHS2):c.686G>A (p.Arg229Gln) rs61747728
NM_014625.3(NPHS2):c.851C>T (p.Ala284Val)
NM_014625.3(NPHS2):c.868G>A (p.Val290Met) rs200482683
NM_014625.3(NPHS2):c.871C>T (p.Arg291Trp) rs74315348
NM_015120.4(ALMS1):c.11086delA (p.Ser3696Alafs) rs1412574975
NM_015120.4(ALMS1):c.5179dup (p.Leu1727Profs) rs1553404020
NM_015120.4(ALMS1):c.8793dup (p.Glu2932Terfs) rs1553409778
NM_015559.3(SETBP1):c.2612T>C (p.Ile871Thr) rs267607038
NM_018848.3(MKKS):c.830T>C (p.Leu277Pro) rs74315398
NM_020732.3(ARID1B):c.1041_1043dup (p.Ala350_Gly351insAla)
NM_020975.4(RET):c.785T>C (p.Val262Ala) rs139790943
NM_022454.3(SOX17):c.532G>T (p.Gly178Cys) rs267607082
NM_022489.3(INF2):c.530G>A (p.Arg177His)
NM_024426.4(WT1):c.745C>T (p.Pro249Ser) rs2234584
NM_030665.4(RAI1):c.832_849del (p.Gln286_Gln291del)
NM_033360.3(KRAS):c.34G>A (p.Gly12Ser) rs121913530
NM_033380.2(COL4A5):c.3427G>A (p.Gly1143Ser) rs104886228
NM_134425.2(SLC26A1):c.554C>T (p.Thr185Met) rs139024319
NM_138694.3(PKHD1):c.1123C>T (p.Arg375Trp) rs376040501
NM_138694.3(PKHD1):c.2414C>T (p.Pro805Leu) rs199531851
NM_138694.3(PKHD1):c.4870C>T (p.Arg1624Trp) rs200391019
NM_138694.3(PKHD1):c.8317G>T (p.Val2773Leu) rs747322128
NM_138694.3(PKHD1):c.9530T>C (p.Ile3177Thr) rs200511261
NM_138959.2(VANGL1):c.821G>A (p.Arg274Gln) rs121918219
NM_139058.2(ARX):c.451_465del15 (p.Ala151_Ala155del)
NM_152618.3(BBS12):c.1151del (p.Ser384Thrfs) rs1553941404
NM_153240.4(NPHP3):c.2694-2_2694-1delAG rs751527253
NM_173689.6(CRB2):c.2400C>G (p.Asn800Lys) rs765676223
NM_175875.4(SIX5):c.472G>A (p.Ala158Thr) rs80356461
NM_198525.2(KIF7):c.3518-1G>C

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