ClinVar Miner

Variants from Centre for Population Genomics, CPG with conflicting interpretations

Location: Australia  Primary collection method: curation
Minimum review status of the submission from Centre for Population Genomics, CPG: Collection method of the submission from Centre for Population Genomics, CPG:
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
225 265 0 118 24 0 66 202

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
Centre for Population Genomics, CPG pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 16 23 0 0
likely pathogenic 94 0 30 0 0
uncertain significance 11 1 0 0 0
likely benign 0 0 11 0 1
benign 1 0 13 7 0

Submitter to submitter summary #

Total submitters: 30
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
RettBASE 0 227 0 82 15 0 62 159
Genetic Services Laboratory, University of Chicago 0 27 0 9 1 0 0 10
Molecular Diagnostics Lab, Nemours Children's Health, Delaware 0 10 0 8 1 0 0 9
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 26 0 3 2 0 1 6
ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel 0 84 0 4 2 0 0 6
OMIM 0 21 0 3 0 0 1 4
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 3 0 3 1 0 0 4
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 7 0 1 1 0 0 2
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital 0 9 0 0 1 0 1 2
Mendelics 0 11 0 2 0 0 0 2
Blueprint Genetics 0 1 0 1 0 0 1 2
Baylor Genetics 0 6 0 0 1 0 0 1
Molecular Genetics Laboratory, Children's Mercy Hospital and Clinics 0 15 0 1 0 0 0 1
Invitae 0 1 0 1 0 0 0 1
Mayo Clinic Laboratories, Mayo Clinic 0 1 0 1 0 0 0 1
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 3 0 1 0 0 0 1
NeuroMeGen, Hospital Clinico Santiago de Compostela 0 0 0 1 0 0 0 1
Center for Human Genetics, University of Leuven 0 0 0 1 0 0 0 1
Centre de Biologie Pathologie Génétique, Centre Hospitalier Universitaire de Lille 0 2 0 1 0 0 0 1
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India 0 3 0 1 0 0 0 1
Neurogenetics Laboratory - MEYER, AOU Meyer 0 1 0 1 0 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 13 0 1 0 0 0 1
SIB Swiss Institute of Bioinformatics 0 1 0 0 1 0 0 1
Laboratoire de Génétique Moléculaire, CHU Bordeaux 0 2 0 1 0 0 0 1
Génétique des Maladies du Développement, Hospices Civils de Lyon 0 3 0 0 0 0 1 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 2 0 1 0 0 0 1
Biochemistry Laboratory of CDMU, Chengde Medical University 0 1 0 1 0 0 0 1
Lifecell International Pvt. Ltd 0 1 0 1 0 0 0 1
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn 0 1 0 1 0 0 0 1
Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 202
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001110792.2(MECP2):c.1225G>A (p.Glu409Lys) rs56268439 0.00308
NM_001110792.2(MECP2):c.638C>T (p.Ala213Val) rs61748381 0.00150
NM_001110792.2(MECP2):c.1162C>T (p.Pro388Ser) rs61752387 0.00108
NM_001110792.2(MECP2):c.1366G>A (p.Ala456Thr) rs61753975 0.00080
