ClinVar Miner

Variants from Paris Brain Institute, Inserm - ICM with conflicting interpretations

Location: France  Primary collection method: clinical testing
Minimum review status of the submission from Paris Brain Institute, Inserm - ICM: Collection method of the submission from Paris Brain Institute, Inserm - ICM:
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
274 90 2 49 4 0 33 84

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
Paris Brain Institute, Inserm - ICM pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 2 49 30 1 0
uncertain significance 2 1 0 2 2
likely benign 0 0 1 0 0

Submitter to submitter summary #

Total submitters: 44
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 80 0 3 1 0 21 25
Genomics England Pilot Project, Genomics England 0 2 0 8 0 0 0 8
MGZ Medical Genetics Center 0 6 0 5 0 0 1 6
Genome-Nilou Lab 0 16 0 6 0 0 0 6
3billion 0 5 0 4 0 0 2 6
GeneDx 0 1 0 1 3 0 1 5
Revvity Omics, Revvity 0 1 0 3 0 0 2 5
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 8 0 3 1 0 1 5
Fulgent Genetics, Fulgent Genetics 0 7 0 3 1 0 1 5
SIB Swiss Institute of Bioinformatics 0 3 0 5 0 0 0 5
Inherited Neuropathy Consortium Ii, University Of Miami 0 0 0 0 0 0 4 4
Baylor Genetics 0 12 0 2 1 0 0 3
Genetic Services Laboratory, University of Chicago 0 4 0 3 0 0 0 3
Illumina Laboratory Services, Illumina 0 2 0 1 1 0 1 3
Neurogenetics Laboratory, GH Pitie Salpetriere APHP 0 0 0 3 0 0 0 3
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 5 0 2 0 0 1 3
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 1 0 3 0 0 0 3
Molecular Genetics, Royal Melbourne Hospital 0 7 0 0 0 0 3 3
Athena Diagnostics Inc 0 3 0 0 2 0 0 2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 2 0 0 2 0 0 2
Counsyl 0 2 0 2 0 0 0 2
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 11 0 2 0 0 0 2
Eurofins Ntd Llc (ga) 0 0 0 0 1 0 1 2
GeneReviews 0 18 2 0 0 0 0 2
Institute of Human Genetics, University of Leipzig Medical Center 0 8 0 2 0 0 0 2
Institute of Human Genetics, University of Goettingen 0 0 0 0 0 0 1 1
PreventionGenetics, part of Exact Sciences 0 0 0 0 1 0 0 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 2 0 0 1 0 0 1
Clinical Genetics, Academic Medical Center 0 0 0 0 1 0 0 1
Mayo Clinic Laboratories, Mayo Clinic 0 1 0 0 0 0 1 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 18 0 1 0 0 0 1
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 0 0 1 0 0 0 1
Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust 0 2 0 1 0 0 0 1
CeGaT Center for Human Genetics Tuebingen 0 3 0 0 1 0 0 1
Undiagnosed Diseases Network, NIH 0 1 0 1 0 0 0 1
Groupe Hospitalier Pitie Salpetriere, UF Genomique du Developpement, Assistance Publique Hopitaux de Paris 0 0 0 1 0 0 0 1
