ClinVar Miner

List of variants reported as likely benign for neurodevelopmental disorder by Illumina Laboratory Services, Illumina

Included ClinVar conditions (780):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 206
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HGVS dbSNP gnomAD frequency
NM_012309.5(SHANK2):c.*4377A>T rs513996 0.96749
NM_012309.5(SHANK2):c.-36A>G rs3020047 0.60032
NM_003097.6(SNRPN):c.-89T>C rs705 0.53733
NM_012309.5(SHANK2):c.*2583T>C rs55678639 0.27352
NM_022807.5(SNRPN):c.-672T>C rs7170796 0.14308
NM_022807.5(SNRPN):c.-579+5G>A rs56684653 0.13434
NM_012309.5(SHANK2):c.385G>A (p.Val129Met) rs73521173 0.05277
NM_002474.3(MYH11):c.*420C>G rs12932063 0.03681
NM_002474.3(MYH11):c.5172-14C>T rs34839877 0.03595
NM_012309.5(SHANK2):c.*4102C>G rs61885874 0.03443
NM_012309.5(SHANK2):c.336C>T (p.Asp112=) rs76014490 0.03111
NM_012309.5(SHANK2):c.520C>T (p.Arg174Cys) rs7926203 0.02486
NM_012309.5(SHANK2):c.483+14G>A rs75938961 0.02166
NM_018136.5(ASPM):c.*60C>T rs1537318 0.02044
NM_018136.5(ASPM):c.-110C>T rs74981632 0.02032
NM_003097.6(SNRPN):c.-39G>A rs75184959 0.01903
NM_018136.5(ASPM):c.2419+12G>A rs77191836 0.01806
NM_022807.5(SNRPN):c.-569C>T rs80135925 0.01706
NM_015192.4(PLCB1):c.*749G>C rs16995375 0.01704
NM_015192.4(PLCB1):c.924A>G (p.Ser308=) rs6056003 0.01487
NM_024596.5(MCPH1):c.23-15A>G rs146351889 0.01440
NM_018136.5(ASPM):c.2751C>T (p.Ala917=) rs33987824 0.01382
NM_002474.3(MYH11):c.4770G>A (p.Lys1590=) rs11648119 0.01341
NM_001083961.2(WDR62):c.2975C>T (p.Ser992Leu) rs74518295 0.00953
NM_018136.5(ASPM):c.7917A>G (p.Lys2639=) rs112647911 0.00953
NM_018136.5(ASPM):c.7353G>A (p.Leu2451=) rs111487086 0.00949
NM_012309.5(SHANK2):c.483+13C>T rs117706585 0.00882
NM_018136.5(ASPM):c.5185C>T (p.Arg1729Trp) rs41299623 0.00808
NM_018136.5(ASPM):c.9773A>G (p.His3258Arg) rs7528827 0.00754
NM_024596.5(MCPH1):c.2453-13G>A rs111713406 0.00748
NM_012309.5(SHANK2):c.*1597T>G rs2154625 0.00746
NM_001083961.2(WDR62):c.*5G>A rs61740165 0.00745
NM_006031.6(PCNT):c.8671G>A (p.Ala2891Thr) rs33956783 0.00733
NM_015192.4(PLCB1):c.*855G>A rs115731722 0.00722
NM_015192.4(PLCB1):c.*1538G>T rs116163517 0.00719
NM_018136.5(ASPM):c.5629G>A (p.Ala1877Thr) rs112230218 0.00719
NM_018136.5(ASPM):c.1987G>T (p.Ala663Ser) rs113611857 0.00689
NM_018136.5(ASPM):c.3742-10T>G rs41299587 0.00665
NM_018136.5(ASPM):c.3741+3A>G rs138558822 0.00656
NM_001194998.2(CEP152):c.4857T>C (p.Asp1619=) rs74986073 0.00651
NM_024596.5(MCPH1):c.*199G>A rs17317651 0.00596
NM_001143979.2(NDE1):c.-353A>G rs138559781 0.00573
NM_001194998.2(CEP152):c.3278G>A (p.Cys1093Tyr) rs74012142 0.00563
NM_006031.6(PCNT):c.6634C>T (p.Arg2212Trp) rs144471022 0.00516
NM_144508.5(KNL1):c.6212+5G>A rs115900739 0.00501
NM_018136.5(ASPM):c.6727G>T (p.Val2243Leu) rs148425392 0.00493
NM_015192.4(PLCB1):c.1167+7T>C rs45466294 0.00492
NM_001048166.1(STIL):c.3378A>G (p.Arg1126=) rs142315727 0.00478
NM_001194998.2(CEP152):c.4914A>G (p.Pro1638=) rs150910683 0.00477
NM_001194998.2(CEP152):c.*194G>A rs144469727 0.00475