NM_001110792.2(MECP2):c.626C>T (p.Thr209Met) rs61749714 0.00064
NM_001110792.2(MECP2):c.*14G>A rs199963992 0.00037
NM_001110792.2(MECP2):c.1174G>A (p.Val392Met) rs267608572 0.00022
NM_001110792.2(MECP2):c.1066C>T (p.Arg356Trp) rs61752361 0.00006
NM_001110792.2(MECP2):c.1198C>T (p.Pro400Ser) rs61753000 0.00006
NM_001110792.2(MECP2):c.1199C>T (p.Pro400Leu) rs61753006 0.00005
NM_001110792.2(MECP2):c.1250C>T (p.Pro417Leu) rs61753016 0.00004
NM_001110792.2(MECP2):c.1477G>A (p.Val493Met) rs193922678 0.00003
NM_001110792.2(MECP2):c.260C>T (p.Pro87Leu) rs267608440 0.00003
NM_001110792.2(MECP2):c.968C>T (p.Thr323Met) rs61751445 0.00003
NM_001110792.2(MECP2):c.1117C>G (p.Pro373Ala) rs61752373 0.00002
NM_001110792.2(MECP2):c.553C>G (p.Pro185Ala) rs61748427 0.00002
NM_001110792.2(MECP2):c.895G>C (p.Ala299Pro) rs61750257 0.00002
NM_001110792.2(MECP2):c.515C>G (p.Thr172Ser) rs61748414 0.00001
NM_001110792.2(MECP2):c.554C>G (p.Pro185Arg) rs267608492 0.00001
NM_001110792.2(MECP2):c.62+5380C>T rs267608324 0.00001
NM_001110792.2(MECP2):c.*122del rs267608342
NM_001110792.2(MECP2):c.*98dup rs267608341
NM_001110792.2(MECP2):c.1000C>G (p.Pro334Ala) rs61751449
NM_001110792.2(MECP2):c.1000C>T (p.Pro334Ser) rs61751449
NM_001110792.2(MECP2):c.1001C>T (p.Pro334Leu) rs61751450
NM_001110792.2(MECP2):c.1030_1034del (p.Ser344fs) rs267608558
NM_001110792.2(MECP2):c.1030_1382del (p.Ser344fs) rs1557135016
NM_001110792.2(MECP2):c.1045_1063del (p.Lys349fs) rs267608559
NM_001110792.2(MECP2):c.1048_1229del (p.Thr350fs) rs1557135426
NM_001110792.2(MECP2):c.1066_1231delinsGT (p.Arg356fs) rs1557135402
NM_001110792.2(MECP2):c.1074C>G (p.Ser358Arg) rs61752365
NM_001110792.2(MECP2):c.1079_1209delinsTG (p.Glu360_Pro403delinsVal) rs1557135603
NM_001110792.2(MECP2):c.1082_1242del (p.Ser361fs) rs1557135268
NM_001110792.2(MECP2):c.1088_1236del (p.Pro363fs) rs1557135338
NM_001110792.2(MECP2):c.1099AGC[2] (p.Ser369del) rs267608564
NM_001110792.2(MECP2):c.1132_1237del (p.His378fs) rs1557135317
NM_001110792.2(MECP2):c.1133_*13del (p.His378_Ter499delinsXaa) rs1557134819
NM_001110792.2(MECP2):c.1133_1239del (p.His378fs) rs1557135285
NM_001110792.2(MECP2):c.1135_1154del (p.His379fs) rs267608567
NM_001110792.2(MECP2):c.1141_1261del (p.His381fs) rs1557135213
NM_001110792.2(MECP2):c.1157_1227del (p.Glu386fs) rs1557135447
NM_001110792.2(MECP2):c.1159_1238del (p.Ser387fs) rs1557135299
NM_001110792.2(MECP2):c.1165_*568delinsCCGTGG (p.Lys389fs) rs1557134378
NM_001110792.2(MECP2):c.1188_*29del (p.Pro396_Ter499delinsXaa) rs1557134779
NM_001110792.2(MECP2):c.1188_1191del (p.Pro397fs) rs267608576
NM_001110792.2(MECP2):c.1189_1226del (p.Pro397fs) rs267608577
NM_001110792.2(MECP2):c.1191_1202del (p.Leu398_Pro401del) rs782174572
NM_001110792.2(MECP2):c.1191_1219del (p.Pro399fs) rs267608580
NM_001110792.2(MECP2):c.1192_1193dup (p.Pro399fs) rs267608584
NM_001110792.2(MECP2):c.1193_*944del (p.Leu398fs)
NM_001110792.2(MECP2):c.1193_1233del (p.Leu398fs) rs267608327
