ClinVar Miner

Variants from Inherited Neuropathy Consortium with conflicting interpretations

Location: United States  Primary collection method: literature only
Minimum review status of the submission from Inherited Neuropathy Consortium: Collection method of the submission from Inherited Neuropathy Consortium:
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
1194 85 0 11 26 0 59 92

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
Inherited Neuropathy Consortium pathogenic likely pathogenic uncertain significance likely benign benign
likely pathogenic 3 0 5 1 0
uncertain significance 36 18 0 14 13
likely benign 0 1 3 0 1
benign 0 0 1 7 0

Submitter to submitter summary #

Total submitters: 38
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
Molecular Genetics Laboratory, London Health Sciences Centre 0 17 0 1 9 0 28 38
GeneDx 0 7 0 4 8 0 2 14
Invitae 0 6 0 2 4 0 6 12
PreventionGenetics, part of Exact Sciences 0 2 0 0 6 0 1 7
Illumina Laboratory Services, Illumina 0 0 0 1 4 0 1 6
CeGaT Center for Human Genetics Tuebingen 0 3 0 2 2 0 2 6
Genesis Genome Database 0 12 0 0 2 0 4 6
OMIM 0 0 0 0 0 0 5 5
Athena Diagnostics Inc 0 4 0 0 4 0 1 5
Clinical Genetics, Academic Medical Center 0 2 0 0 5 0 0 5
Natera, Inc. 0 5 0 0 0 0 4 4
Fulgent Genetics, Fulgent Genetics 0 0 0 1 0 0 3 4
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 0 0 1 0 0 2 3
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 2 0 0 2 0 1 3
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 0 1 2 0 0 3
Revvity Omics, Revvity 0 0 0 0 0 0 2 2
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 1 0 0 2 0 0 2
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen 0 0 0 0 0 0 2 2
Practice for Gait Abnormalities, David Pomarino, Competency Network Toe Walking c/o Practice Pomarino 0 0 0 0 0 0 2 2
Genetic Services Laboratory, University of Chicago 0 0 0 1 0 0 0 1
Institute of Human Genetics, Cologne University 0 0 0 0 0 0 1 1
MGZ Medical Genetics Center 0 0 0 0 0 0 1 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 0 0 0 1 0 0 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 0 0 0 0 0 1 1
Mendelics 0 0 0 0 1 0 0 1
Eurofins Ntd Llc (ga) 0 1 0 0 0 0 1 1
GeneReviews 0 6 0 0 0 0 1 1
Mayo Clinic Laboratories, Mayo Clinic 0 0 0 0 0 0 1 1
Department Of Translational Genomics (developmental Genetics Section), King Faisal Specialist Hospital & Research Centre 0 0 0 0 0 0 1 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 0 0 0 0 0 1 1
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 0 0 0 0 0 0 1 1
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ 0 1 0 0 1 0 0 1
Department of Human Genetics, University Hospital Magdeburg 0 0 0 0 0 0 1 1
AiLife Diagnostics, AiLife Diagnostics 0 0 0 0 0 0 1 1
3billion 0 0 0 0 0 0 1 1
