ClinVar Miner

Variants from APRT Deficiency Research Program of the Rare Kidney Stone Consortium, Landspitali, National University Hospital of Iceland with conflicting interpretations

Location: Iceland  Primary collection method: literature only
Minimum review status of the submission from APRT Deficiency Research Program of the Rare Kidney Stone Consortium, Landspitali, National University Hospital of Iceland: Collection method of the submission from APRT Deficiency Research Program of the Rare Kidney Stone Consortium, Landspitali, National University Hospital of Iceland:
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
43 12 0 5 0 0 1 6

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
APRT Deficiency Research Program of the Rare Kidney Stone Consortium, Landspitali, National University Hospital of Iceland likely pathogenic uncertain significance
pathogenic 5 1

Submitter to submitter summary #

Total submitters: 3
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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
Fulgent Genetics, Fulgent Genetics 0 3 0 3 0 0 0 3
Revvity Omics, Revvity 0 1 0 1 0 0 1 2
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 6
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HGVS dbSNP gnomAD frequency
NM_000485.3(APRT):c.250G>A (p.Val84Met) rs200392753 0.00003
NM_000485.3(APRT):c.188G>A (p.Gly63Asp) rs1909091672
NM_000485.3(APRT):c.200G>A (p.Arg67Gln) rs762509151
NM_000485.3(APRT):c.280_286del (p.Gly94fs) rs776240467
NM_000485.3(APRT):c.439C>T (p.Gln147Ter) rs745872435
NM_000485.3(APRT):c.518TCT[1] (p.Phe174del) rs121912681

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