ClinVar Miner

List of variants reported as benign for Nephronophthisis

Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 214
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_032575.3(GLIS2):c.864T>C (p.Tyr288=) rs669561 0.97986
NM_015102.5(NPHP4):c.2818-2= rs1217117155 0.84829
NM_001023570.4(IQCB1):c.574C>T (p.Leu192=) rs4543051 0.64838
NM_014425.5(INVS):c.2412T>C (p.Ser804=) rs2787374 0.53208
NM_153240.4(NPHP3):c.-69A>G rs13099099 0.49619
NM_001128178.3(NPHP1):c.654G>A (p.Glu218=) rs11675767 0.38033
NM_015102.5(NPHP4):c.2802C>T (p.Arg934=) rs3747992 0.36928
NM_015102.5(NPHP4):c.3570A>G (p.Glu1190=) rs555164 0.35094
NM_014425.5(INVS):c.1235-5T>C rs2245216 0.30271
NM_032575.3(GLIS2):c.1311A>C (p.Ala437=) rs3810817 0.27719
NM_001023570.4(IQCB1):c.1301G>A (p.Cys434Tyr) rs17849995 0.25469
NM_014425.5(INVS):c.274-15_274-14del rs61147858 0.18785
NM_014425.5(INVS):c.-110T>G rs7024375 0.17693
NM_015102.5(NPHP4):c.1441+13A>G rs7520105 0.17476
NM_153240.5(NPHP3):c.3759G>A (p.Leu1253=) rs6794496 0.13621
NM_015102.5(NPHP4):c.2643G>A (p.Ala881=) rs3747990 0.11763
NM_015102.5(NPHP4):c.1926G>A (p.Glu642=) rs12120967 0.11732
NM_001023570.4(IQCB1):c.1178T>A (p.Ile393Asn) rs1141528 0.09226
NM_032575.3(GLIS2):c.1474A>G (p.Thr492Ala) rs8057701 0.06483
NM_015102.5(NPHP4):c.1470C>T (p.Leu490=) rs12116997 0.04804
NM_015102.5(NPHP4):c.86C>T (p.Thr29Met) rs12142270 0.04382
NM_153240.5(NPHP3):c.2610G>A (p.Pro870=) rs16839515 0.04323
NM_001128178.3(NPHP1):c.771+39C>T rs73954628 0.03266
NM_015102.5(NPHP4):c.2724G>A (p.Ser908=) rs114545322 0.03032
NM_153240.5(NPHP3):c.2571-7T>C rs62292468 0.02974
NM_014425.5(INVS):c.2402G>A (p.Gly801Glu) rs76868679 0.02854
NM_015102.5(NPHP4):c.1631C>G (p.Ala544Gly) rs12093500 0.02840
NM_001128178.3(NPHP1):c.115C>A (p.Pro39Thr) rs33958626 0.02731
NM_015102.5(NPHP4):c.2219G>A (p.Arg740His) rs34248917 0.02256
NM_014425.5(INVS):c.616-19T>C rs78038572 0.01891
NM_032575.3(GLIS2):c.223G>T (p.Ala75Ser) rs72766563 0.01854
NM_153240.5(NPHP3):c.864T>A (p.Thr288=) rs147932449 0.01825
NM_153240.5(NPHP3):c.3913C>T (p.Arg1305Cys) rs35485382 0.01709
NM_015102.5(NPHP4):c.3243G>C (p.Gly1081=) rs41280800 0.01658
NM_015102.5(NPHP4):c.1611+9C>T rs114900019 0.01637
NM_015102.5(NPHP4):c.2542C>T (p.Arg848Trp) rs17472401 0.01606
NM_153240.5(NPHP3):c.1986G>A (p.Arg662=) rs77533254 0.01496
NM_015102.5(NPHP4):c.2808G>A (p.Thr936=) rs17028857 0.01235
NM_001023570.4(IQCB1):c.1303C>T (p.Arg435Cys) rs11920543 0.01165