NM_001110792.2(MECP2):c.1195_1494del (p.Pro399_Ser498del) rs1557134858
NM_001110792.2(MECP2):c.1196_1236del (p.Pro399fs) rs267608592
NM_001110792.2(MECP2):c.1198CCACCT[1] (p.Pro402_Pro403del) rs61753008
NM_001110792.2(MECP2):c.1199_1233del (p.Pro400fs) rs267608589
NM_001110792.2(MECP2):c.1199_1252del (p.Pro400_Pro417del) rs1557135234
NM_001110792.2(MECP2):c.1200_1208del (p.Pro401_Pro403del) rs267608604
NM_001110792.2(MECP2):c.1200_1244del (p.Pro401_Pro415del) rs267608605
NM_001110792.2(MECP2):c.1200del (p.Pro401fs) rs267608606
NM_001110792.2(MECP2):c.1206_1243del (p.Pro402_Pro403insTer) rs267608609
NM_001110792.2(MECP2):c.1209_1243del (p.Pro403_Glu404insTer) rs2148659508
NM_001110792.2(MECP2):c.1216_1217insT (p.Glu406fs) rs786205021
NM_001110792.2(MECP2):c.1226dup (p.Asp410fs) rs267608610
NM_001110792.2(MECP2):c.1232_1302del (p.Pro411fs) rs1557135137
NM_001110792.2(MECP2):c.1233dup (p.Thr412fs) rs267608612
NM_001110792.2(MECP2):c.1238dup (p.Ser413fs) rs267608614
NM_001110792.2(MECP2):c.1259_1301del (p.Leu420fs) rs63749038
NM_001110792.2(MECP2):c.1271_1296del (p.Val424fs) rs267608617
NM_001110792.2(MECP2):c.127del (p.Lys42_Val43insTer) rs61754427
NM_001110792.2(MECP2):c.1301_1325delinsAGCGGCCG (p.Gly434fs) rs63749064
NM_001110792.2(MECP2):c.143_149del (p.Lys48fs) rs267608424
NM_001110792.2(MECP2):c.1444_1447delinsTG (p.Asn482fs) rs786205023
NM_001110792.2(MECP2):c.1486_*12del (p.Arg496_Ter499del) rs267608637
NM_001110792.2(MECP2):c.1490_1493del (p.Val497fs) rs267608640
NM_001110792.2(MECP2):c.1497A>C (p.Ter499Cys) rs267608642
NM_001110792.2(MECP2):c.155_156del (p.Glu52fs) rs267608428
NM_001110792.2(MECP2):c.162dup (p.His55fs) rs61754430
NM_001110792.2(MECP2):c.1A>G (p.Met1Val) rs587783132
NM_001110792.2(MECP2):c.1A>T (p.Met1Leu) rs587783132
NM_001110792.2(MECP2):c.230C>G (p.Ser77Ter) rs61754437
NM_001110792.2(MECP2):c.237del (p.Ser80fs) rs61754438
NM_001110792.2(MECP2):c.239C>G (p.Ser80Ter) rs267608438
NM_001110792.2(MECP2):c.2T>C (p.Met1Thr) rs2066907057
NM_001110792.2(MECP2):c.30delinsGA (p.Ser10fs) rs786205040
NM_001110792.2(MECP2):c.310G>T (p.Gly104Ter) rs267608445
NM_001110792.2(MECP2):c.325G>T (p.Asp109Tyr) rs61754448
NM_001110792.2(MECP2):c.331_333del (p.Thr111del) rs267608449
NM_001110792.2(MECP2):c.334C>G (p.Leu112Val) rs28935168
NM_001110792.2(MECP2):c.337C>T (p.Pro113Ser) rs61754452
NM_001110792.2(MECP2):c.338C>A (p.Pro113His) rs61754453
NM_001110792.2(MECP2):c.338C>G (p.Pro113Arg) rs61754453
NM_001110792.2(MECP2):c.338C>T (p.Pro113Leu) rs61754453
NM_001110792.2(MECP2):c.33AGG[7] (p.Gly15_Gly16dup) rs587783744
NM_001110792.2(MECP2):c.347G>A (p.Trp116Ter) rs61754455
NM_001110792.2(MECP2):c.347_359del (p.Trp116fs) rs63749010
NM_001110792.2(MECP2):c.352C>G (p.Arg118Gly) rs28934907
NM_001110792.2(MECP2):c.352C>T (p.Arg118Trp) rs28934907
NM_001110792.2(MECP2):c.353G>T (p.Arg118Leu) rs61754457
NM_001110792.2(MECP2):c.359T>A (p.Leu120His) rs61754458
NM_001110792.2(MECP2):c.367A>G (p.Arg123Gly) rs61754459
