ClinVar Miner

Variants with conflicting interpretations studied for Nephronophthisis

Coded as:
Minimum review status of the submission for Nephronophthisis: Y axis collection method of the submission for 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
205 289 1 71 80 2 4 143

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
Nephronophthisis pathogenic likely pathogenic uncertain significance likely benign benign risk factor
pathogenic 0 2 1 1 1 0
uncertain significance 1 1 0 41 31 2
likely benign 1 0 25 1 42 1
benign 0 0 22 49 0 0

Condition to condition summary #

Total conditions: 16
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 specified 0 33 0 62 53 0 1 107
Nephronophthisis 578 10 0 22 27 0 0 49
Renal dysplasia and retinal aplasia 0 97 0 14 14 0 1 29
not provided 0 100 1 5 19 0 1 25
Meckel-Gruber syndrome 0 152 0 6 5 0 0 11
Renal-hepatic-pancreatic dysplasia 0 54 0 6 4 0 0 10
Joubert syndrome 0 116 0 3 5 0 1 8
Joubert syndrome; Meckel-Gruber syndrome 0 6 0 3 6 0 0 8
Infantile nephronophthisis 0 4 0 1 1 0 1 3
Nephronophthisis 9 0 1 0 1 2 0 0 3
Bardet-Biedl syndrome 14, modifier of 0 0 0 0 0 1 0 1
Congenital ocular coloboma; Global developmental delay; Visual impairment; Nystagmus; Absent speech; Barrel-shaped chest; Nephropathy; Cerebellar vermis hypoplasia; Tremor; Pancreatitis; Cerebellar malformation; Peritonitis; Infantile muscular hypotonia; Intellectual disability, severe 0 0 0 1 0 0 0 1
Joubert syndrome 4; Nephronophthisis 1; Senior-Loken syndrome 1 0 1 0 0 1 0 0 1
Joubert syndrome; Oligohydramnios; Renal cyst 0 0 0 1 0 0 0 1
Nephronophthisis 4 0 2 0 0 1 0 0 1
Retinitis pigmentosa in ciliopathies, modifier of 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 143
Download table as spreadsheet
HGVS dbSNP
NM_000272.3(NPHP1):c.1121C>T (p.Thr374Ile) rs140469160
NM_000272.3(NPHP1):c.115C>A (p.Pro39Thr) rs33958626
NM_000272.3(NPHP1):c.1437+9G>A rs13414551
NM_000272.3(NPHP1):c.1438-4C>T rs151204566
NM_000272.3(NPHP1):c.14G>T (p.Arg5Leu) rs190983114
NM_000272.3(NPHP1):c.1637G>A (p.Arg546Lys) rs149887461
NM_000272.3(NPHP1):c.1698-10delT rs779032904
NM_000272.3(NPHP1):c.2081A>G (p.Gln694Arg) rs186950965
NM_000272.3(NPHP1):c.2118G>A (p.Leu706=) rs144850331
NM_000272.3(NPHP1):c.232T>C (p.Tyr78His) rs140446520
NM_000272.3(NPHP1):c.654G>A (p.Glu218=) rs11675767
NM_000272.3(NPHP1):c.689C>T (p.Ala230Val) rs113450177
NM_000272.3(NPHP1):c.810C>T (p.Cys270=) rs73954628
NM_000272.3(NPHP1):c.830G>A (p.Arg277Gln) rs143174377
NM_001023570.3(IQCB1):c.1178T>A (p.Ile393Asn) rs1141528
NM_001023570.3(IQCB1):c.1303C>T (p.Arg435Cys) rs11920543
NM_001023570.3(IQCB1):c.1549A>T (p.Asn517Tyr) rs139468837
NM_001023570.3(IQCB1):c.394-15_394-10dupATCTTT rs768572151
NM_014425.3(INVS):c.2782C>T (p.Arg928Ter) rs376879175
NM_014425.4(INVS):c.114T>C (p.Ser38=) rs114056499
NM_014425.4(INVS):c.1925A>G (p.Lys642Arg) rs116314059
NM_014425.4(INVS):c.2116A>G (p.Arg706Gly) rs116222916
NM_014425.4(INVS):c.2310C>T (p.His770=) rs116606949
NM_014425.4(INVS):c.2402G>A (p.Gly801Glu) rs76868679
NM_014425.4(INVS):c.2803C>T (p.His935Tyr) rs139768159
