ClinVar Miner

Variants from Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL) with conflicting interpretations

Location: Spain  Primary collection method: research
Minimum review status of the submission from Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL): Collection method of the submission from Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL):
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
50 23 0 23 0 0 13 33

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
Neurometabolic Diseases Laboratory, Bellvitge Biomedical Research Institute (IDIBELL) pathogenic likely pathogenic uncertain significance likely benign
pathogenic 0 16 8 1
likely pathogenic 7 0 4 0

Submitter to submitter summary #

Total submitters: 35
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 19 0 2 0 0 5 7
Genetic Services Laboratory, University of Chicago 0 1 0 2 0 0 2 4
OMIM 0 19 0 2 0 0 1 3
PreventionGenetics, part of Exact Sciences 0 0 0 3 0 0 0 3
MGZ Medical Genetics Center 0 1 0 3 0 0 0 3
Genome-Nilou Lab 0 3 0 0 0 0 3 3
Ambry Genetics 0 0 0 0 0 0 2 2
Revvity Omics, Revvity 0 5 0 2 0 0 0 2
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 5 0 1 0 0 1 2
SIB Swiss Institute of Bioinformatics 0 2 0 2 0 0 0 2
3billion 0 2 0 2 0 0 0 2
Baylor Genetics 0 4 0 1 0 0 0 1
Institute of Human Genetics, Cologne University 0 0 0 1 0 0 0 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 1 0 1 0 0 0 1
Clinical Genetics, Academic Medical Center 0 0 0 0 0 0 1 1
Mendelics 0 2 0 1 0 0 0 1
Eurofins Ntd Llc (ga) 0 0 0 1 0 0 0 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 4 0 1 0 0 0 1
Fulgent Genetics, Fulgent Genetics 0 3 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
UW Hindbrain Malformation Research Program, University of Washington 0 1 0 1 0 0 0 1
Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics 0 1 0 1 0 0 0 1
CeGaT Center for Human Genetics Tuebingen 0 3 0 0 0 0 1 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 0 0 1 0 0 0 1
Undiagnosed Diseases Network, NIH 0 0 0 1 0 0 0 1
Wong Mito Lab, Molecular and Human Genetics, Baylor College of Medicine 0 0 0 1 0 0 0 1
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 1 0 0 0 0 1 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 1 0 1 0 0 0 1
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill 0 1 0 1 0 0 0 1
Codex Genetics Limited 0 0 0 1 0 0 0 1
Paris Brain Institute, Inserm - ICM 0 9 0 1 0 0 0 1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 2 0 1 0 0 0 1
Genomics England Pilot Project, Genomics England 0 2 0 1 0 0 0 1
Inherited Neuropathy Consortium Ii, University Of Miami 0 0 0 0 0 0 1 1
Tumer Group, Copenhagen University Hospital, Rigshospitalet 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 33
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000303.3(PMM2):c.422G>A (p.Arg141His) rs28936415 0.00338
NM_007055.4(POLR3A):c.1909+22G>A rs191875469 0.00156
NM_024570.4(RNASEH2B):c.529G>A (p.Ala177Thr) rs75184679 0.00141
NM_004369.4(COL6A3):c.7447A>G (p.Lys2483Glu) rs139260335 0.00057
NM_001378615.1(CC2D2A):c.4667A>T (p.Asp1556Val) rs201502401 0.00020
NM_005186.4(CAPN1):c.1605+5G>A rs375817528 0.00012
NM_006567.5(FARS2):c.1082C>T (p.Pro361Leu) rs751459058 0.00011
NM_001253852.3(AP4B1):c.577G>A (p.Val193Ile) rs376478015 0.00009
NM_025137.4(SPG11):c.733_734del (p.Met245fs) rs312262720 0.00005
NM_001253852.3(AP4B1):c.1558C>T (p.Arg520Cys) rs200276550 0.00004
NM_002693.3(POLG):c.911T>G (p.Leu304Arg) rs121918044 0.00004
NM_021930.6(RINT1):c.1555C>T (p.Arg519Ter) rs759853907 0.00004
NM_004553.6(NDUFS6):c.309+5G>A rs763535523 0.00001
NM_015915.5(ATL1):c.1483C>T (p.Arg495Trp) rs864622269 0.00001
NM_020919.4(ALS2):c.2606A>C (p.Gln869Pro) rs1355321952 0.00001
NM_000303.3(PMM2):c.640-23A>G rs981372486
NM_001114748.2(TMEM240):c.509C>T (p.Pro170Leu) rs606231451
NM_001130438.3(SPTAN1):c.55C>T (p.Arg19Trp) rs748232676
NM_001244008.2(KIF1A):c.773C>T (p.Thr258Met) rs1553638086
NM_001321075.3(DLG4):c.1592-1G>A rs2142825829
NM_003119.3(SPG7):c.1454_1462delGGCGGGAGA (p.Arg485_Glu487del) rs768823392
NM_005412.6(SHMT2):c.1495C>G (p.Pro499Ala) rs2037465152
NM_006513.4(SARS1):c.969+1_969+3del
NM_007055.4(POLR3A):c.1771-7C>G rs201314157
NM_007055.4(POLR3A):c.1862G>A (p.Gly621Asp) rs757718124
NM_014946.4(SPAST):c.1507C>T (p.Arg503Trp) rs864622162
NM_015915.5(ATL1):c.466A>C (p.Thr156Pro) rs2140205433
NM_015915.5(ATL1):c.715C>T (p.Arg239Cys) rs119476046
NM_020810.3(TRMT5):c.312_315del (p.Ile105fs) rs755184077
NM_020810.3(TRMT5):c.665T>C (p.Ile222Thr) rs766935145
NM_021930.6(RINT1):c.1672-1G>C
NM_025137.4(SPG11):c.6477+4A>G rs312262780
NM_025137.4(SPG11):c.7150A>T (p.Lys2384Ter) rs1555446078

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