NM_001110792.2(MECP2):c.381del (p.Ser128fs) rs61755761
NM_001110792.2(MECP2):c.400G>A (p.Val134Met) rs267608455
NM_001110792.2(MECP2):c.408G>C (p.Leu136Phe) rs61755763
NM_001110792.2(MECP2):c.408G>T (p.Leu136Phe) rs61755763
NM_001110792.2(MECP2):c.413+2T>G rs267608458
NM_001110792.2(MECP2):c.414-3C>G rs267608465
NM_001110792.2(MECP2):c.416C>T (p.Pro139Leu) rs267608387
NM_001110792.2(MECP2):c.419A>C (p.Gln140Pro) rs61748383
NM_001110792.2(MECP2):c.422G>T (p.Gly141Val) rs61748384
NM_001110792.2(MECP2):c.428C>A (p.Ala143Asp) rs267608470
NM_001110792.2(MECP2):c.433C>G (p.Arg145Gly) rs28934904
NM_001110792.2(MECP2):c.434G>A (p.Arg145His) rs61748389
NM_001110792.2(MECP2):c.434G>C (p.Arg145Pro) rs61748389
NM_001110792.2(MECP2):c.434G>T (p.Arg145Leu) rs61748389
NM_001110792.2(MECP2):c.436T>C (p.Ser146Pro) rs267608471
NM_001110792.2(MECP2):c.437C>G (p.Ser146Cys) rs61748390
NM_001110792.2(MECP2):c.437C>T (p.Ser146Phe) rs61748390
NM_001110792.2(MECP2):c.439A>G (p.Lys147Glu) rs61748391
NM_001110792.2(MECP2):c.446A>G (p.Glu149Gly) rs61748392
NM_001110792.2(MECP2):c.447del (p.Glu149fs) rs61748393
NM_001110792.2(MECP2):c.449T>A (p.Leu150Ter) rs267608475
NM_001110792.2(MECP2):c.456del (p.Tyr153fs) rs267608476
NM_001110792.2(MECP2):c.458A>G (p.Tyr153Cys) rs61748395
NM_001110792.2(MECP2):c.464_465insT (p.Glu155fs) rs61748398
NM_001110792.2(MECP2):c.475del (p.Asp159fs) rs62952161
NM_001110792.2(MECP2):c.487del (p.Asp163fs) rs61748402
NM_001110792.2(MECP2):c.488A>G (p.Asp163Gly) rs61748403
NM_001110792.2(MECP2):c.48_55dup (p.Glu19fs) rs786205043
NM_001110792.2(MECP2):c.499T>A (p.Phe167Ile) rs61748406
NM_001110792.2(MECP2):c.500T>C (p.Phe167Ser) rs28934905
NM_001110792.2(MECP2):c.500T>G (p.Phe167Cys) rs28934905
NM_001110792.2(MECP2):c.503A>C (p.Asp168Ala) rs61748407
NM_001110792.2(MECP2):c.503A>G (p.Asp168Gly) rs61748407
NM_001110792.2(MECP2):c.505T>A (p.Phe169Ile) rs61748410
NM_001110792.2(MECP2):c.506dup (p.Thr170fs) rs267608482
NM_001110792.2(MECP2):c.507C>G (p.Phe169Leu) rs267608484
NM_001110792.2(MECP2):c.508A>G (p.Thr170Ala) rs61748411
NM_001110792.2(MECP2):c.509C>T (p.Thr170Met) rs28934906
NM_001110792.2(MECP2):c.511del (p.Thr170_Val171insTer) rs267608485
NM_001110792.2(MECP2):c.516del (p.Arg174fs) rs61748415
NM_001110792.2(MECP2):c.517G>T (p.Gly173Trp) rs61748416
NM_001110792.2(MECP2):c.518G>A (p.Gly173Glu) rs61748417
NM_001110792.2(MECP2):c.518G>T (p.Gly173Val) rs61748417
NM_001110792.2(MECP2):c.519del (p.Arg174fs) rs61748418
NM_001110792.2(MECP2):c.535C>T (p.Arg179Trp) rs61748420
NM_001110792.2(MECP2):c.567del (p.Lys189fs) rs61749703
NM_001110792.2(MECP2):c.590del (p.Gly197fs) rs61749707
NM_001110792.2(MECP2):c.5C>T (p.Ala2Val) rs179363901
NM_001110792.2(MECP2):c.610A>T (p.Lys204Ter) rs193922679
NM_001110792.2(MECP2):c.62+1G>A rs786205048
NM_001110792.2(MECP2):c.62+2_62+3del rs786205049
NM_001110792.2(MECP2):c.63-6C>G rs267608411
NM_001110792.2(MECP2):c.637dup (p.Ala213fs) rs267608503