NM_001048166.1(STIL):c.3786G>A (p.Thr1262=) rs146387723 0.00460
NM_001194998.2(CEP152):c.1866G>T (p.Leu622=) rs61737684 0.00460
NM_006031.6(PCNT):c.4285C>T (p.Arg1429Cys) rs62224222 0.00437
NM_018136.5(ASPM):c.5741A>G (p.Gln1914Arg) rs113325473 0.00427
NM_018136.5(ASPM):c.-28G>A rs111299108 0.00419
NM_001083961.2(WDR62):c.3946C>G (p.Gln1316Glu) rs35811023 0.00416
NM_007254.4(PNKP):c.-50G>C rs3739166 0.00413
NM_002474.3(MYH11):c.4117-80G>C rs7196012 0.00411
NM_144508.5(KNL1):c.6034A>G (p.Ile2012Val) rs74970544 0.00405
NM_024596.5(MCPH1):c.1845A>C (p.Thr615=) rs186547090 0.00403
NM_018136.5(ASPM):c.4213C>T (p.Arg1405Cys) rs139367209 0.00396
NM_018136.5(ASPM):c.7554A>G (p.Arg2518=) rs140248383 0.00393
NM_144508.5(KNL1):c.5799-9G>A rs114041699 0.00385
NM_001194998.2(CEP152):c.4094-9A>T rs80090788 0.00380
NM_006031.6(PCNT):c.4345C>G (p.Gln1449Glu) rs139432601 0.00379
NM_018136.5(ASPM):c.3791G>A (p.Arg1264His) rs150125249 0.00378
NM_001194998.2(CEP152):c.3325G>C (p.Ala1109Pro) rs115832709 0.00373
NM_018451.5(CPAP):c.1233G>A (p.Pro411=) rs112133852 0.00368
NM_007254.4(PNKP):c.783G>A (p.Pro261=) rs145307985 0.00353
NM_144508.5(KNL1):c.6131C>T (p.Pro2044Leu) rs116439389 0.00341
NM_001126121.2(SLC25A19):c.*96G>C rs143419896 0.00335
NM_018136.5(ASPM):c.6775T>C (p.Leu2259=) rs140922974 0.00333
NM_018451.5(CPAP):c.*570T>C rs139596189 0.00313
NM_002474.3(MYH11):c.5757C>T (p.Arg1919=) rs138168272 0.00312
NM_001083961.2(WDR62):c.3812C>T (p.Ala1271Val) rs111294536 0.00310
NM_024596.5(MCPH1):c.1495G>A (p.Val499Met) rs146586991 0.00302
NM_007254.4(PNKP):c.939T>C (p.Phe313=) rs149731642 0.00290
NM_006031.6(PCNT):c.6933C>T (p.Val2311=) rs148444313 0.00289
NM_018136.5(ASPM):c.9444+8T>G rs140150599 0.00278
NM_001194998.2(CEP152):c.5115A>G (p.Pro1705=) rs1048042 0.00273
NM_006031.6(PCNT):c.1784C>T (p.Ala595Val) rs143028464 0.00265
NM_000817.3(GAD1):c.-39A>C rs45617531 0.00262
NM_015192.4(PLCB1):c.2673T>G (p.Pro891=) rs142813933 0.00260
NM_006031.6(PCNT):c.3748C>T (p.Arg1250Trp) rs117987006 0.00257
NM_018136.5(ASPM):c.9996T>C (p.Thr3332=) rs139927527 0.00253
NM_015192.4(PLCB1):c.3116T>C (p.Ile1039Thr) rs75820839 0.00251
NM_006031.6(PCNT):c.9707G>A (p.Arg3236Gln) rs113591604 0.00249
NM_006031.6(PCNT):c.7495-13A>G rs114588443 0.00240
NM_006031.6(PCNT):c.8224G>C (p.Glu2742Gln) rs35557109 0.00238
NM_002474.3(MYH11):c.3859-768T>C rs140080894 0.00221
NM_006031.6(PCNT):c.4142C>T (p.Ala1381Val) rs114383833 0.00221
NM_002474.3(MYH11):c.3928G>A (p.Val1310Met) rs7196804 0.00216
NM_001083961.2(WDR62):c.4312-5T>G rs182467995 0.00215
NM_001126121.2(SLC25A19):c.483C>T (p.Ala161=) rs142281464 0.00215
NM_001143979.2(NDE1):c.-687C>T rs373275027 0.00215
NM_000702.4(ATP1A2):c.25T>A (p.Tyr9Asn) rs55858252 0.00211
NM_001126121.2(SLC25A19):c.797T>G (p.Met266Arg) rs148372053 0.00204
NM_007254.4(PNKP):c.416G>A (p.Arg139His) rs34472250 0.00185
NM_001083961.2(WDR62):c.4338C>T (p.Thr1446=) rs149289227 0.00183
NM_007254.4(PNKP):c.1433T>G (p.Val478Gly) rs3739206 0.00181
