ClinVar Miner

Variants from SingHealth Duke-NUS Institute of Precision Medicine with conflicting interpretations

Location: Singapore  Primary collection method: curation
Minimum review status of the submission from SingHealth Duke-NUS Institute of Precision Medicine: Collection method of the submission from SingHealth Duke-NUS Institute of Precision Medicine:
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
34 15 0 16 12 1 10 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
SingHealth Duke-NUS Institute of Precision Medicine pathogenic likely pathogenic uncertain significance likely benign benign other
pathogenic 0 2 2 0 0 0
likely pathogenic 11 0 1 0 0 0
uncertain significance 7 2 0 5 9 1
likely benign 0 0 1 0 3 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 11 0 12 7 1 3 23
Natera, Inc. 0 9 0 6 3 0 2 11
Baylor Genetics 0 9 0 4 0 0 5 9
Illumina Laboratory Services, Illumina 0 6 0 2 5 0 1 8
Genome-Nilou Lab 0 4 0 3 3 0 2 8
Counsyl 0 7 0 3 0 0 4 7
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 6 0 5 0 0 2 7
Mendelics 0 1 0 0 5 0 2 7
OMIM 0 5 0 2 0 0 3 5
Revvity Omics, Revvity 0 4 0 2 1 0 2 5
Fulgent Genetics, Fulgent Genetics 0 6 0 3 1 0 1 5
3billion 0 2 0 2 0 0 2 4
Neuberg Centre For Genomic Medicine, NCGM 0 0 0 1 1 0 1 3
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 1 0 1 0 0 1 2
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 2 0 0 1 0 1 2
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center 0 1 0 0 1 0 1 2
Genetic Services Laboratory, University of Chicago 0 0 0 0 0 0 1 1
MGZ Medical Genetics Center 0 0 0 0 0 0 1 1
Centogene AG - the Rare Disease Company 0 0 0 0 0 0 1 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 0 1 0 0 0 0 1 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 0 0 0 0 0 1 1
Institute of Human Genetics Munich, Klinikum Rechts Der Isar, TU München 0 1 0 1 0 0 0 1
Division of Human Genetics, Children's Hospital of Philadelphia 0 0 0 0 0 0 1 1
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 0 0 0 0 0 1 1
Color Diagnostics, LLC DBA Color Health 0 0 0 0 1 0 0 1
Genetics and Molecular Pathology, SA Pathology 0 1 0 0 0 0 1 1
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego 0 0 0 0 0 0 1 1
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 1 0 0 0 1
Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center 0 0 0 1 0 0 0 1
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 0 0 0 0 0 1 1
Variantyx, Inc. 0 0 0 0 0 0 1 1
ClinGen PAH Variant Curation Expert Panel 0 1 0 0 1 0 0 1
Broad Center for Mendelian Genomics, Broad Institute of MIT and Harvard 0 0 0 0 1 0 0 1
Clinical Genomics Program, Stanford Medicine 0 0 0 0 0 0 1 1
Institute of Human Genetics, University Hospital Muenster 0 0 0 0 0 0 1 1
New York Genome Center 0 0 0 0 0 0 1 1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 1 0 0 0 0 1 1
DASA 0 0 0 0 0 0 1 1
Molecular Genetics, Royal Melbourne Hospital 0 0 0 0 1 0 0 1
Provincial Medical Genetics Program of British Columbia, University of British Columbia 0 1 0 1 0 0 0 1
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 0 0 0 0 0 0 1 1
Molecular Biology Laboratory, Department of Zoology, Quaid-i-azam University 0 0 0 0 0 0 1 1
Neonatal Disease Screening Center, Medical Genetics Center, Huaihua City Maternal and Child Health Care Hospital 0 1 0 0 1 0 0 1
All of Us Research Program, National Institutes of Health 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 33
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000487.6(ARSA):c.*96A>G rs6151429 0.05120
NM_001370658.1(BTD):c.1270G>C (p.Asp424His) rs13078881 0.03225
NM_000531.6(OTC):c.809A>G (p.Gln270Arg) rs1800328 0.02868
NM_000203.5(IDUA):c.1225G>C (p.Gly409Arg) rs11934801 0.01974
NM_016729.3(FOLR1):c.493+2T>C rs144637717 0.00134
NM_000277.3(PAH):c.158G>A (p.Arg53His) rs118092776 0.00091
NM_001081.4(CUBN):c.1951C>G (p.Arg651Gly) rs182512508 0.00086
NM_000531.6(OTC):c.298+5G>C rs72554348 0.00058
NM_000436.4(OXCT1):c.173C>T (p.Thr58Met) rs75134564 0.00053
NM_001081.4(CUBN):c.5428C>T (p.Arg1810Ter) rs143944436 0.00019
NM_001360.3(DHCR7):c.725G>A (p.Arg242His) rs80338857 0.00004
NM_004453.4(ETFDH):c.250G>A (p.Ala84Thr) rs121964954 0.00004
NM_001358921.2(COQ2):c.440G>A (p.Arg147His) rs121918231 0.00003
NM_000263.4(NAGLU):c.1562C>T (p.Pro521Leu) rs104894595 0.00002
NM_000360.4(TH):c.364C>T (p.Arg122Ter) rs771610752 0.00002
NM_000053.4(ATP7B):c.2621C>T (p.Ala874Val) rs121907994 0.00001
NM_000317.3(PTS):c.155A>G (p.Asn52Ser) rs104894275 0.00001
NM_001352514.2(HLCS):c.2451-1G>A rs1158898827 0.00001
NM_001370658.1(BTD):c.577del (p.His193fs) rs780874850 0.00001
NM_001370658.1(BTD):c.697C>T (p.Pro233Ser) rs397514383 0.00001
NM_025243.4(SLC19A3):c.111del (p.Tyr38fs) rs1559252723 0.00001
NM_183050.4(BCKDHB):c.1159C>T (p.Arg387Ter) rs751599203 0.00001
NM_000170.3(GLDC):c.1545G>A (p.Arg515=) rs121964976
NM_000181.4(GUSB):c.1916_1918dup (p.Val639dup) rs770237165
NM_000271.5(NPC1):c.2974G>T (p.Gly992Trp) rs80358254
NM_000360.4(TH):c.714_715del (p.Leu239fs) rs1564918287
NM_000528.4(MAN2B1):c.2398G>C (p.Gly800Arg) rs398123456
NM_001875.5(CPS1):c.-4_-3insTTC rs61509952
NM_001985.3(ETFB):c.58-57dup rs74357706
NM_002225.5(IVD):c.457-2A>G rs771914739
NM_004453.4(ETFDH):c.380T>A (p.Leu127His) rs121964956
NM_006516.4(SLC2A1):c.274C>A (p.Arg92=) rs202060209
NM_030943.4(AMN):c.1343_1348dup (p.Gly448_Ala449dup) rs36040113

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