ClinVar Miner

Variants with conflicting interpretations studied for Familial aplasia of the vermis; Meckel-Gruber syndrome; Nephronophthisis

Coded as:
Minimum review status of the submission for Familial aplasia of the vermis; Meckel-Gruber syndrome; Nephronophthisis: Collection method of the submission for Familial aplasia of the vermis; 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 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
2747 299 0 34 13 0 1 47

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
Familial aplasia of the vermis; Meckel-Gruber syndrome; Nephronophthisis pathogenic likely pathogenic uncertain significance likely benign
pathogenic 0 26 0 0
likely pathogenic 2 0 1 0
uncertain significance 0 0 0 1
likely benign 0 0 11 0
benign 0 0 1 6

Condition to condition summary #

Total conditions: 5
Download table as spreadsheet
Condition 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
Leber congenital amaurosis 10; Meckel syndrome, type 4; Senior-Loken syndrome 6; Joubert syndrome 5; Bardet-Biedl syndrome 14 0 241 0 30 5 0 0 35
Inborn genetic diseases 0 78 0 1 5 0 1 7
Leber congenital amaurosis 10; Meckel syndrome, type 4; Senior-Loken syndrome 6; Joubert syndrome 5 0 12 0 1 6 0 0 7
Familial aplasia of the vermis; Polycystic kidney disease; Abnormality of the kidney; Cerebellar vermis hypoplasia; Cerebellar cyst; Hyperechogenic kidneys 0 1 0 1 0 0 0 1
Meckel syndrome, type 4; Senior-Loken syndrome 6; Joubert syndrome 5; Bardet-Biedl syndrome 14 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 47
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_025114.4(CEP290):c.1624-5T>C rs142742071 0.00704
NM_025114.4(CEP290):c.5322C>T (p.Leu1774=) rs117370446 0.00329
NM_025114.4(CEP290):c.6960+10G>A rs75011402 0.00305
NM_025114.4(CEP290):c.943-4C>T rs199770158 0.00037
NM_025114.4(CEP290):c.2479C>G (p.Leu827Val) rs201569048 0.00036
NM_025114.4(CEP290):c.1908A>T (p.Lys636Asn) rs199747962 0.00032
NM_025114.4(CEP290):c.4250A>G (p.Gln1417Arg) rs201504946 0.00030
NM_025114.4(CEP290):c.6392A>G (p.Glu2131Gly) rs184323010 0.00020
NM_025114.4(CEP290):c.671C>T (p.Thr224Ile) rs200587974 0.00013
NM_025114.4(CEP290):c.4938A>G (p.Lys1646=) rs371582975 0.00010
NM_025114.4(CEP290):c.5164A>G (p.Thr1722Ala) rs375817905 0.00010
NM_025114.4(CEP290):c.343A>G (p.Asn115Asp) rs140236736 0.00007
NM_025114.4(CEP290):c.6645+1G>A rs201218801 0.00006
NM_025114.4(CEP290):c.2174A>C (p.Glu725Ala) rs375038986 0.00005
NM_025114.4(CEP290):c.6523-6T>C rs794727692 0.00003
NM_025114.4(CEP290):c.1711+1G>A rs587783009 0.00001
NM_025114.4(CEP290):c.2551G>A (p.Val851Ile) rs764963626 0.00001
NM_025114.4(CEP290):c.2587-19T>C rs755086278 0.00001
NM_025114.4(CEP290):c.2T>A (p.Met1Lys) rs368984997 0.00001
NM_025114.4(CEP290):c.7324G>T (p.Glu2442Ter) rs1374014119 0.00001
NM_025114.4(CEP290):c.1254_1255del (p.Lys419fs) rs897997464
NM_025114.4(CEP290):c.1624-5T>G rs142742071
NM_025114.4(CEP290):c.180+1G>A rs758593134
NM_025114.4(CEP290):c.1915G>T (p.Glu639Ter) rs1555220625
NM_025114.4(CEP290):c.251-11del rs752284551
NM_025114.4(CEP290):c.2632del (p.Ile878fs) rs1404507934
NM_025114.4(CEP290):c.3104-2A>G rs773386777
NM_025114.4(CEP290):c.3240T>G (p.Tyr1080Ter) rs886042467
NM_025114.4(CEP290):c.3285del (p.Phe1095fs) rs1017496924
NM_025114.4(CEP290):c.3488_3494dup (p.Val1166fs) rs2036977719
NM_025114.4(CEP290):c.369del (p.Gln123fs) rs773622064
NM_025114.4(CEP290):c.4028del (p.Lys1343fs) rs1213286417
NM_025114.4(CEP290):c.4621del (p.Thr1541fs) rs587779733
NM_025114.4(CEP290):c.5227-23dup rs747878752
NM_025114.4(CEP290):c.5777G>C (p.Arg1926Pro) rs778030031
NM_025114.4(CEP290):c.583_584del (p.Leu195fs) rs1277316340
NM_025114.4(CEP290):c.584del (p.Leu195fs) rs1277316340
NM_025114.4(CEP290):c.6448_6455del (p.Gln2150fs) rs1364945778
NM_025114.4(CEP290):c.7153del (p.Lys2384_Ile2385insTer) rs781310385
NM_025114.4(CEP290):c.7198C>T (p.Gln2400Ter) rs1478582091
NM_025114.4(CEP290):c.7233dup (p.Glu2412fs) rs2033254449
NM_025114.4(CEP290):c.7263dup (p.Glu2422Ter) rs1219184437
NM_025114.4(CEP290):c.7283_7286dup (p.Tyr2429Ter) rs773642187
NM_025114.4(CEP290):c.7328_7332dup (p.Val2445fs) rs747138345
NM_025114.4(CEP290):c.7341dup (p.Leu2448fs) rs281865189
NM_025114.4(CEP290):c.734_735del (p.Glu245fs) rs1592671672
NM_025114.4(CEP290):c.829G>T (p.Glu277Ter) rs45502896

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