ClinVar Miner

Variants from Sydney Genome Diagnostics, Children's Hospital Westmead with conflicting interpretations

Location: Australia  Primary collection method: clinical testing
Minimum review status of the submission from Sydney Genome Diagnostics, Children's Hospital Westmead: Collection method of the submission from Sydney Genome Diagnostics, Children's Hospital Westmead:
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
251 29 0 22 3 1 6 32

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
Sydney Genome Diagnostics, Children's Hospital Westmead pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 13 1 0 0
likely pathogenic 9 0 3 0 0
uncertain significance 2 1 0 2 1
risk factor 0 0 0 1 0

Submitter to submitter summary #

Total submitters: 22
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 8 2 0 1 11
Yale Center for Mendelian Genomics, Yale University 0 1 0 5 0 0 0 5
Genome Diagnostics Laboratory, The Hospital for Sick Children 0 0 0 0 0 1 1 2
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 2 0 2 0 0 0 2
Natera, Inc. 0 5 0 0 1 0 1 2
Fulgent Genetics, Fulgent Genetics 0 7 0 1 0 0 1 2
Juha Muilu Group; Institute for Molecular Medicine Finland (FIMM) 0 0 0 2 0 0 0 2
UNC Molecular Genetics Laboratory, University of North Carolina at Chapel Hill 0 2 0 1 0 0 1 2
DASA 0 0 0 1 0 0 1 2
Baylor Genetics 0 3 0 1 0 0 0 1
Athena Diagnostics Inc 0 0 0 1 0 0 0 1
GeneDx 0 1 0 0 0 0 1 1
Revvity Omics, Revvity 0 3 0 1 0 0 0 1
Counsyl 0 0 0 0 0 0 1 1
Blueprint Genetics 0 0 0 0 0 0 1 1
CSER _CC_NCGL, University of Washington 0 0 0 1 0 0 0 1
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 0 0 1 0 0 0 1
Laboratorio de Imunogenetica e Histocompatibilidade, Universidade Federal do Parana 0 0 0 1 0 0 0 1
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City 0 0 0 1 0 0 0 1
Molecular Biology Laboratory, Fundació Puigvert 0 0 0 1 0 0 0 1
Laboratory of Molecular Genetics, Children's Memorial Health Institute 0 2 0 1 0 0 0 1
Arcensus 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 32
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_015102.5(NPHP4):c.3329C>T (p.Ala1110Val) rs139767853 0.00374
NM_000361.3(THBD):c.127G>A (p.Ala43Thr) rs1800576 0.00255
NM_014270.5(SLC7A9):c.544G>A (p.Ala182Thr) rs79389353 0.00238
NM_015102.5(NPHP4):c.2965G>A (p.Glu989Lys) rs116606479 0.00068
NM_000361.3(THBD):c.1483C>T (p.Pro495Ser) rs1800578 0.00057
NM_014625.4(NPHS2):c.413G>A (p.Arg138Gln) rs74315342 0.00054
NM_000092.5(COL4A4):c.2241C>T (p.Pro747=) rs374510402 0.00048
NM_138694.4(PKHD1):c.107C>T (p.Thr36Met) rs137852944 0.00048
NM_000091.5(COL4A3):c.4981C>T (p.Arg1661Cys) rs201697532 0.00039
NM_014270.5(SLC7A9):c.313G>A (p.Gly105Arg) rs121908480 0.00017
NM_024753.5(TTC21B):c.626C>T (p.Pro209Leu) rs140511594 0.00011
NM_004646.4(NPHS1):c.3478C>T (p.Arg1160Ter) rs267606919 0.00010
NM_138694.4(PKHD1):c.4870C>T (p.Arg1624Trp) rs200391019 0.00006
NM_138694.4(PKHD1):c.5912G>A (p.Gly1971Asp) rs180675584 0.00006
NM_153704.6(TMEM67):c.1046T>C (p.Leu349Ser) rs386834180 0.00004
NM_172351.3(CD46):c.286+2T>G rs769742294 0.00004
NM_176824.3(BBS7):c.187G>A (p.Gly63Arg) rs754579374 0.00004
NM_033380.3(COL4A5):c.5048G>A (p.Arg1683Gln) rs104886308 0.00002
NM_138694.4(PKHD1):c.5830G>A (p.Asp1944Asn) rs774290802 0.00002
NM_004183.4(BEST1):c.400C>G (p.Leu134Val) rs753614067 0.00001
NM_015102.5(NPHP4):c.1075C>T (p.Gln359Ter) rs1430741326 0.00001
NM_138694.4(PKHD1):c.8411T>A (p.Met2804Lys) rs794727759 0.00001
NM_176824.3(BBS7):c.878A>C (p.Gln293Pro) rs889417696 0.00001
NM_000091.5(COL4A3):c.2323_2340del (p.772LPG[1]) rs1306992119
NM_000092.5(COL4A4):c.81_86del (p.27IL[1]) rs771943519
NM_001023570.4(IQCB1):c.897_900dup (p.Ile301fs) rs745340459
NM_001174147.2(LMX1B):c.737G>A (p.Arg246Gln) rs1191455921
NM_004621.6(TRPC6):c.523C>T (p.Arg175Trp) rs869025541
NM_004646.4(NPHS1):c.3250dup (p.Val1084fs) rs386833935
NM_024685.4(BBS10):c.2122_2123del (p.Lys708fs) rs1951753208
NM_138694.4(PKHD1):c.1032_1033del (p.Glu345fs) rs1446729264
NM_153704.6(TMEM67):c.2301del (p.Asp768fs) rs386834191

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