ClinVar Miner

Variants from Centre for Inherited Metabolic Diseases, Karolinska University Hospital with conflicting interpretations

Location: Sweden  Primary collection method: clinical testing
Minimum review status of the submission from Centre for Inherited Metabolic Diseases, Karolinska University Hospital: Collection method of the submission from Centre for Inherited Metabolic Diseases, Karolinska University Hospital:
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
73 46 0 46 0 0 16 57

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 Inherited Metabolic Diseases, Karolinska University Hospital pathogenic likely pathogenic uncertain significance
pathogenic 0 34 13
likely pathogenic 12 0 3

Submitter to submitter summary #

Total submitters: 42
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
Counsyl 0 3 0 8 0 0 4 12
Invitae 0 44 0 8 0 0 2 10
OMIM 0 25 0 6 0 0 0 6
Baylor Genetics 0 25 0 5 0 0 1 6
Revvity Omics, Revvity 0 18 0 3 0 0 2 5
Genome-Nilou Lab 0 10 0 4 0 0 1 5
Laboratory of Diagnosis and Therapy of Lysosomal Disorders, University of Padova 0 3 0 3 0 0 0 3
Natera, Inc. 0 19 0 2 0 0 0 2
Mendelics 0 4 0 2 0 0 0 2
Illumina Laboratory Services, Illumina 0 7 0 2 0 0 0 2
SIB Swiss Institute of Bioinformatics 0 0 0 2 0 0 0 2
Myriad Genetics, Inc. 0 12 0 2 0 0 0 2
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 7 0 2 0 0 0 2
Genomics England Pilot Project, Genomics England 0 1 0 2 0 0 0 2
ClinGen ACADVL Variant Curation Expert Panel, ClinGen 0 0 0 2 0 0 0 2
Clinical Molecular Genetics Laboratory, Johns Hopkins All Children's Hospital 0 0 0 1 0 0 0 1
Genetic Services Laboratory, University of Chicago 0 4 0 1 0 0 0 1
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 20 0 1 0 0 0 1
Fulgent Genetics, Fulgent Genetics 0 17 0 0 0 0 1 1
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 0 0 0 1 0 0 0 1
Genomic Research Center, Shahid Beheshti University of Medical Sciences 0 2 0 1 0 0 0 1
Foundation for Research in Genetics and Endocrinology, FRIGE's Institute of Human Genetics 0 3 0 0 0 0 1 1
Institute for Medical Genetics and Human Genetics, Charité - Universitätsmedizin Berlin 0 1 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 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
Daryl Scott Lab, Baylor College of Medicine 0 0 0 0 0 0 1 1
Undiagnosed Diseases Network, NIH 0 0 0 0 0 0 1 1
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 0 2 0 0 0 0 1 1
Genetics and Molecular Pathology, SA Pathology 0 3 0 1 0 0 0 1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 5 0 1 0 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 6 0 0 0 0 1 1
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 2 0 1 0 0 0 1
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 2 0 1 0 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 4 0 0 0 0 1 1
ClinGen PAH Variant Curation Expert Panel 0 0 0 0 0 0 1 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 5 0 0 0 0 1 1
Pathology and Clinical Laboratory Medicine, King Fahad Medical City 0 1 0 0 0 0 1 1
3billion 0 9 0 1 0 0 0 1
DASA 0 1 0 1 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 0 3 0 1 0 0 0 1
Department of Biotechnology and Genetic Engineering, Kohat University of Science and Technology 0 0 0 1 0 0 0 1
Inherited Neuropathy Consortium Ii, University Of Miami 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 57
