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 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
1356 100 1 45 16 7 44 104

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 risk factor other
pathogenic 0 27 8 1 0 1 3 1
likely pathogenic 17 0 17 1 0 0 0 0
uncertain significance 8 8 1 9 3 2 0 0
likely benign 1 1 4 0 1 0 0 0

Submitter to submitter summary #

Total submitters: 25
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
Invitae 0 25 0 16 4 0 17 37
GeneDx 0 55 0 12 3 0 6 21
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics 0 17 0 4 3 0 6 13
Athena Diagnostics Inc 0 26 0 6 0 0 3 9
Ambry Genetics 0 11 0 1 6 0 1 8
CeGaT Praxis fuer Humangenetik Tuebingen 0 16 0 3 2 0 3 8
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 8 0 0 4 0 1 5
OMIM 0 0 0 0 0 4 0 4
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 11 0 2 0 0 2 4
Integrated Genetics/Laboratory Corporation of America 0 8 0 0 2 0 2 4
Blueprint Genetics 0 14 0 2 1 0 0 3
Department of Pathology and Laboratory Medicine,Sinai Health System 0 6 0 0 1 0 2 3
Molecular Genetics of Inherited Kidney Disorders Laboratory,Garvan Institute of Medical Research 0 2 0 2 0 0 1 3
Mayo Clinic Laboratories, Mayo Clinic 0 3 0 2 0 0 0 2
Illumina Clinical Services Laboratory,Illumina 0 4 0 0 1 0 1 2
Albrecht-Kossel-Institute,Medical University Rostock 0 0 0 0 0 2 0 2
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 4 0 0 0 0 2 2
Centre for Mendelian Genomics,University Medical Centre Ljubljana 0 1 0 2 0 0 0 2
Biesecker Lab/Clinical Genomics Section,National Institutes of Health 0 0 1 0 0 0 0 1
Genetic Services Laboratory, University of Chicago 0 0 0 0 1 0 0 1
Quest Diagnostics Nichols Institute San Juan Capistrano 0 13 0 1 0 0 0 1
PharmGKB 0 0 0 0 0 1 0 1
Stanford Center for Inherited Cardiovascular Disease, Stanford University 0 5 0 1 0 0 0 1
Sharon lab,Hadassah-Hebrew University Medical Center 0 1 0 1 0 0 0 1
Ocular Genomics Institute, Massachusetts Eye and Ear 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 104
Download table as spreadsheet
HGVS dbSNP
NM_000059.3(BRCA2):c.9593_9594del (p.Cys3198fs) rs1566260198
NM_000059.4(BRCA2):c.5946del (p.Ser1982fs) rs80359550
NM_000059.4(BRCA2):c.8488-1G>A rs397507404
NM_000091.4(COL4A3):c.1096G>A (p.Gly366Arg) rs539765620
NM_000091.4(COL4A3):c.1201G>A (p.Gly401Arg) rs1559878824
NM_000091.4(COL4A3):c.1354G>A (p.Gly452Arg) rs772958162
NM_000091.4(COL4A3):c.1855G>A (p.Gly619Arg) rs773515249
NM_000091.4(COL4A3):c.190G>C (p.Gly64Arg) rs917643323
NM_000091.4(COL4A3):c.2452G>A (p.Gly818Arg) rs868002181
