ClinVar Miner

Variants with conflicting interpretations studied for Joubert syndrome; Meckel-Gruber syndrome; Nephronophthisis

Coded as:
Minimum review status of the submission for Joubert syndrome; Meckel-Gruber syndrome; Nephronophthisis: Y axis collection method of the submission for Joubert syndrome; Meckel-Gruber syndrome; Nephronophthisis:
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 Variants with at least 2 submissions 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 kind of conflict
63 46 1 24 26 0 3 45

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 conditions
Joubert syndrome; Meckel-Gruber syndrome; Nephronophthisis pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 1 7 0 0 0
likely pathogenic 1 0 3 0 0
uncertain significance 0 0 0 3 0
likely benign 0 0 11 0 1
benign 0 0 12 15 0

Condition to condition summary #

Total conditions: 13
Download table as spreadsheet
Condition Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
not provided 0 30 0 10 13 0 1 21
Bardet-Biedl syndrome 0 4 0 6 13 0 0 19
Joubert syndrome 0 4 0 6 13 0 0 19
Leber congenital amaurosis 0 6 0 6 13 0 0 19
Meckel-Gruber syndrome 0 7 0 6 13 0 0 19
Renal dysplasia and retinal aplasia 0 4 0 6 13 0 0 19
not specified 0 21 0 15 5 0 0 17
CEP290-Related Disorders 0 1 0 2 1 0 1 4
Meckel syndrome type 4 0 1 0 3 0 0 0 3
Leber congenital amaurosis 10 0 1 1 0 0 0 0 1
Retinal dystrophy 0 1 0 1 0 0 0 1
Retinitis pigmentosa 0 3 0 0 1 0 0 1
Retinopathy 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 45
Download table as spreadsheet
HGVS dbSNP
NM_025114.3(CEP290):c.1079G>A (p.Arg360Gln) rs188164241
NM_025114.3(CEP290):c.1092T>G (p.Ile364Met) rs201988582
NM_025114.3(CEP290):c.1199C>T (p.Thr400Ile) rs773578133
NM_025114.3(CEP290):c.1429C>T (p.Arg477Ter) rs1170451277
NM_025114.3(CEP290):c.1624-5T>C rs142742071
NM_025114.3(CEP290):c.1716A>G (p.Leu572=) rs372349042
NM_025114.3(CEP290):c.1729C>T (p.Leu577=) rs201295052
NM_025114.3(CEP290):c.1984C>T (p.Gln662Ter) rs386834152
NM_025114.3(CEP290):c.1991A>G (p.Asp664Gly) rs79705698
NM_025114.3(CEP290):c.2052+1_2052+2delGT rs747835249
NM_025114.3(CEP290):c.226G>A (p.Ala76Thr) rs373913704
NM_025114.3(CEP290):c.2484-8_2484-4dupGTTTT rs745522483
NM_025114.3(CEP290):c.251-10A>T rs190383141
NM_025114.3(CEP290):c.2717T>G (p.Leu906Trp) rs7970228
NM_025114.3(CEP290):c.2991+1655A>G rs281865192
NM_025114.3(CEP290):c.3465G>A (p.Leu1155=) rs150138016
NM_025114.3(CEP290):c.3594G>A (p.Ser1198=) rs376645523
NM_025114.3(CEP290):c.3654T>C (p.Leu1218=) rs201838492
NM_025114.3(CEP290):c.3710G>A (p.Arg1237His) rs7307793
NM_025114.3(CEP290):c.3790C>T (p.Arg1264Cys) rs139998038
NM_025114.3(CEP290):c.384_387delTAGA (p.Asp128Glufs) rs386834157
NM_025114.3(CEP290):c.3955T>C (p.Leu1319=) rs182851622
NM_025114.3(CEP290):c.4068T>G (p.Leu1356=) rs377227262
NM_025114.3(CEP290):c.4087C>T (p.Arg1363Trp) rs181121175
NM_025114.3(CEP290):c.4102G>A (p.Asp1368Asn) rs184143186
NM_025114.3(CEP290):c.4119A>G (p.Lys1373=) rs117122459
NM_025114.3(CEP290):c.4237G>C (p.Asp1413His) rs183655276
NM_025114.3(CEP290):c.4437+1G>A rs760915898
NM_025114.3(CEP290):c.4438-3delC rs747323414
NM_025114.3(CEP290):c.451C>T (p.Arg151Ter) rs757641323
NM_025114.3(CEP290):c.4966G>T (p.Glu1656Ter) rs62638179
NM_025114.3(CEP290):c.503G>A (p.Arg168His) rs200063017
NM_025114.3(CEP290):c.5199A>G (p.Gln1733=) rs79644671
NM_025114.3(CEP290):c.5237G>A (p.Arg1746Gln) rs61941020
NM_025114.3(CEP290):c.523C>A (p.Gln175Lys) rs202159966
NM_025114.3(CEP290):c.5322C>T (p.Leu1774=) rs117370446
NM_025114.3(CEP290):c.5493delA (p.Ala1832Profs) rs386834158
NM_025114.3(CEP290):c.5506A>G (p.Ile1836Val) rs11104729
NM_025114.3(CEP290):c.6401T>C (p.Ile2134Thr) rs117852025
NM_025114.3(CEP290):c.6452T>C (p.Leu2151Ser) rs191613017
NM_025114.3(CEP290):c.6645+1G>A rs201218801
NM_025114.3(CEP290):c.7186G>T (p.Asp2396Tyr) rs189556433
NM_025114.3(CEP290):c.829G>C (p.Glu277Gln) rs45502896
NM_025114.3(CEP290):c.943-4C>T rs199770158
NM_025114.3(CEP290):c.943-8A>T rs200729812

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