NM_015102.5(NPHP4):c.3479C>T (p.Pro1160Leu) rs113445782 0.01143
NM_001128178.3(NPHP1):c.689C>T (p.Ala230Val) rs113450177 0.01140
NM_153240.5(NPHP3):c.57G>C (p.Thr19=) rs192633696 0.01128
NM_001023570.4(IQCB1):c.424T>C (p.Phe142Leu) rs11926958 0.01125
NM_015102.5(NPHP4):c.2031C>T (p.Pro677=) rs34373111 0.01102
NM_015102.5(NPHP4):c.2876G>A (p.Arg959Gln) rs12084067 0.01099
NM_001128178.3(NPHP1):c.1529+19C>T rs112090979 0.01096
NM_153240.5(NPHP3):c.154G>A (p.Ala52Thr) rs145643112 0.01037
NM_015102.5(NPHP4):c.1852G>A (p.Glu618Lys) rs571655 0.01009
NM_015102.5(NPHP4):c.3876C>T (p.Gly1292=) rs115526767 0.00982
NM_032575.3(GLIS2):c.1259C>T (p.Pro420Leu) rs75495782 0.00923
NM_153240.5(NPHP3):c.450G>A (p.Ala150=) rs78527322 0.00906
NM_032575.3(GLIS2):c.70C>A (p.Arg24=) rs34543395 0.00866
NM_001128178.3(NPHP1):c.772-17G>A rs146343637 0.00862
NM_032575.3(GLIS2):c.894C>T (p.Pro298=) rs112926217 0.00791
NM_153240.5(NPHP3):c.3550G>A (p.Ala1184Thr) rs34391943 0.00744
NM_015102.5(NPHP4):c.1542G>A (p.Pro514=) rs35264155 0.00677
NM_153240.5(NPHP3):c.3941G>C (p.Ser1314Thr) rs75316802 0.00658
NM_153240.5(NPHP3):c.3252A>G (p.Thr1084=) rs11915053 0.00629
NM_032575.3(GLIS2):c.1476G>A (p.Thr492=) rs140403969 0.00608
NM_015102.5(NPHP4):c.1442-7C>T rs146078470 0.00599
NM_015102.5(NPHP4):c.3674C>T (p.Thr1225Met) rs144624477 0.00576
NM_014425.5(INVS):c.102C>T (p.Ile34=) rs115640267 0.00549
NM_014425.5(INVS):c.740A>G (p.Asn247Ser) rs41312220 0.00526
NM_014425.5(INVS):c.725C>T (p.Ser242Leu) rs2491097 0.00485
NM_015102.5(NPHP4):c.3894C>T (p.Ala1298=) rs60094861 0.00477
NM_032575.3(GLIS2):c.1464G>A (p.Leu488=) rs149580171 0.00467
NM_015102.5(NPHP4):c.2812G>A (p.Val938Met) rs184961418 0.00460
NM_015102.5(NPHP4):c.1705C>G (p.Gln569Glu) rs113413307 0.00443
NM_015102.5(NPHP4):c.2293G>A (p.Val765Ile) rs149244006 0.00420
NM_015102.5(NPHP4):c.2681A>G (p.His894Arg) rs113097479 0.00418
NM_015102.5(NPHP4):c.511G>A (p.Ala171Thr) rs113765431 0.00408
NM_153240.5(NPHP3):c.2089-9C>T rs141397228 0.00404
NM_015102.5(NPHP4):c.279+11G>A rs113902159 0.00401
NM_014425.5(INVS):c.1948G>C (p.Ala650Pro) rs147452898 0.00394
NM_014425.5(INVS):c.2116A>G (p.Arg706Gly) rs116222916 0.00384
NM_015102.5(NPHP4):c.3329C>T (p.Ala1110Val) rs139767853 0.00374
NM_015102.5(NPHP4):c.1503+10G>A rs41307782 0.00367
NM_001128178.3(NPHP1):c.14G>T (p.Arg5Leu) rs190983114 0.00366
NM_153240.5(NPHP3):c.520-10C>G rs200144727 0.00362