NM_000091.4(COL4A3):c.2810G>A (p.Gly937Glu) rs1559899600
NM_000091.4(COL4A3):c.3546_3548dup (p.Gly1183dup) rs1175052474
NM_000091.4(COL4A3):c.4981C>T (p.Arg1661Cys) rs201697532
NM_000091.4(COL4A3):c.898G>A (p.Gly300Arg) rs772708743
NM_000092.4(COL4A4):c.1223G>A (p.Gly408Glu) rs1026613471
NM_000092.4(COL4A4):c.2092G>A (p.Gly698Arg) rs1241404192
NM_000092.4(COL4A4):c.4082-1G>T rs1559438651
NM_000092.4(COL4A4):c.5045G>A (p.Arg1682Gln) rs368404711
NM_000124.4(ERCC6):c.809del (p.Gly270fs) rs923535659
NM_000168.6(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.926C>T (p.Ala309Val) rs869312155
NM_000169.3(GLA):c.352C>T (p.Arg118Cys) rs148158093
NM_000169.3(GLA):c.376A>G (p.Ser126Gly) rs149391489
NM_000179.3(MSH6):c.1483C>T rs587779212
NM_000179.3(MSH6):c.3716_3717del (p.Ile1239fs) rs1064794384
NM_000216.4(ANOS1):c.555G>C (p.Lys185Asn) rs140670828
NM_000255.4(MMUT):c.912-1G>A rs1561957527
NM_000256.3(MYBPC3):c.3815-1G>A rs397516044
NM_000297.4(PKD2):c.2208_2213del (p.Leu736_Asn737del) rs778896252
NM_000334.4(SCN4A):c.1173del (p.Phe392fs) rs1235665641
NM_000388.4(CASR):c.1189G>A (p.Gly397Arg) rs1064794291
NM_000435.3(NOTCH3):c.2182C>T (p.Arg728Cys) rs1057519101
NM_000441.2(SLC26A4):c.1708-1G>A rs759414956
NM_000458.4(HNF1B):c.1006C>G (p.His336Asp)
NM_000478.6(ALPL):c.994G>T (p.Glu332Ter) rs768976020
NM_000503.6(EYA1):c.865G>T (p.Asp289Tyr) rs201504674
NM_000518.5(HBB):c.20A>T (p.Glu7Val) rs334
NM_000540.3(RYR1):c.7300G>A (p.Gly2434Arg) rs121918593
NM_000551.4(VHL):c.241C>T (p.Pro81Ser) rs104893829
NM_001009944.3(PKD1):c.10420C>T (p.Gln3474Ter) rs1064794206
NM_001009944.3(PKD1):c.12691C>T (p.Gln4231Ter) rs755496450
NM_001009944.3(PKD1):c.2180T>C (p.Leu727Pro) rs1616940
NM_001009944.3(PKD1):c.3496G>A (p.Gly1166Ser) rs573566419
NM_001009944.3(PKD1):c.3955G>A (p.Gly1319Arg) rs747362311
NM_001009944.3(PKD1):c.7546C>T (p.Arg2516Cys) rs797044902
NM_001009944.3(PKD1):c.8218G>T (p.Gly2740Ter) rs1555451368
NM_001009944.3(PKD1):c.8311G>A (p.Glu2771Lys) rs1057518897
NM_001009944.3(PKD1):c.8447T>C (p.Leu2816Pro) rs1567177684
NM_001009944.3(PKD1):c.9829C>T (p.Arg3277Cys) rs148812376
NM_001110556.2(FLNA):c.2609A>G (p.His870Arg) rs200679107
NM_001126108.2(SLC12A3):c.1844C>T (p.Ser615Leu) rs779160677
NM_001126108.2(SLC12A3):c.1928C>T (p.Pro643Leu) rs140012781
NM_001126108.2(SLC12A3):c.2191G>A (p.Gly731Arg) rs752101663
NM_001126108.2(SLC12A3):c.2864G>A (p.Arg955Gln) rs202114767
NM_001126108.2(SLC12A3):c.363G>C (p.Glu121Asp) rs146632606
NM_001177316.2(SLC34A3):c.575C>T (p.Ser192Leu) rs199690076
NM_001360.2(DHCR7):c.199G>A (p.Ala67Thr) rs143999854