Beijing Key Laboratry for Genetics of Birth Defects, Beijing Children's Hospital 0 0 0 0 0 0 1 1
Concord Molecular Medicine Laboratory, Concord Repatriation General Hospital 0 0 0 0 0 0 1 1
Inherited Neuropathy Consortium Ii, University Of Miami 0 51 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 92
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_002529.4(NTRK1):c.1887C>T (p.Ala629=) rs6337 0.53946
NM_018972.4(GDAP1):c.507T>G (p.Ser169=) rs11554166 0.27295
NM_001136472.2(LITAF):c.274A>G (p.Ile92Val) rs4280262 0.15945
NM_181882.3(PRX):c.306C>T (p.Thr102=) rs744389 0.12409
NM_000399.5(EGR2):c.1086A>C (p.Arg362=) rs45602133 0.04462
NM_016156.6(MTMR2):c.1504G>C (p.Glu502Gln) rs61735578 0.03636
NM_002180.3(IGHMBP2):c.180C>T (p.Tyr60=) rs34617762 0.00959
NM_014874.4(MFN2):c.957C>T (p.Gly319=) rs41278632 0.00690
NM_006158.5(NEFL):c.667C>T (p.Leu223=) rs60156239 0.00494
NM_022041.4(GAN):c.1684C>G (p.Pro562Ala) rs79901179 0.00388
NM_000304.4(PMP22):c.353C>T (p.Thr118Met) rs104894619 0.00378
NM_024577.4(SH3TC2):c.3686A>T (p.Asp1229Val) rs146920285 0.00306
NM_000304.4(PMP22):c.-141C>G rs560442424 0.00204
NM_000166.6(GJB1):c.235C>T (p.Leu79=) rs144717157 0.00186
NM_021625.5(TRPV4):c.649G>T (p.Ala217Ser) rs187864727 0.00172
NM_181882.3(PRX):c.1574T>C (p.Val525Ala) rs149715830 0.00136
NM_024577.4(SH3TC2):c.137A>C (p.Gln46Pro) rs146162276 0.00114
NM_002693.3(POLG):c.2209G>C (p.Gly737Arg) rs121918054 0.00096
NM_001136472.2(LITAF):c.146C>T (p.Thr49Met) rs141862602 0.00086
NM_006158.5(NEFL):c.1402G>A (p.Asp468Asn) rs57153321 0.00081
NM_006158.5(NEFL):c.639C>G (p.Ile213Met) rs62636522 0.00065
NM_001136472.2(LITAF):c.330C>T (p.Asn110=) rs139116481 0.00062
NM_014874.4(MFN2):c.2146G>A (p.Ala716Thr) rs144860227 0.00032
NM_000166.6(GJB1):c.30C>T (p.Leu10=) rs183702021 0.00018
NM_018972.4(GDAP1):c.487C>T (p.Gln163Ter) rs104894077 0.00015
NM_018972.4(GDAP1):c.692C>T (p.Pro231Leu) rs121908114 0.00015
NM_006158.5(NEFL):c.423G>A (p.Gln141=) rs59161567 0.00012
NM_006158.5(NEFL):c.1212C>T (p.Ser404=) rs60547413 0.00008
NM_006158.5(NEFL):c.1458C>T (p.Ala486=) rs61726486 0.00007
NM_000166.6(GJB1):c.441C>T (p.Ala147=) rs765686240 0.00006
NM_000530.8(MPZ):c.637G>C (p.Gly213Arg) rs202176679 0.00005
NM_018972.4(GDAP1):c.715C>T (p.Leu239Phe) rs104894080 0.00004
NM_001005373.4(LRSAM1):c.1913-1G>A rs756880678 0.00003
NM_022041.4(GAN):c.805C>T (p.Arg269Trp) rs776397915 0.00003
NM_024577.4(SH3TC2):c.3325C>T (p.Arg1109Ter) rs80338934 0.00003
NM_024577.4(SH3TC2):c.3512G>T (p.Arg1171Leu) rs200728983 0.00003
NM_006158.5(NEFL):c.279G>A (p.Gln93=) rs60737254 0.00002
NM_000166.6(GJB1):c.14G>T (p.Gly5Val) rs1064793139 0.00001
NM_000166.6(GJB1):c.462T>C (p.Tyr154=) rs879254098 0.00001
NM_000166.6(GJB1):c.83T>A (p.Ile28Asn) rs768834663 0.00001
NM_000304.4(PMP22):c.327C>T (p.Cys109=) rs863225028 0.00001