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000303.3(PMM2):c.422G>A (p.Arg141His) rs28936415 0.00338
NM_183050.4(BCKDHB):c.832G>A (p.Gly278Ser) rs386834233 0.00061
NM_020117.11(LARS1):c.1292T>A (p.Val431Asp) rs150429680 0.00041
NM_000199.5(SGSH):c.734G>A (p.Arg245His) rs104894635 0.00039
NM_000199.5(SGSH):c.220C>T (p.Arg74Cys) rs104894636 0.00021
NM_000271.5(NPC1):c.3019C>G (p.Pro1007Ala) rs80358257 0.00021
NM_183050.4(BCKDHB):c.853C>T (p.Arg285Ter) rs398124598 0.00015
NM_001282225.2(ADA2):c.139G>A (p.Gly47Arg) rs202134424 0.00010
NM_000153.4(GALC):c.1586C>T (p.Thr529Met) rs200960659 0.00009
NM_002437.5(MPV17):c.191C>G (p.Pro64Arg) rs375401970 0.00008
NM_000310.4(PPT1):c.541G>A (p.Val181Met) rs148412181 0.00006
NM_000017.4(ACADS):c.1138C>T (p.Arg380Trp) rs28940875 0.00004
NM_020247.5(COQ8A):c.811C>T (p.Arg271Cys) rs145034527 0.00004
NM_000481.4(AMT):c.217C>T (p.Arg73Cys) rs386833679 0.00003
NM_017570.5(OPLAH):c.659C>T (p.Ser220Leu) rs781785267 0.00003
NM_000199.5(SGSH):c.364G>A (p.Gly122Arg) rs761607612 0.00002
NM_000512.5(GALNS):c.245C>T (p.Ser82Leu) rs371429653 0.00002
NM_206933.4(USH2A):c.15017C>T (p.Thr5006Met) rs757676723 0.00002
NM_000018.4(ACADVL):c.1405C>T (p.Arg469Trp) rs113994170 0.00001
NM_000018.4(ACADVL):c.1468G>C (p.Ala490Pro) rs759775666 0.00001
NM_000153.4(GALC):c.1591C>T (p.Arg531Cys) rs749893889 0.00001
NM_000255.4(MMUT):c.2206C>T (p.Leu736Phe) rs753461919 0.00001
NM_000545.8(HNF1A):c.1501G>A (p.Ala501Thr) rs371807951 0.00001
NM_001918.5(DBT):c.5C>T (p.Ala2Val) rs398123672 0.00001
NM_002936.6(RNASEH1):c.424G>A (p.Val142Ile) rs766294940 0.00001
NM_005957.5(MTHFR):c.680C>T (p.Thr227Met) rs748571395 0.00001
NM_013339.4(ALG6):c.250G>A (p.Ala84Thr) rs762643273 0.00001
NM_018359.5(UFSP2):c.344T>A (p.Val115Glu) rs142500730 0.00001
NM_000052.7(ATP7A):c.1639C>T (p.Arg547Ter) rs797045332
NM_000162.5(GCK):c.704T>C (p.Met235Thr) rs193922323
NM_000271.5(NPC1):c.1843C>T (p.Arg615Cys) rs745777805
NM_000277.3(PAH):c.473G>C (p.Arg158Pro) rs5030843
NM_000282.4(PCCA):c.2040G>A (p.Ala680=) rs369982920
NM_000303.3(PMM2):c.317A>T (p.Tyr106Phe) rs387906824
NM_000303.3(PMM2):c.44G>C (p.Gly15Ala) rs958073558
NM_000487.6(ARSA):c.1114C>T (p.Arg372Trp) rs74315476
NM_000744.7(CHRNA4):c.851C>T (p.Ser284Leu) rs28931591
NM_001165963.4(SCN1A):c.1118T>C (p.Leu373Ser) rs1553547448
NM_001165963.4(SCN1A):c.602+1G>A
NM_001170535.3(ATAD3A):c.1361A>G (p.Asn454Ser) rs2100677960
NM_001184880.2(PCDH19):c.707C>T (p.Pro236Leu) rs1060502176
NM_002074.5(GNB1):c.239T>C (p.Ile80Thr) rs752746786
NM_002641.4(PIGA):c.1352T>C (p.Ile451Thr) rs2147714706
NM_002769.5(PRSS1):c.346C>T (p.Arg116Cys) rs387906698
NM_003850.3(SUCLA2):c.998A>G (p.Asp333Gly)
NM_005654.6(NR2F1):c.437G>A (p.Cys146Tyr) rs1753213218
NM_007055.4(POLR3A):c.1771-7C>G rs201314157
NM_013328.4(PYCR2):c.773T>C (p.Val258Ala) rs886037932
NM_014233.4(UBTF):c.628G>A (p.Glu210Lys) rs1555582065
NM_014363.6(SACS):c.8793dup (p.Arg2932fs) rs767871841
NM_015937.6(PIGT):c.547A>C (p.Thr183Pro) rs587777027
NM_017882.3(CLN6):c.791CCT[1] (p.Ser265del) rs768422260
NM_020708.5(SLC12A5):c.1208T>C (p.Leu403Pro) rs863225304
NM_020708.5(SLC12A5):c.1583G>A (p.Gly528Asp) rs863225305
NM_022132.5(MCCC2):c.739-2A>G rs2112427637
NM_030632.3(ASXL3):c.3349C>T (p.Arg1117Ter) rs868044680
NM_206933.4(USH2A):c.10450C>T (p.Arg3484Ter) rs111033379

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