ClinVar Miner

Variants from PROSPAX: an integrated multimodal progression chart in spastic ataxias, Center for Neurology; Hertie-Institute for Clinical Brain Research with conflicting interpretations

Location: Germany  Primary collection method: research
Minimum review status of the submission from PROSPAX: an integrated multimodal progression chart in spastic ataxias, Center for Neurology; Hertie-Institute for Clinical Brain Research: Collection method of the submission from PROSPAX: an integrated multimodal progression chart in spastic ataxias, Center for Neurology; Hertie-Institute for Clinical Brain Research:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:

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
112 67 0 70 0 0 25 93

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
PROSPAX: an integrated multimodal progression chart in spastic ataxias, Center for Neurology; Hertie-Institute for Clinical Brain Research pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 44 2 0 0
likely pathogenic 26 0 10 4 8
uncertain significance 1 5 0 0 0

Submitter to submitter summary #

Total submitters: 47
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
Natera, Inc. 0 26 0 15 0 0 13 28
Counsyl 0 15 0 16 0 0 3 19
Fulgent Genetics, Fulgent Genetics 0 32 0 16 0 0 2 18
Labcorp Genetics (formerly Invitae), Labcorp 0 35 0 10 0 0 6 16
Baylor Genetics 0 32 0 11 0 0 2 13
Genome-Nilou Lab 0 25 0 4 0 0 7 11
Solve-RD Consortium 0 1 0 10 0 0 1 11
Revvity Omics, Revvity 0 4 0 5 0 0 3 8
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 31 0 7 0 0 0 7
MGZ Medical Genetics Center 0 3 0 3 0 0 2 5
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 4 0 4 0 0 0 4
Paris Brain Institute, Inserm - ICM 0 36 0 3 0 0 1 4
Kariminejad - Najmabadi Pathology & Genetics Center 0 3 0 3 0 0 0 3
Mendelics 0 4 0 2 0 0 1 3
Genetic Services Laboratory, University of Chicago 0 4 0 2 0 0 0 2
Genomics England Pilot Project, Genomics England 0 4 0 2 0 0 0 2
Illumina Laboratory Services, Illumina 0 3 0 0 0 0 2 2
Institute of Human Genetics, Heidelberg University 0 0 0 2 0 0 0 2
Molecular Medicine for Neurodegenerative and Neuromuscular Diseases Unit, IRCCS Fondazione Stella Maris 0 4 0 2 0 0 0 2
Service de Génétique Médicale, Centre Hospitalier Universitaire de Nice-Université Côte d'Azur 0 0 0 2 0 0 0 2
Variantyx, Inc. 0 8 0 2 0 0 0 2
3billion 0 8 0 1 0 0 0 1
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 2 0 0 0 0 1 1
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 0 0 1 0 0 0 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 0 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 0 0 1 0 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 2 0 0 0 0 1 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 0 0 1 0 0 0 1
Genetic Diseases Diagnostic Center, Koc University Hospital 0 0 0 1 0 0 0 1
Genetic Foundation of Khorasan Razavi (GFKR) 0 1 0 1 0 0 0 1
Genetics and Genomic Medicine Centre, NeuroGen Healthcare, NeuroGen Healthcare 0 2 0 0 0 0 1 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 1 0 0 0 0 1 1
Imagene.me medical diagnostic laboratory, IMAGENE.ME SA 0 0 0 1 0 0 0 1