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 1 0 0 1 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 2 0 0 1 0 0 1
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill 0 0 0 1 0 0 0 1
Department of Rehabilitation Medicine, Incheon St. Mary’s Hospital, College of Medicine, The Catholic University of Korea 0 0 0 1 0 0 0 1
Lifecell International Pvt. Ltd 0 0 0 1 0 0 0 1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 1 0 1 0 0 0 1
DASA 0 3 0 1 0 0 0 1
Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL) 0 9 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 84
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_015046.7(SETX):c.2975A>G (p.Lys992Arg) rs61742937 0.01445
NM_003119.4(SPG7):c.1529C>T (p.Ala510Val) rs61755320 0.00361
NM_003119.4(SPG7):c.1045G>A (p.Gly349Ser) rs141659620 0.00103
NM_004820.5(CYP7B1):c.1456C>T (p.Arg486Cys) rs116171274 0.00051
NM_024306.5(FA2H):c.232G>A (p.Glu78Lys) rs527421775 0.00024
NM_001244008.2(KIF1A):c.882+8G>A rs376552408 0.00019
NM_003119.4(SPG7):c.233T>A (p.Leu78Ter) rs121918358 0.00014
NM_006612.6(KIF1C):c.2920G>A (p.Asp974Asn) rs550136320 0.00014
NM_005186.4(CAPN1):c.1605+5G>A rs375817528 0.00012
NM_025137.4(SPG11):c.5381T>C (p.Leu1794Pro) rs201689565 0.00011
NM_006612.6(KIF1C):c.1346A>G (p.Lys449Arg) rs142046798 0.00009
NM_004820.5(CYP7B1):c.334C>T (p.Arg112Ter) rs200737038 0.00007
NM_003119.4(SPG7):c.2228T>C (p.Ile743Thr) rs752623413 0.00006
NM_015214.3(DDHD2):c.1978G>C (p.Asp660His) rs375168720 0.00006
NM_025137.4(SPG11):c.733_734del (p.Met245fs) rs312262720 0.00005
NM_183075.3(CYP2U1):c.1376C>T (p.Pro459Leu) rs747965749 0.00005
NM_003119.4(SPG7):c.861+2dup rs771256761 0.00004
NM_025137.4(SPG11):c.2834+1G>T rs312262749 0.00003
NM_183075.3(CYP2U1):c.1462C>T (p.Arg488Trp) rs141431913 0.00003
NM_015214.3(DDHD2):c.724C>T (p.Arg242Cys) rs1380005347 0.00002
NM_015214.3(DDHD2):c.725G>A (p.Arg242His) rs767497993 0.00002
NM_003119.4(SPG7):c.1409G>A (p.Arg470Gln) rs756535079 0.00001
NM_003119.4(SPG7):c.1730G>A (p.Gly577Asp) rs1329063851 0.00001
NM_004820.5(CYP7B1):c.1061G>A (p.Ser354Asn) rs753708048 0.00001
NM_014363.6(SACS):c.12973C>T (p.Arg4325Ter) rs762947018 0.00001
NM_015915.5(ATL1):c.1483C>T (p.Arg495Trp) rs864622269 0.00001
NM_020919.4(ALS2):c.575C>T (p.Pro192Leu) rs778003334 0.00001
NM_020944.3(GBA2):c.1905G>A (p.Thr635=) rs369401526 0.00001
NM_025137.4(SPG11):c.3039-5T>G rs763224175 0.00001
NM_001244008.2(KIF1A):c.206C>T (p.Ser69Leu) rs786200949
NM_001244008.2(KIF1A):c.232G>A (p.Gly78Ser) rs1057518760
NM_001244008.2(KIF1A):c.32G>A (p.Arg11Gln) rs1575654528
NM_001244008.2(KIF1A):c.500G>A (p.Arg167His) rs2054757914
NM_001244008.2(KIF1A):c.773C>T (p.Thr258Met) rs1553638086
NM_001244008.2(KIF1A):c.865-24CT[2] rs140674901
