ClinVar Miner

Variants from TIDEX, University of British Columbia with conflicting interpretations

Location: Canada  Primary collection method: research
Minimum review status of the submission from TIDEX, University of British Columbia: Collection method of the submission from TIDEX, University of British Columbia:
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
28 13 0 4 4 0 2 9

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
TIDEX, University of British Columbia pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 2 1 0 0
likely pathogenic 2 0 1 0 0
uncertain significance 0 0 0 3 3

Submitter to submitter summary #

Total submitters: 9
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 8 0 1 3 0 1 5
OMIM 0 3 0 1 0 0 0 1
PreventionGenetics, part of Exact Sciences 0 0 0 0 1 0 0 1
RettBASE 0 0 0 1 0 0 0 1
Illumina Laboratory Services, Illumina 0 0 0 0 1 0 0 1
UCLA Clinical Genomics Center, UCLA 0 0 0 1 0 0 0 1
CeGaT Center for Human Genetics Tuebingen 0 0 0 0 1 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 1 0 0 1 0 0 1
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 9
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_001199267.2(DGKZ):c.2660C>G (p.Thr887Arg) rs76583617 0.00449
NM_170606.3(KMT2C):c.8502A>T (p.Glu2834Asp) rs138845109 0.00321
NM_000429.3(MAT1A):c.712G>A (p.Glu238Lys) rs116528173 0.00022
NM_002578.5(PAK3):c.1579A>G (p.Ser527Gly) rs200474454 0.00021
NM_001163435.3(TBCK):c.2060-2A>G rs62321379 0.00005
NM_000159.4(GCDH):c.533G>A (p.Gly178Glu) rs786204627
NM_001110792.2(MECP2):c.455C>T (p.Ala152Val) rs28934908
NM_006087.4(TUBB4A):c.763G>A (p.Val255Ile) rs767399782
NM_014946.4(SPAST):c.1477G>C (p.Asp493His) rs1060499939

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