Institute of Human Genetics Munich, TUM University Hospital 0 6 0 1 0 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 6 0 1 0 0 0 1
Intergen Genetics and Rare Diseases Diagnosis Center 0 0 0 1 0 0 0 1
Laboratory of Medical Genetics, National & Kapodistrian University of Athens 0 0 0 0 0 0 1 1
Lifecell International Pvt. Ltd 0 0 0 1 0 0 0 1
Medical Genetics Laboratory, Tarbiat Modares University 0 1 0 1 0 0 0 1
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota 0 0 0 1 0 0 0 1
Molecular Genetics Laboratory, BC Children's and BC Women's Hospitals 0 2 0 1 0 0 0 1
Molecular Genetics, Royal Melbourne Hospital 0 3 0 0 0 0 1 1
Myriad Genetics, Inc. 0 1 0 1 0 0 0 1
Neurogenetics of motion laboratory, Montreal Neurological Institute 0 6 0 1 0 0 0 1
OMIM 0 13 0 1 0 0 0 1
Pars Genome Lab 0 0 0 0 0 0 1 1
SIB Swiss Institute of Bioinformatics 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 93
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_014363.6(SACS):c.909A>G (p.Ala303=) rs41315020 0.03313
NM_014363.6(SACS):c.1839G>A (p.Gln613=) rs35840595 0.02663
NM_014363.6(SACS):c.2080G>A (p.Ala694Thr) rs17325713 0.02472
NM_003119.4(SPG7):c.120G>A (p.Gly40=) rs187330648 0.00779
NM_014363.6(SACS):c.4466A>G (p.Asn1489Ser) rs147099630 0.00597
NM_003119.4(SPG7):c.1529C>T (p.Ala510Val) rs61755320 0.00364
NM_014363.6(SACS):c.13717A>C (p.Asn4573His) rs34382952 0.00326
NM_014363.6(SACS):c.10611A>G (p.Ala3537=) rs137856939 0.00236
NM_014363.6(SACS):c.8393C>A (p.Pro2798Gln) rs140551762 0.00178
NM_003119.4(SPG7):c.1045G>A (p.Gly349Ser) rs141659620 0.00102
NM_003119.4(SPG7):c.233T>A (p.Leu78Ter) rs121918358 0.00019
NM_014363.6(SACS):c.7394C>T (p.Ser2465Leu) rs747676277 0.00008
NM_014363.6(SACS):c.10954C>A (p.Pro3652Thr) rs201505036 0.00007
NM_003119.4(SPG7):c.2228T>C (p.Ile743Thr) rs752623413 0.00005
NM_003119.4(SPG7):c.2014G>A (p.Gly672Arg) rs369503365 0.00004
NM_014363.6(SACS):c.2439_2440del (p.Val815fs) rs775059063 0.00004
NM_014363.6(SACS):c.8315G>C (p.Gly2772Ala) rs763504656 0.00004
NM_003119.4(SPG7):c.1553-2_1553-1del rs772828460 0.00003
NM_003119.4(SPG7):c.878C>T (p.Ala293Val) rs201723702 0.00003
NM_014363.6(SACS):c.9508C>T (p.Arg3170Ter) rs202199411 0.00003
NM_003119.4(SPG7):c.1192C>T (p.Arg398Ter) rs1373388852 0.00002
NM_014363.6(SACS):c.4723C>T (p.Arg1575Trp) rs1426756976 0.00002
NM_003119.4(SPG7):c.1054G>A (p.Gly352Ser) rs537421502 0.00001
NM_003119.4(SPG7):c.1408C>T (p.Arg470Ter) rs748555510 0.00001
NM_003119.4(SPG7):c.1420C>T (p.His474Tyr) rs1567926386 0.00001
NM_003119.4(SPG7):c.1702C>T (p.Gln568Ter) rs946925151 0.00001
NM_003119.4(SPG7):c.1730G>A (p.Gly577Asp) rs1329063851 0.00001
NM_003119.4(SPG7):c.1972G>A (p.Ala658Thr) rs2058661391 0.00001
NM_003119.4(SPG7):c.1A>G (p.Met1Val) rs794726906 0.00001
NM_003119.4(SPG7):c.2084T>C (p.Leu695Pro) rs864622094 0.00001
NM_003119.4(SPG7):c.2249C>T (p.Pro750Leu) rs879253797 0.00001
NM_003119.4(SPG7):c.376+1G>T rs746053679 0.00001
NM_003119.4(SPG7):c.415C>T (p.Arg139Ter) rs370777371 0.00001
NM_003119.4(SPG7):c.861+1G>C rs1412575396 0.00001
NM_014363.6(SACS):c.10136T>G (p.Leu3379Ter) rs1057517250 0.00001
NM_014363.6(SACS):c.10907G>A (p.Arg3636Gln) rs281865119 0.00001
NM_014363.6(SACS):c.12973C>T (p.Arg4325Ter) rs762947018 0.00001