NM_014425.4(INVS):c.3017-5T>G rs201018893
NM_014425.4(INVS):c.3027C>T (p.His1009=) rs201136636
NM_014425.4(INVS):c.740A>G (p.Asn247Ser) rs41312220
NM_014425.4(INVS):c.913G>A (p.Val305Ile) rs116438342
NM_015102.3(NPHP4):c.1196A>G (p.Glu399Gly) rs117898549
NM_015102.4(NPHP4):c.1024C>T (p.Arg342Cys) rs190940697
NM_015102.4(NPHP4):c.136-4delC rs143323188
NM_015102.4(NPHP4):c.1441+13A>G rs7520105
NM_015102.4(NPHP4):c.1442-7C>T rs146078470
NM_015102.4(NPHP4):c.1470C>T (p.Leu490=) rs12116997
NM_015102.4(NPHP4):c.1482G>A (p.Gln494=) rs199557439
NM_015102.4(NPHP4):c.1490C>G (p.Pro497Arg) rs375051705
NM_015102.4(NPHP4):c.1611+9C>T rs114900019
NM_015102.4(NPHP4):c.1622C>T (p.Pro541Leu) rs145255635
NM_015102.4(NPHP4):c.1631C>G (p.Ala544Gly) rs12093500
NM_015102.4(NPHP4):c.1852G>A (p.Glu618Lys) rs571655
NM_015102.4(NPHP4):c.1867A>G (p.Thr623Ala) rs35959882
NM_015102.4(NPHP4):c.1926G>A (p.Glu642=) rs12120967
NM_015102.4(NPHP4):c.1935A>G (p.Leu645=) rs200104274
NM_015102.4(NPHP4):c.1966G>A (p.Asp656Asn) rs191602135
NM_015102.4(NPHP4):c.2031C>T (p.Pro677=) rs34373111
NM_015102.4(NPHP4):c.2219G>A (p.Arg740His) rs34248917
NM_015102.4(NPHP4):c.2257G>A (p.Asp753Asn) rs148424288
NM_015102.4(NPHP4):c.2557G>T (p.Asp853Tyr) rs199875059
NM_015102.4(NPHP4):c.2643G>A (p.Ala881=) rs3747990
NM_015102.4(NPHP4):c.2724G>A (p.Ser908=) rs114545322
NM_015102.4(NPHP4):c.279+11G>A rs113902159
NM_015102.4(NPHP4):c.2808G>A (p.Thr936=) rs17028857
NM_015102.4(NPHP4):c.2820G>A (p.Ala940=) rs35575973
NM_015102.4(NPHP4):c.2868C>T (p.Ala956=) rs138025088
NM_015102.4(NPHP4):c.2876G>A (p.Arg959Gln) rs12084067
NM_015102.4(NPHP4):c.2940G>A (p.Thr980=) rs146948888
NM_015102.4(NPHP4):c.3243G>C (p.Gly1081=) rs41280800
NM_015102.4(NPHP4):c.3329C>T (p.Ala1110Val) rs139767853
NM_015102.4(NPHP4):c.3479C>T (p.Pro1160Leu) rs113445782
NM_015102.4(NPHP4):c.3574C>T (p.Arg1192Trp) rs139022622
NM_015102.4(NPHP4):c.3777G>A (p.Arg1259=) rs369566680
NM_015102.4(NPHP4):c.3837C>T (p.Phe1279=) rs375237454
NM_015102.4(NPHP4):c.3851G>A (p.Arg1284His) rs61739637
NM_015102.4(NPHP4):c.3876C>T (p.Gly1292=) rs115526767
NM_015102.4(NPHP4):c.4075C>T (p.Arg1359Trp) rs369162678
NM_015102.4(NPHP4):c.4114C>T (p.Leu1372=) rs374146357
NM_015102.4(NPHP4):c.4141-11C>T rs139203183
NM_015102.4(NPHP4):c.4179T>A (p.Phe1393Leu) rs35641267
NM_015102.4(NPHP4):c.4237G>A (p.Asp1413Asn) rs115910810
NM_015102.4(NPHP4):c.86C>T (p.Thr29Met) rs12142270
NM_015272.4(RPGRIP1L):c.1341G>A (p.Leu447=) rs61743997
NM_015272.4(RPGRIP1L):c.1960G>A (p.Glu654Lys) rs141979202
NM_015272.4(RPGRIP1L):c.2231G>A (p.Arg744Gln) rs2302677
NM_015272.4(RPGRIP1L):c.2240G>A (p.Arg747Gln) rs142349647
NM_015272.4(RPGRIP1L):c.2658G>A (p.Ser886=) rs775153934
NM_015272.4(RPGRIP1L):c.2682A>G (p.Ser894=) rs141608712
NM_015272.4(RPGRIP1L):c.2925A>G (p.Val975=) rs144313291
NM_015272.4(RPGRIP1L):c.2959-15T>C rs11863101
NM_015272.4(RPGRIP1L):c.3073G>A (p.Gly1025Ser) rs2111119
NM_015272.4(RPGRIP1L):c.3312C>T (p.Pro1104=) rs568801926
NM_015272.4(RPGRIP1L):c.3428C>G (p.Thr1143Ser) rs111775292
NM_015272.4(RPGRIP1L):c.3624C>T (p.Tyr1208=) rs138724933
