ClinVar Miner

Variants from NxGen MDx with conflicting interpretations

Location: United States  Primary collection method: clinical testing
Minimum review status of the submission from NxGen MDx: Collection method of the submission from NxGen MDx:
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
18 6 0 9 0 0 3 11

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
NxGen MDx pathogenic likely pathogenic uncertain significance
likely pathogenic 9 0 2
uncertain significance 0 1 0

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 3 0 4 0 0 0 4
Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences 0 0 0 3 0 0 0 3
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 1 0 2 0 0 0 2
Baylor Genetics 0 0 0 1 0 0 0 1
Ambry Genetics 0 2 0 1 0 0 0 1
Counsyl 0 0 0 0 0 0 1 1
Natera, Inc. 0 0 0 1 0 0 0 1
Mendelics 0 1 0 0 0 0 1 1
ClinGen Lysosomal Storage Disorder Variant Curation Expert Panel 0 1 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 11
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000478.6(ALPL):c.575T>C (p.Met192Thr) rs765011829 0.00007
NM_000441.2(SLC26A4):c.165-1G>A rs759792660 0.00005
NM_000187.4(HGD):c.367G>A (p.Gly123Arg) rs564979861 0.00002
NM_000051.4(ATM):c.8584+2T>C rs730881326 0.00001
NM_000152.5(GAA):c.2783A>G (p.Tyr928Cys) rs1403885484 0.00001
NM_000187.4(HGD):c.343G>C (p.Gly115Arg) rs755734596 0.00001
NM_000152.5(GAA):c.1847dup (p.Asp616fs) rs1475559733
NM_000159.4(GCDH):c.1220T>C (p.Leu407Pro) rs1555751379
NM_000187.4(HGD):c.566G>T (p.Ser189Ile) rs2107510544
NM_000441.2(SLC26A4):c.1439T>A (p.Val480Asp) rs1314376649
NM_000492.4(CFTR):c.3068T>G (p.Ile1023Arg) rs756219310

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