NM_153240.5(NPHP3):c.1189C>T (p.Arg397Cys) rs141477666 0.00334
NM_015102.5(NPHP4):c.2914A>G (p.Ser972Gly) rs187947581 0.00330
NM_015102.5(NPHP4):c.4237G>A (p.Asp1413Asn) rs115910810 0.00328
NM_014425.5(INVS):c.1284T>C (p.His428=) rs77465715 0.00312
NM_032575.3(GLIS2):c.775+20C>T rs116598071 0.00297
NM_015102.5(NPHP4):c.3559-19del rs201335783 0.00292
NM_015102.5(NPHP4):c.3036C>T (p.Pro1012=) rs34265978 0.00283
NM_001023570.4(IQCB1):c.588T>C (p.Ser196=) rs80015876 0.00267
NM_015102.5(NPHP4):c.1622C>T (p.Pro541Leu) rs145255635 0.00265
NM_032575.3(GLIS2):c.415G>A (p.Gly139Arg) rs147175353 0.00265
NM_001023570.4(IQCB1):c.1549A>T (p.Asn517Tyr) rs139468837 0.00237
NM_014425.5(INVS):c.2803C>T (p.His935Tyr) rs139768159 0.00232
NM_153240.5(NPHP3):c.2693+17A>G rs200046908 0.00212
NM_001128178.3(NPHP1):c.133A>C (p.Ile45Leu) rs145479679 0.00211
NM_015102.5(NPHP4):c.2882G>A (p.Arg961His) rs183885357 0.00200
NM_015102.5(NPHP4):c.2868C>T (p.Ala956=) rs138025088 0.00188
NM_001128178.3(NPHP1):c.1270-4C>T rs151204566 0.00181
NM_014425.5(INVS):c.3017-5T>G rs201018893 0.00177
NM_015102.5(NPHP4):c.810+14A>C rs201977545 0.00173
NM_014425.5(INVS):c.2193C>T (p.Gly731=) rs148758887 0.00158
NM_032575.3(GLIS2):c.1011G>A (p.Pro337=) rs200814551 0.00156
NM_153240.5(NPHP3):c.449C>T (p.Ala150Val) rs142663818 0.00142
NM_032575.3(GLIS2):c.1010C>T (p.Pro337Leu) rs140544340 0.00128
NM_015102.5(NPHP4):c.3911A>G (p.His1304Arg) rs115488133 0.00124
NM_153240.5(NPHP3):c.2883+13G>C rs112375565 0.00122
NM_153240.5(NPHP3):c.3189A>G (p.Lys1063=) rs112386774 0.00121
NM_153240.5(NPHP3):c.3570+9G>T rs112749193 0.00121
NM_153240.5(NPHP3):c.3093A>G (p.Glu1031=) rs112300370 0.00120
NM_015102.5(NPHP4):c.1024C>T (p.Arg342Cys) rs190940697 0.00113
NM_015102.5(NPHP4):c.945G>A (p.Thr315=) rs115272639 0.00113
NM_153240.5(NPHP3):c.3664T>C (p.Leu1222=) rs142616619 0.00107
NM_015102.5(NPHP4):c.3232-12C>T rs370840400 0.00101
NM_153240.5(NPHP3):c.3663C>T (p.Ala1221=) rs112144165 0.00099
NM_032575.3(GLIS2):c.477G>A (p.Ser159=) rs148123444 0.00096
NM_001128178.3(NPHP1):c.1269+9G>A rs13414551 0.00089
NM_153240.5(NPHP3):c.105G>A (p.Lys35=) rs377060857 0.00085
NM_015102.5(NPHP4):c.2820G>A (p.Ala940=) rs35575973 0.00078
NM_015102.5(NPHP4):c.3843G>T (p.Leu1281=) rs9662691 0.00076
NM_015102.5(NPHP4):c.2257G>A (p.Asp753Asn) rs148424288 0.00074
NM_014425.5(INVS):c.1704G>A (p.Gly568=) rs114645869 0.00073
NM_014425.5(INVS):c.2775C>T (p.Arg925=) rs146360442 0.00071