NM_001360.2(DHCR7):c.91C>T (p.Arg31Cys) rs367585401
NM_001374828.1(ARID1B):c.1281GGC[5] (p.Ala433dup) rs764418312
NM_001567.4(INPPL1):c.1893_1894delinsAA (p.Leu632Ile) rs1565392009
NM_002968.2(SALL1):c.466_477dup (p.Ser159_Gly160insSerSerSerSer) rs113614842
NM_003000.2(SDHB):c.136C>T (p.Arg46Ter) rs74315370
NM_003361.3(UMOD):c.317G>T (p.Cys106Phe) rs398123697
NM_004525.3(LRP2):c.6473A>C (p.Asn2158Thr) rs34052957
NM_004572.3(PKP2):c.1440_1444del (p.Asn480fs) rs775995156
NM_004572.3(PKP2):c.837_838del (p.Val280fs) rs772220644
NM_004621.6(TRPC6):c.643C>T (p.Arg215Trp) rs768210838
NM_004646.3(NPHS1):c.2335-1G>A rs150038620
NM_004985.5(KRAS):c.108A>G (p.Ile36Met) rs727503109
NM_004985.5(KRAS):c.34G>A (p.Gly12Ser) rs121913530
NM_005912.3(MC4R):c.466C>T (p.Gln156Ter) rs369841551
NM_006005.3(WFS1):c.1371G>T (p.Arg457Ser) rs113446173
NM_014270.5(SLC7A9):c.1353C>A (p.Tyr451Ter) rs1007096305
NM_014625.3(NPHS2):c.451+2T>A rs786204708
NM_014625.3(NPHS2):c.686G>A (p.Arg229Gln) rs61747728
NM_014625.4(NPHS2):c.868G>A (p.Val290Met) rs200482683
NM_015559.3(SETBP1):c.2612T>C (p.Ile871Thr) rs267607038
NM_018668.4(VPS33B):c.96+1G>T rs1567232168
NM_018848.3(MKKS):c.830T>C (p.Leu277Pro) rs74315398
NM_019892.6(INPP5E):c.1787G>C (p.Arg596Thr) rs765327224
NM_020975.6(RET):c.785T>C (p.Val262Ala) rs139790943
NM_022042.4(SLC26A1):c.1073C>T (p.Ser358Leu) rs148832260
NM_024753.5(TTC21B):c.626C>T (p.Pro209Leu) rs140511594
NM_030665.4(RAI1):c.834GCA[7] (p.Gln286_Gln291del) rs371983878
NM_033380.3(COL4A5):c.1276G>A (p.Gly426Arg) rs104886111
NM_033380.3(COL4A5):c.1607G>A (p.Gly536Asp) rs104886125
NM_033380.3(COL4A5):c.2510-2A>G rs760109866
NM_033380.3(COL4A5):c.2965_2982del (p.Asp989_Gly994del) rs104886374
NM_033380.3(COL4A5):c.3427G>A (p.Gly1143Ser) rs104886228
NM_033380.3(COL4A5):c.4282C>T (p.Arg1428Cys) rs144282156
NM_033380.3(COL4A5):c.4567C>A (p.Pro1523Thr) rs201220208
NM_033380.3(COL4A5):c.5048G>A (p.Arg1683Gln) rs104886308
NM_033380.3(COL4A5):c.546+2dup rs1569489353
NM_033380.3(COL4A5):c.647G>A (p.Gly216Glu) rs104886074
NM_138694.4(PKHD1):c.2414C>T (p.Pro805Leu) rs199531851
NM_138694.4(PKHD1):c.4870C>T (p.Arg1624Trp) rs200391019
NM_138694.4(PKHD1):c.9530T>C (p.Ile3177Thr) rs200511261
NM_139058.3(ARX):c.451_465del (p.Ala151_Ala155del) rs757588621
NM_144696.6(AXDND1):c.3032-1887G>A rs780761368
NM_153240.5(NPHP3):c.2694-2_2694-1del rs751527253
NM_173689.7(CRB2):c.2400C>G (p.Asn800Lys) rs765676223
NM_181798.1(KCNQ1):c.416T>C (p.Leu139Pro) rs199473460
NM_181798.1(KCNQ1):c.884del (p.Lys295fs) rs397508083

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