NM_001253852.3(AP4B1):c.1160_1161del (p.Thr387fs) rs587779388
NM_003119.3(SPG7):c.1454_1462delGGCGGGAGA (p.Arg485_Glu487del) rs768823392
NM_003119.4(SPG7):c.1033G>C (p.Ala345Pro) rs368373840
NM_003119.4(SPG7):c.1169T>C (p.Val390Ala) rs2058357964
NM_003119.4(SPG7):c.1763C>T (p.Thr588Met) rs778387199
NM_003119.4(SPG7):c.759-11_759-8del rs758385553
NM_003384.3(VRK1):c.788A>G (p.Asp263Gly) rs1428656431
NM_004820.5(CYP7B1):c.1249C>T (p.Arg417Cys) rs367916692
NM_004984.4(KIF5A):c.416A>G (p.Tyr139Cys) rs2140159368
NM_007126.5(VCP):c.283C>T (p.Arg95Cys) rs121909332
NM_014363.6(SACS):c.11374C>T (p.Arg3792Ter) rs565203731
NM_014363.6(SACS):c.12923_12927del (p.Lys4308fs) rs1057517294
NM_014363.6(SACS):c.6172del (p.Ser2058fs) rs1214399996
NM_014363.6(SACS):c.699del (p.Asp235fs) rs1415870785
NM_014846.4(WASHC5):c.1771T>C (p.Ser591Pro) rs1554593901
NM_014846.4(WASHC5):c.1876G>T (p.Val626Phe) rs80338867
NM_014855.3(AP5Z1):c.1573A>C (p.Lys525Gln) rs186003800
NM_014946.4(SPAST):c.1173G>A (p.Leu391=) rs1679218212
NM_014946.4(SPAST):c.1174-1G>A rs1553317024
NM_014946.4(SPAST):c.1196C>T (p.Ser399Leu) rs1553317025
NM_014946.4(SPAST):c.1216A>G (p.Ile406Val) rs587777757
NM_014946.4(SPAST):c.1276C>T (p.Leu426Phe) rs1060502227
NM_014946.4(SPAST):c.1340T>C (p.Leu447Ser) rs2148753950
NM_014946.4(SPAST):c.1413+1_1413+2del rs1679558544
NM_014946.4(SPAST):c.1413+3_1413+6del rs570685843
NM_014946.4(SPAST):c.1437_1438del (p.Arg479fs) rs864622268
NM_014946.4(SPAST):c.1483G>T (p.Ala495Ser) rs1060502228
NM_014946.4(SPAST):c.1496G>A (p.Arg499His) rs878854991
NM_014946.4(SPAST):c.1550T>C (p.Leu517Ser) rs2148759388
NM_014946.4(SPAST):c.1553T>C (p.Leu518Pro) rs1553319290
NM_014946.4(SPAST):c.1616+5G>A rs2148759485
NM_014946.4(SPAST):c.1715T>C (p.Met572Thr) rs138146982
NM_014946.4(SPAST):c.1742G>C (p.Arg581Pro) rs749484350
NM_014946.4(SPAST):c.67_85dup (p.Leu29fs) rs1676388641
NM_015346.4(ZFYVE26):c.1129del (p.Cys377fs) rs2140250002
NM_015915.5(ATL1):c.1220A>T (p.Lys407Met) rs2039539459
NM_015915.5(ATL1):c.1243C>T (p.Arg415Trp) rs119476050
NM_015915.5(ATL1):c.1306A>G (p.Asn436Asp) rs2140239163
NM_015915.5(ATL1):c.715C>T (p.Arg239Cys) rs119476046
NM_015915.5(ATL1):c.751C>A (p.Gln251Lys) rs1595615134
NM_015915.5(ATL1):c.757G>A (p.Val253Ile) rs864622520
NM_020919.4(ALS2):c.3619del (p.Lys1206_Met1207insTer) rs386134187
NM_020919.4(ALS2):c.4832G>A (p.Arg1611Gln) rs1689578912
NM_024306.5(FA2H):c.822del (p.Val275fs) rs2144601954
NM_025137.4(SPG11):c.1235C>G (p.Ser412Ter) rs312262723
NM_025137.4(SPG11):c.1837_1838insA (p.Leu613fs) rs312262735
NM_025137.4(SPG11):c.5989_5992del (p.Leu1997fs) rs312262776
NM_144599.5(NIPA1):c.403G>A (p.Val135Met) rs763295984
NM_183075.3(CYP2U1):c.784T>C (p.Cys262Arg) rs397514515

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