NM_015102.5(NPHP4):c.4141-11C>T rs139203183 0.00066
NM_153240.5(NPHP3):c.2769C>T (p.Phe923=) rs116174472 0.00066
NM_015102.5(NPHP4):c.1482G>A (p.Gln494=) rs199557439 0.00064
NM_015102.5(NPHP4):c.2557G>T (p.Asp853Tyr) rs199875059 0.00064
NM_032575.3(GLIS2):c.1105G>A (p.Gly369Ser) rs200720013 0.00056
NM_015102.5(NPHP4):c.1966G>A (p.Asp656Asn) rs191602135 0.00050
NM_032575.3(GLIS2):c.1350G>A (p.Ser450=) rs150464446 0.00046
NM_001023570.4(IQCB1):c.877-11C>T rs192296154 0.00045
NM_015102.5(NPHP4):c.3045-5C>T rs2297790 0.00038
NM_001128178.3(NPHP1):c.836C>T (p.Thr279Met) rs200201945 0.00033
NM_015102.5(NPHP4):c.944C>T (p.Thr315Met) rs200684272 0.00033
NM_001023570.4(IQCB1):c.987-17C>T rs187649158 0.00029
NM_015102.5(NPHP4):c.138C>T (p.Gly46=) rs201069164 0.00028
NM_015102.5(NPHP4):c.3705C>T (p.Arg1235=) rs199925943 0.00028
NM_015102.5(NPHP4):c.1089G>T (p.Val363=) rs201464887 0.00026
NM_015102.5(NPHP4):c.1632C>T (p.Ala544=) rs201903713 0.00025
NM_153240.5(NPHP3):c.1629-17C>A rs145056102 0.00024
NM_015102.5(NPHP4):c.3145C>T (p.Pro1049Ser) rs759609852 0.00022
NM_015102.5(NPHP4):c.1196A>G (p.Glu399Gly) rs117898549 0.00020
NM_015102.5(NPHP4):c.1120-13G>T rs192450719 0.00019
NM_015102.5(NPHP4):c.3044+20C>T rs372051668 0.00019
NM_015102.5(NPHP4):c.2445G>A (p.Ser815=) rs764367617 0.00017
NM_015102.5(NPHP4):c.3777G>A (p.Arg1259=) rs369566680 0.00016
NM_015102.5(NPHP4):c.3817-20C>T rs573999865 0.00016
NM_001023570.4(IQCB1):c.1311A>G (p.Lys437=) rs142536967 0.00015
NM_001023570.4(IQCB1):c.588-5A>G rs370451583 0.00015
NM_153240.5(NPHP3):c.3126-8T>G rs201592109 0.00015
NM_015102.5(NPHP4):c.902C>T (p.Pro301Leu) rs527701970 0.00014
NM_001128178.3(NPHP1):c.1270-18A>G rs534210307 0.00011
NM_015102.5(NPHP4):c.122C>T (p.Pro41Leu) rs754311690 0.00011
NM_153240.5(NPHP3):c.2132A>G (p.Asn711Ser) rs117872197 0.00011
NM_015102.5(NPHP4):c.2807C>T (p.Thr936Met) rs201074950 0.00008
NM_014425.5(INVS):c.1374C>A (p.Thr458=) rs114912725 0.00007
NM_001023570.4(IQCB1):c.1509C>G (p.Ala503=) rs149259534 0.00006
NM_015102.5(NPHP4):c.1490C>G (p.Pro497Arg) rs375051705 0.00006
NM_032575.3(GLIS2):c.849C>T (p.His283=) rs200829928 0.00006
NM_015102.5(NPHP4):c.1120-9T>A rs570380438 0.00004
NM_015102.5(NPHP4):c.1764-5C>T rs370899989 0.00004
NM_153240.5(NPHP3):c.1083T>C (p.Ser361=) rs781244729 0.00004
NM_014425.5(INVS):c.2604C>T (p.Ser868=) rs751765105 0.00003
NM_153240.5(NPHP3):c.1357C>T (p.Leu453=) rs535110862 0.00002