NM_014363.6(SACS):c.4744G>A (p.Asp1582Asn) rs1160357920 0.00001
NM_014363.6(SACS):c.5629C>T (p.Arg1877Ter) rs761089024 0.00001
NM_014363.6(SACS):c.562G>A (p.Gly188Arg) rs780184251 0.00001
NM_014363.6(SACS):c.623G>T (p.Ser208Ile) rs911764681 0.00001
NM_014363.6(SACS):c.7205_7206del (p.Leu2402fs) rs773182375 0.00001
NM_014363.6(SACS):c.8132C>T (p.Ser2711Leu) rs1213203489 0.00001
NM_014363.6(SACS):c.814C>T (p.Arg272Cys) rs374128662 0.00001
NM_014363.6(SACS):c.9305T>A (p.Leu3102Ter) rs886041949 0.00001
NM_003119.4(SPG7):c.1049_1077del (p.Pro350fs) rs775364547
NM_003119.4(SPG7):c.1053del (p.Gly352fs) rs760818649
NM_003119.4(SPG7):c.1053dup (p.Gly352fs) rs760818649
NM_003119.4(SPG7):c.1231G>A (p.Asp411Asn) rs745444834
NM_003119.4(SPG7):c.1450-1_1457del rs768823392
NM_003119.4(SPG7):c.1763C>T (p.Thr588Met) rs778387199
NM_003119.4(SPG7):c.1779+1G>T
NM_003119.4(SPG7):c.1861C>T (p.Gln621Ter) rs769258044
NM_003119.4(SPG7):c.1894G>A (p.Gly632Arg) rs368541637
NM_003119.4(SPG7):c.1940C>A (p.Ala647Glu) rs776380988
NM_003119.4(SPG7):c.1A>C (p.Met1Leu)
NM_003119.4(SPG7):c.2075G>C (p.Ser692Thr) rs121918357
NM_003119.4(SPG7):c.2104-2A>G rs1567934754
NM_003119.4(SPG7):c.273_274del (p.Trp92fs) rs2543672662
NM_003119.4(SPG7):c.292_295del (p.Thr98fs)
NM_003119.4(SPG7):c.335_336insTA (p.Glu112fs)
NM_003119.4(SPG7):c.958G>T (p.Glu320Ter)
NM_014363.6(SACS):c.10497C>A (p.Tyr3499Ter) rs755186798
NM_014363.6(SACS):c.10686_10689del (p.Phe3562fs) rs779338945
NM_014363.6(SACS):c.11012_11013del (p.Gln3671fs) rs1883576381
NM_014363.6(SACS):c.11374C>T (p.Arg3792Ter) rs565203731
NM_014363.6(SACS):c.11539ATT[1] (p.Ile3848del) rs2137565671
NM_014363.6(SACS):c.11914C>T (p.Arg3972Ter) rs781491486
NM_014363.6(SACS):c.1228_1229del (p.Leu410fs) rs1057516365
NM_014363.6(SACS):c.12835_12836del (p.Leu4279fs) rs1555249425
NM_014363.6(SACS):c.12923_12927del (p.Lys4308fs) rs1057517294
NM_014363.6(SACS):c.13132C>T (p.Arg4378Ter) rs747868017
NM_014363.6(SACS):c.2182C>T (p.Arg728Ter) rs752059006
NM_014363.6(SACS):c.2224C>T (p.Arg742Ter) rs1057517285
NM_014363.6(SACS):c.2881C>T (p.Arg961Ter) rs1593133395
NM_014363.6(SACS):c.3484G>T (p.Glu1162Ter) rs1246013998
NM_014363.6(SACS):c.4108C>T (p.Gln1370Ter)
NM_014363.6(SACS):c.4145A>G (p.His1382Arg) rs550057119
NM_014363.6(SACS):c.429_430del (p.Trp144fs) rs1555255328
NM_014363.6(SACS):c.4756_4760del (p.Asn1586fs) rs765361868
NM_014363.6(SACS):c.4954C>T (p.Gln1652Ter) rs2542273834
NM_014363.6(SACS):c.5836T>C (p.Trp1946Arg) rs137853017
NM_014363.6(SACS):c.6172del (p.Ser2058fs) rs1214399996
NM_014363.6(SACS):c.6186dup (p.Pro2063fs) rs2137611917
NM_014363.6(SACS):c.6290del (p.Cys2097fs) rs1868755540
NM_014363.6(SACS):c.6663del (p.Lys2221fs) rs1555251699
NM_014363.6(SACS):c.699del (p.Asp235fs) rs1415870785
NM_014363.6(SACS):c.7162_7163del (p.Thr2388fs) rs1555251539
NM_014363.6(SACS):c.7276C>T (p.Arg2426Ter) rs786204750
NM_014363.6(SACS):c.815G>A (p.Arg272His) rs745907077
NM_014363.6(SACS):c.8873A>G (p.Lys2958Arg) rs11839380
NM_014363.6(SACS):c.9561_9564del (p.Leu3187_Phe3188insTer) rs1060503431
NM_014363.6(SACS):c.9625_9628del (p.Phe3209fs) rs1555250557

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