NM_015272.4(RPGRIP1L):c.3790G>A (p.Asp1264Asn) rs3213758
NM_015272.4(RPGRIP1L):c.3936C>T (p.Asp1312=) rs4784320
NM_015272.4(RPGRIP1L):c.685G>A (p.Ala229Thr) rs61747071
NM_032575.2(GLIS2):c.-11G>A rs28449480
NM_032575.2(GLIS2):c.1011G>A (p.Pro337=) rs200814551
NM_032575.2(GLIS2):c.1180G>A (p.Gly394Ser) rs775114398
NM_032575.2(GLIS2):c.1259C>T (p.Pro420Leu) rs75495782
NM_032575.2(GLIS2):c.1413C>G (p.Ser471Arg) rs201182025
NM_032575.2(GLIS2):c.1474A>G (p.Thr492Ala) rs8057701
NM_032575.2(GLIS2):c.1476G>A (p.Thr492=) rs140403969
NM_032575.2(GLIS2):c.223G>T (p.Ala75Ser) rs72766563
NM_032575.2(GLIS2):c.693C>T (p.Asn231=) rs150071733
NM_032575.2(GLIS2):c.894C>T (p.Pro298=) rs112926217
NM_153240.4(NPHP3):c.105G>A (p.Lys35=) rs377060857
NM_153240.4(NPHP3):c.1157A>G (p.Asn386Ser) rs142021049
NM_153240.4(NPHP3):c.1189C>T (p.Arg397Cys) rs141477666
NM_153240.4(NPHP3):c.1525-5delT rs762115717
NM_153240.4(NPHP3):c.154G>A (p.Ala52Thr) rs145643112
NM_153240.4(NPHP3):c.1887+6G>A rs79113972
NM_153240.4(NPHP3):c.189G>C (p.Gly63=) rs750280281
NM_153240.4(NPHP3):c.1986G>A (p.Arg662=) rs77533254
NM_153240.4(NPHP3):c.2089-9C>T rs141397228
NM_153240.4(NPHP3):c.255G>A (p.Glu85=) rs146839563
NM_153240.4(NPHP3):c.2571-7T>C rs62292468
NM_153240.4(NPHP3):c.2610G>A (p.Pro870=) rs16839515
NM_153240.4(NPHP3):c.2688T>C (p.Tyr896=) rs150489788
NM_153240.4(NPHP3):c.2694-2_2694-1delAG rs751527253
NM_153240.4(NPHP3):c.2769C>T (p.Phe923=) rs116174472
NM_153240.4(NPHP3):c.3093A>G (p.Glu1031=) rs112300370
NM_153240.4(NPHP3):c.3189A>G (p.Lys1063=) rs112386774
NM_153240.4(NPHP3):c.3500G>A (p.Arg1167His) rs111727307
NM_153240.4(NPHP3):c.3550G>A (p.Ala1184Thr) rs34391943
NM_153240.4(NPHP3):c.3570+9G>T rs112749193
NM_153240.4(NPHP3):c.3663C>T (p.Ala1221=) rs112144165
NM_153240.4(NPHP3):c.3697-7delT rs564013823
NM_153240.4(NPHP3):c.3913C>T (p.Arg1305Cys) rs35485382
NM_153240.4(NPHP3):c.3941G>C (p.Ser1314Thr) rs75316802
NM_153240.4(NPHP3):c.3971T>C (p.Phe1324Ser) rs113364886
NM_153240.4(NPHP3):c.408G>A (p.Thr136=) rs141410951
NM_153240.4(NPHP3):c.449C>T (p.Ala150Val) rs142663818
NM_153240.4(NPHP3):c.450G>A (p.Ala150=) rs78527322
NM_153240.4(NPHP3):c.520-10C>G rs200144727
NM_153240.4(NPHP3):c.57G>C (p.Thr19=) rs192633696
NM_153240.4(NPHP3):c.621A>G (p.Val207=) rs139693694
NM_153240.4(NPHP3):c.670+13C>T rs202228115
NM_153240.4(NPHP3):c.864T>A (p.Thr288=) rs147932449
NM_153704.5(TMEM67):c.-33delG rs145334032
NM_153704.5(TMEM67):c.1066-3C>T rs3097427
NM_153704.5(TMEM67):c.120T>C (p.Ser40=) rs767999682
NM_153704.5(TMEM67):c.1810A>G (p.Ile604Val) rs3134031
NM_153704.5(TMEM67):c.1843T>C (p.Cys615Arg) rs201893408
NM_153704.5(TMEM67):c.186T>C (p.Cys62=) rs115660279
NM_153704.5(TMEM67):c.2241G>A (p.=) rs115563233
NM_153704.5(TMEM67):c.2448G>A (p.Leu816=) rs886038738
NM_153704.5(TMEM67):c.2892A>C (p.Thr964=) rs16916221
NM_153704.5(TMEM67):c.869+9A>G rs372597584
NM_153704.5(TMEM67):c.958A>T (p.Ser320Cys) rs111619594
NM_178170.3(NEK8):c.1641C>T (p.Ala547=) rs8073738
NM_178170.3(NEK8):c.1938A>C (p.Gly646=) rs138629865
NM_178170.3(NEK8):c.2052G>A (p.Ser684=) rs145898152

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