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 Variants with at least 2 submissions 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 kind of conflict
37 12 4 12 11 1 12 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 4 0 2 0 0 0
likely pathogenic 8 0 2 0 0 0
uncertain significance 6 2 0 6 8 1
likely benign 0 0 1 0 4 0
benign 1 0 1 0 0 0

Submitter to submitter summary #

Total submitters: 28
Download table as spreadsheet
Submitter Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
Invitae 0 8 0 6 5 1 2 14
OMIM 0 7 0 5 0 0 4 9
GeneReviews 0 1 4 3 0 0 2 9
GeneDx 0 7 0 3 3 0 1 7
Counsyl 0 11 0 3 0 0 4 7
Illumina Clinical Services Laboratory,Illumina 0 6 0 1 5 0 1 7
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 0 10 0 0 3 1 2 6
PreventionGenetics 0 1 0 1 4 0 0 5
Integrated Genetics/Laboratory Corporation of America 0 6 0 3 2 0 0 5
Center for Pediatric Genomic Medicine,Children's Mercy Hospital and Clinics 0 2 0 1 2 0 1 4
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 0 0 0 2 0 1 3
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 1 0 1 1 0 1 3
Mayo Clinic Genetic Testing Laboratories,Mayo Clinic 0 0 0 1 2 0 0 3
Genetic Services Laboratory, University of Chicago 0 0 0 0 1 0 1 2
Ambry Genetics 0 2 0 0 2 0 0 2
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center 0 2 0 0 1 0 1 2
Diagnostic Laboratory, Department of Genetics,University Medical Center Groningen 0 0 0 1 0 0 1 2
Athena Diagnostics Inc 0 0 0 0 1 0 0 1
Division of Genomic Diagnostics,The Children's Hospital of Philadelphia 0 1 0 0 1 0 0 1
Genome Diagnostics Laboratory,University Medical Center Utrecht 0 0 0 0 0 0 1 1
Fulgent Genetics 0 3 0 0 0 0 1 1
Quest Diagnostics Nichols Institute San Juan Capistrano 0 0 0 0 0 0 1 1
ClinVar Staff, National Center for Biotechnology Information (NCBI) 0 0 0 0 0 0 1 1
GenMed Metabolism Lab 0 0 0 0 0 0 1 1
Division of Human Genetics,Children's Hospital of Philadelphia 0 0 0 0 0 0 1 1
ARUP Institute,ARUP Laboratories 0 1 0 0 0 0 1 1
DNA and Cytogenetics Diagnostics Unit,Erasmus Medical Center 0 0 0 1 0 0 0 1
ClinGen PAH Variant Curation Expert Panel, 0 1 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 33
Download table as spreadsheet
HGVS dbSNP
NM_000053.3(ATP7B):c.2333G>T (p.Arg778Leu) rs28942074
NM_000053.3(ATP7B):c.2621C>T (p.Ala874Val) rs121907994
NM_000170.2(GLDC):c.1545G>A (p.Arg515=) rs121964976
NM_000203.4(IDUA):c.1225G>C (p.Gly409Arg) rs11934801
NM_000263.3(NAGLU):c.1562C>T (p.Pro521Leu) rs104894595
NM_000271.4(NPC1):c.2974G>T (p.Gly992Trp) rs80358254
NM_000277.3(PAH):c.158G>A (p.Arg53His) rs118092776
NM_000317.2(PTS):c.155A>G (p.Asn52Ser) rs104894275
NM_000436.3(OXCT1):c.173C>T (p.Thr58Met) rs75134564
NM_000487.5(ARSA):c.*96A>G rs6151429
NM_000487.5(ARSA):c.1178C>G (p.Thr393Ser) rs743616
NM_000528.3(MAN2B1):c.2398G>C (p.Gly800Arg) rs398123456
NM_000531.5(OTC):c.298+5G>C rs72554348
NM_000531.5(OTC):c.809A>G (p.Gln270Arg) rs1800328
NM_001014763.1(ETFB):c.278dupC (p.Pro94Thrfs) rs74357706
NM_001081.3(CUBN):c.5428C>T (p.Arg1810Ter)
NM_001159508.2(IVD):c.367-2A>G rs771914739
NM_001281723.2(BTD):c.763C>T (p.Pro255Ser) rs397514383
NM_001281724.2(BTD):c.1336G>C (p.Asp446His) rs13078881
NM_001360.2(DHCR7):c.725G>A (p.Arg242His) rs80338857
NM_001875.4(CPS1):c.-4_-3insTTC rs61509952
NM_001918.3(DBT):c.1150G>A (p.Gly384Ser) rs12021720
NM_001985.2(ETFB):c.58-313_58-312insCTGTGG rs61361626
NM_004453.3(ETFDH):c.250G>A (p.Ala84Thr) rs121964954
NM_004453.3(ETFDH):c.380T>A (p.Leu127His) rs121964956
NM_006516.3(SLC2A1):c.274C>A (p.Arg92=) rs202060209
NM_014251.2(SLC25A13):c.615+5G>A rs80338717
NM_014251.2(SLC25A13):c.852_855delTATG (p.Met285Profs) rs80338720
NM_015697.8(COQ2):c.590G>A (p.Arg197His) rs121918231
NM_015697.8(COQ2):c.64A>T (p.Arg22Ter) rs112033303
NM_016725.2(FOLR1):c.493+2T>C rs144637717
NM_199292.2(TH):c.457C>T (p.Arg153Ter) rs771610752
NM_199292.2(TH):c.698G>A (p.Arg233His) rs80338892

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