NM_153240.5(NPHP3):c.3813-10T>C rs372263313 0.00002
NM_001023570.4(IQCB1):c.776G>A (p.Arg259His) rs374034270 0.00001
NM_001128178.3(NPHP1):c.294C>T (p.Gly98=) rs747950591 0.00001
NM_001128178.3(NPHP1):c.438T>C (p.Asn146=) rs548684868 0.00001
NM_001128178.3(NPHP1):c.859+5T>C rs374379957 0.00001
NM_014425.5(INVS):c.1980A>G (p.Gly660=) rs139314036 0.00001
NM_014425.5(INVS):c.3027C>T (p.His1009=) rs201136636 0.00001
NM_015102.5(NPHP4):c.3645-15C>T rs558429618 0.00001
NC_000002.11:g.(?_110849180)_(110962545_?)dup
NC_000002.11:g.(?_110879913)_(110963639_?)dup
NC_000002.11:g.(?_110881368)_(110937261_?)dup
NM_000272.3(NPHP1):c.(?_-1)_(*1_?)dup
NM_000272.3(NPHP1):c.625-3dup rs200118387
NM_001023570.4(IQCB1):c.1279-8del rs758519096
NM_001023570.4(IQCB1):c.1568-19del rs148949254
NM_001023570.4(IQCB1):c.394-15_394-10dup rs768572151
NM_001023570.4(IQCB1):c.488-13del rs753164790
NM_001023570.4(IQCB1):c.488-13dup rs753164790
NM_001023570.4(IQCB1):c.588-16del rs574290389
NM_001023570.4(IQCB1):c.588-25dup rs574290389
NM_001023570.4(IQCB1):c.775C>T (p.Arg259Cys) rs778777181
NM_001023570.4(IQCB1):c.986+9del
NM_001128178.3(NPHP1):c.144-11del
NM_001128178.3(NPHP1):c.144-11dup rs762119782
NM_001128178.3(NPHP1):c.1530-13dup
NM_001128178.3(NPHP1):c.729-11dup
NM_014425.5(INVS):c.2069-18_2069-16del rs577372332
NM_014425.5(INVS):c.2582G>C (p.Arg861Thr) rs760537423
NM_014425.5(INVS):c.2719C>A (p.Arg907=) rs267607185
NM_014425.5(INVS):c.273+13del
NM_014425.5(INVS):c.2786+14del
NM_014425.5(INVS):c.3182dup (p.Asn1061fs) rs760013326
NM_014425.5(INVS):c.448-10G>A
NM_015102.5(NPHP4):c.136-4del rs143323188
NM_015102.5(NPHP4):c.1503+17dup rs756154468
NM_015102.5(NPHP4):c.3144C>G (p.Ala1048=) rs540738356
NM_015102.5(NPHP4):c.3997-12del rs1325812736
NM_015102.5(NPHP4):c.4140+11dup rs779059295
NM_032575.3(GLIS2):c.173-16T>C
NM_032575.3(GLIS2):c.523-20A>T
NM_032575.3(GLIS2):c.657-17C>T
NM_153240.5(NPHP3):c.1118+16del rs560151715
NM_153240.5(NPHP3):c.1118+16dup rs560151715
NM_153240.5(NPHP3):c.1276-7del rs2107987665
NM_153240.5(NPHP3):c.1525-13dup rs762115717
NM_153240.5(NPHP3):c.2884-16dup rs2107967791
NM_153240.5(NPHP3):c.3125+7dup rs11396595
NM_153240.5(NPHP3):c.3126-4del rs398124547
NM_153240.5(NPHP3):c.3571-3dup
NM_153240.5(NPHP3):c.3697-14dup rs564013823
NM_153240.5(NPHP3):c.3697-7del rs564013823
NM_153240.5(NPHP3):c.3813-12del rs2107960657
Single allele

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