NM_001110792.2(MECP2):c.644_645insA (p.Ser216fs) rs267608506
NM_001110792.2(MECP2):c.64G>T (p.Glu22Ter) rs61754421
NM_001110792.2(MECP2):c.652_1158del (p.Gly218_Glu386del) rs1557135847
NM_001110792.2(MECP2):c.653del (p.Gly218fs) rs61749727
NM_001110792.2(MECP2):c.6CGC[4] (p.Ala7_Ala8del) rs398123566
NM_001110792.2(MECP2):c.6CGC[8] (p.Ala7_Ala8dup) rs398123566
NM_001110792.2(MECP2):c.709C>A (p.Pro237Thr) rs267608513
NM_001110792.2(MECP2):c.710C>G (p.Pro237Arg) rs61749715
NM_001110792.2(MECP2):c.710C>T (p.Pro237Leu) rs61749715
NM_001110792.2(MECP2):c.725_792del (p.Pro242fs) rs1557136493
NM_001110792.2(MECP2):c.747_1305del (p.Gly250fs) rs1557135125
NM_001110792.2(MECP2):c.767_1202del (p.Gln256fs) rs1557135670
NM_001110792.2(MECP2):c.772_779delinsGTG (p.Met258fs) rs267608520
NM_001110792.2(MECP2):c.784_785insT (p.Arg262fs) rs1557136549
NM_001110792.2(MECP2):c.785G>A (p.Arg262His) rs61750227
NM_001110792.2(MECP2):c.788_789dup (p.Gly264fs) rs61749751
NM_001110792.2(MECP2):c.789dup (p.Gly264fs) rs61749751
NM_001110792.2(MECP2):c.799C>T (p.Arg267Ter) rs61749721
NM_001110792.2(MECP2):c.828_829del (p.Pro277fs) rs267608526
NM_001110792.2(MECP2):c.848_854del (p.Lys283fs) rs61750242
NM_001110792.2(MECP2):c.858_1220del (p.Val287_Ser407del) rs1557135541
NM_001110792.2(MECP2):c.870_975del (p.Ala291fs) rs1557136146
NM_001110792.2(MECP2):c.885_1272del (p.Lys296fs) rs1557135197
NM_001110792.2(MECP2):c.887_1224del (p.Lys296fs) rs1557135499
NM_001110792.2(MECP2):c.901A>T (p.Lys301Ter) rs61750259
NM_001110792.2(MECP2):c.901_902del (p.Lys301fs) rs267608536
NM_001110792.2(MECP2):c.907_1080del (p.Ile305_Ser362del) rs1557136013
NM_001110792.2(MECP2):c.916C>T (p.Arg306Ter) rs61751362
NM_001110792.2(MECP2):c.916_920del (p.Arg306fs) rs61751364
NM_001110792.2(MECP2):c.919del (p.Ser307fs) rs267608541
NM_001110792.2(MECP2):c.92dup (p.Leu33fs) rs267608417
NM_001110792.2(MECP2):c.930_1131del (p.Glu310fs) rs1557135907
NM_001110792.2(MECP2):c.934_940del (p.Val312fs) rs267608543
NM_001110792.2(MECP2):c.934del (p.Val312fs) rs267608544
NM_001110792.2(MECP2):c.940C>A (p.Pro314Thr) rs61751373
NM_001110792.2(MECP2):c.940C>G (p.Pro314Ala) rs61751373
NM_001110792.2(MECP2):c.940C>T (p.Pro314Ser) rs61751373
NM_001110792.2(MECP2):c.941C>A (p.Pro314His) rs61749723
NM_001110792.2(MECP2):c.941C>G (p.Pro314Arg) rs61749723
NM_001110792.2(MECP2):c.941C>T (p.Pro314Leu) rs61749723
NM_001110792.2(MECP2):c.942_1174delinsAC (p.Ile315_Val392delinsLeu) rs1557135788
NM_001110792.2(MECP2):c.945C>G (p.Ile315Met) rs61751439
NM_001110792.2(MECP2):c.946A>G (p.Lys316Glu) rs61751440
NM_001110792.2(MECP2):c.949A>G (p.Lys317Glu) rs267608551
NM_001110792.2(MECP2):c.950A>G (p.Lys317Arg) rs61751441
NM_001110792.2(MECP2):c.950_1208del (p.Lys317fs) rs1557135622
NM_001110792.2(MECP2):c.953G>A (p.Arg318His) rs61751443
NM_001110792.2(MECP2):c.961C>T (p.Arg321Trp) rs61751444
NM_004992.4(MECP2):c.26+2T>A rs267608409

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