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
40 12 3 13 8 1 10 30

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 3 0 2 0 0 0
likely pathogenic 10 0 1 0 0 0
uncertain significance 6 2 0 3 6 1
likely benign 0 0 1 0 3 0

Submitter to submitter summary #

Total submitters: 26
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 10 0 10 4 1 3 18
Illumina Clinical Services Laboratory,Illumina 0 6 0 2 5 0 1 8
Counsyl 0 8 0 3 0 0 4 7
Natera, Inc. 0 5 0 5 2 0 0 7
Mendelics 0 1 0 0 5 0 2 7
GeneReviews 0 1 3 2 0 0 2 7
OMIM 0 4 0 4 0 0 2 6
Integrated Genetics/Laboratory Corporation of America 0 5 0 2 0 0 2 4
Baylor Genetics 0 5 0 2 0 0 0 2
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 0 0 0 1 0 1 2
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center 0 1 0 0 1 0 1 2
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 1 0 0 1 2
Genetic Services Laboratory, University of Chicago 0 0 0 0 0 0 1 1
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine 0 0 0 0 0 0 1 1
Genome Diagnostics Laboratory,University Medical Center Utrecht 0 0 0 0 0 0 1 1
Centogene AG - the Rare Disease Company 0 0 0 0 0 0 1 1
Fulgent Genetics,Fulgent Genetics 0 2 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, Klinikum rechts der Isar 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
Research and Development, 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
Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City 0 0 0 0 0 0 1 1
ClinGen PAH Variant Curation Expert Panel 0 1 0 0 1 0 0 1
Broad Institute Rare Disease Group, Broad Institute 0 0 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 30
Download table as spreadsheet
HGVS dbSNP
NM_000053.4(ATP7B):c.2333G>T (p.Arg778Leu) rs28942074
NM_000053.4(ATP7B):c.2621C>T (p.Ala874Val) rs121907994
NM_000170.2(GLDC):c.1545G>A (p.Arg515=) rs121964976
NM_000203.5(IDUA):c.1225G>C (p.Gly409Arg) rs11934801
NM_000263.4(NAGLU):c.1562C>T (p.Pro521Leu) rs104894595
NM_000271.5(NPC1):c.2974G>T (p.Gly992Trp) rs80358254
NM_000277.3(PAH):c.158G>A (p.Arg53His) rs118092776
NM_000317.3(PTS):c.155A>G (p.Asn52Ser) rs104894275
NM_000360.4(TH):c.364C>T (p.Arg122Ter) rs771610752
NM_000360.4(TH):c.605G>A (p.Arg202His) rs80338892
NM_000360.4(TH):c.714_715del (p.Leu239fs) rs1564918287
NM_000436.4(OXCT1):c.173C>T (p.Thr58Met) rs75134564
NM_000487.6(ARSA):c.*96A>G rs6151429
NM_000528.4(MAN2B1):c.2398G>C (p.Gly800Arg) rs398123456
NM_000531.6(OTC):c.298+5G>C rs72554348
NM_000531.6(OTC):c.809A>G (p.Gln270Arg) rs1800328
NM_001081.3(CUBN):c.5428C>T (p.Arg1810Ter) rs143944436
NM_001163817.2(DHCR7):c.725G>A (p.Arg242His) rs80338857
NM_001370658.1(BTD):c.1270G>C (p.Asp424His) rs13078881
NM_001370658.1(BTD):c.697C>T (p.Pro233Ser) rs397514383
NM_001875.5(CPS1):c.-4_-3insTTC rs61509952
NM_002225.5(IVD):c.457-2A>G rs771914739
NM_004453.4(ETFDH):c.250G>A (p.Ala84Thr) rs121964954
NM_004453.4(ETFDH):c.380T>A (p.Leu127His) rs121964956
NM_006516.3(SLC2A1):c.274C>A (p.Arg92=) rs202060209
NM_014251.3(SLC25A13):c.615+5G>A rs80338717
NM_015697.8(COQ2):c.590G>A (p.Arg197His) rs121918231
NM_016729.3(FOLR1):c.493+2T>C rs144637717
NM_025243.4(SLC19A3):c.111del (p.Tyr38fs) rs1559252723
NM_183050.4(BCKDHB):c.1159C>T (p.Arg387Ter) rs751599203

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