NM_000530.8(MPZ):c.418T>A (p.Ser140Thr) rs572010627 0.00001
NM_001540.5(HSPB1):c.250G>C (p.Gly84Arg) rs770272088 0.00001
NM_002693.3(POLG):c.926G>A (p.Arg309His) rs780953863 0.00001
NM_014874.4(MFN2):c.1724G>A (p.Arg575His) rs564375950 0.00001
NM_018972.4(GDAP1):c.458C>T (p.Pro153Leu) rs538412810 0.00001
NM_018972.4(GDAP1):c.767A>G (p.His256Arg) rs1476856429 0.00001
NM_022041.4(GAN):c.806G>A (p.Arg269Gln) rs759581558 0.00001
NM_022041.4(GAN):c.877C>T (p.Arg293Ter) rs370358470 0.00001
NM_024577.4(SH3TC2):c.3511C>T (p.Arg1171Cys) rs759785462 0.00001
NM_000166.6(GJB1):c.187G>A (p.Val63Ile) rs116840818
NM_000166.6(GJB1):c.283G>A (p.Val95Met) rs104894821
NM_000166.6(GJB1):c.381C>G (p.Ile127Met) rs1602349264
NM_000166.6(GJB1):c.43C>T (p.Arg15Trp) rs116840815
NM_000166.6(GJB1):c.50C>G (p.Ser17Cys) rs1555937009
NM_000166.6(GJB1):c.64C>T (p.Arg22Ter) rs1555937020
NM_000166.6(GJB1):c.65G>A (p.Arg22Gln) rs1060501002
NM_000166.6(GJB1):c.73C>T (p.Leu25Phe) rs1602348662
NM_000166.6(GJB1):c.8G>C (p.Trp3Ser) rs1555936989
NM_000304.4(PMP22):c.179-2A>G rs1597608225
NM_000304.4(PMP22):c.281dup (p.Arg95fs) rs80338763
NM_000304.4(PMP22):c.298G>A (p.Gly100Arg) rs1597607651
NM_000304.4(PMP22):c.392C>G (p.Ser131Cys) rs1597597627
NM_000399.5(EGR2):c.1075C>T (p.Arg359Trp) rs104894161
NM_000399.5(EGR2):c.1352G>T (p.Gly451Val) rs138967272
NM_000530.8(MPZ):c.131C>T (p.Ser44Phe) rs121913598
NM_000530.8(MPZ):c.245A>G (p.Tyr82Cys) rs1553259707
NM_000530.8(MPZ):c.296T>C (p.Ile99Thr) rs1571819182
NM_000530.8(MPZ):c.380G>A (p.Cys127Tyr) rs797044941
NM_000530.8(MPZ):c.419C>T (p.Ser140Phe) rs863224449
NM_000530.8(MPZ):c.435T>A (p.Tyr145Ter) rs1571818632
NM_000530.8(MPZ):c.499G>C (p.Gly167Arg) rs121913586
NM_000530.8(MPZ):c.703AAG[1] (p.Lys236del) rs755446743
NM_001136472.2(LITAF):c.332C>G (p.Ala111Gly) rs281865134
NM_001540.5(HSPB1):c.116C>T (p.Pro39Leu) rs557327165
NM_001540.5(HSPB1):c.407G>T (p.Arg136Leu) rs863225022
NM_002047.4(GARS1):c.1171C>T (p.Arg391Cys) rs370057212
NM_002180.3(IGHMBP2):c.2911_2912del (p.Arg971fs) rs724159994
NM_002972.4(SBF1):c.1327G>A (p.Asp443Asn) rs690016543
NM_004208.4(AIFM1):c.1019T>C (p.Met340Thr) rs1057518895
NM_006415.4(SPTLC1):c.1160G>C (p.Gly387Ala) rs119482084
NM_014874.4(MFN2):c.272T>G (p.Val91Gly) rs1569816262
NM_014874.4(MFN2):c.751C>G (p.Pro251Ala) rs28940295
NM_014874.4(MFN2):c.775C>T (p.Arg259Cys) rs587777875
NM_018972.4(GDAP1):c.558del (p.Ile186fs) rs770658701
NM_018972.4(GDAP1):c.579+1G>A rs864622501
NM_022041.4(GAN):c.1012A>T (p.Lys338Ter) rs1181977802
NM_022041.4(GAN):c.1502+1G>T rs1555511978
NM_022041.4(GAN):c.18_19insA (p.Val7fs) rs1597385624
NM_022041.4(GAN):c.413G>A (p.Arg138His) rs119485092
NM_022041.4(GAN):c.484C>T (p.Arg162Ter) rs1300267158
NM_181882.3(PRX):c.3198del (p.Phe1066fs) rs1599651549

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