NM_000817.3(GAD1):c.1612-3A>G rs113828797 0.00179
NM_144508.5(KNL1):c.5271C>T (p.Cys1757=) rs191249840 0.00173
NM_000817.3(GAD1):c.1473T>C (p.Tyr491=) rs146199288 0.00168
NM_006031.6(PCNT):c.1519C>G (p.Arg507Gly) rs138036524 0.00165
NM_024596.5(MCPH1):c.1349A>C (p.Lys450Thr) rs77959215 0.00160
NM_006031.6(PCNT):c.-25G>C rs202239640 0.00159
NM_006031.6(PCNT):c.6080A>G (p.Gln2027Arg) rs147189224 0.00157
NM_007254.4(PNKP):c.636+7G>A rs3739187 0.00154
NM_006031.6(PCNT):c.6125G>A (p.Arg2042His) rs149264703 0.00151
NM_006031.6(PCNT):c.9949T>C (p.Leu3317=) rs111389121 0.00148
NM_018451.5(CPAP):c.646T>C (p.Cys216Arg) rs143260721 0.00148
NM_144508.5(KNL1):c.4170T>A (p.Asp1390Glu) rs141726041 0.00141
NM_018451.5(CPAP):c.656C>T (p.Pro219Leu) rs139844197 0.00140
NM_001083961.2(WDR62):c.1359C>T (p.Asn453=) rs148667984 0.00138
NM_007254.4(PNKP):c.1491C>T (p.Ala497=) rs116192442 0.00133
NM_018451.5(CENPJ):c.*556A>C rs188324716 0.00124
NM_018136.5(ASPM):c.-114C>A rs78280885 0.00121
NM_018136.5(ASPM):c.1732G>A (p.Asp578Asn) rs60950503 0.00119
NM_018136.5(ASPM):c.-177G>A rs80055790 0.00118
NM_007254.4(PNKP):c.650C>G (p.Thr217Ser) rs115259839 0.00112
NM_001143979.1(NDE1):c.-773G>A rs376603273 0.00111
NM_018136.5(ASPM):c.-9G>T rs141108591 0.00105
NM_018451.5(CPAP):c.2298T>A (p.Asp766Glu) rs79951875 0.00096
NM_018451.5(CPAP):c.2571C>G (p.Ser857Arg) rs78628025 0.00094
NM_006031.6(PCNT):c.2033A>G (p.Lys678Arg) rs149623054 0.00088
NM_018451.5(CPAP):c.2806A>G (p.Ser936Gly) rs75008861 0.00070
NM_018136.5(ASPM):c.1007C>A (p.Thr336Lys) rs112113370 0.00066
NM_018136.5(ASPM):c.844A>C (p.Asn282His) rs113777932 0.00066
NM_018136.5(ASPM):c.905G>A (p.Cys302Tyr) rs77736715 0.00066
NM_152296.5(ATP1A3):c.2838C>T (p.Phe946=) rs141421692 0.00065
NM_018136.5(ASPM):c.9492T>C (p.Tyr3164=) rs143931757 0.00061
NM_018136.5(ASPM):c.8449G>T (p.Ala2817Ser) rs117963393 0.00059
NM_001143979.2(NDE1):c.-535C>A rs187630586 0.00056
NM_000702.4(ATP1A2):c.1474G>A (p.Glu492Lys) rs142348542 0.00055
NM_144508.5(KNL1):c.3405C>T (p.Ala1135=) rs142853192 0.00055
NM_017668.3(NDE1):c.872C>T (p.Ser291Phe) rs146284370 0.00053
NM_018451.5(CPAP):c.763A>G (p.Thr255Ala) rs150932292 0.00053
NM_018249.6(CDK5RAP2):c.2294C>G (p.Pro765Arg) rs139706626 0.00052
NM_001126121.2(SLC25A19):c.*301C>T rs543638381 0.00051
NM_018136.5(ASPM):c.8166T>C (p.Tyr2722=) rs78315399 0.00046
NM_018451.5(CENPJ):c.600G>T (p.Gln200His) rs200061825 0.00043
NM_001143979.2(NDE1):c.-302A>G rs117057165 0.00040
NM_006031.6(PCNT):c.2264T>G (p.Met755Arg) rs201827977 0.00039
NM_018136.5(ASPM):c.581C>A (p.Ala194Asp) rs141532484 0.00038
NM_018136.5(ASPM):c.7475G>A (p.Arg2492Lys) rs118010078 0.00037
NM_001048166.1(STIL):c.*730A>G rs184977531 0.00035
NM_001194998.2(CEP152):c.2681C>T (p.Ser894Phe) rs145138194 0.00034
NM_018136.5(ASPM):c.2267A>G (p.Tyr756Cys) rs201066146 0.00031
NM_018136.5(ASPM):c.937A>G (p.Ile313Val) rs12025066 0.00029
NM_001126121.2(SLC25A19):c.288+8G>C rs144563813 0.00024
NM_002474.3(MYH11):c.3859-202G>A rs149894916 0.00022
NM_144508.5(KNL1):c.5433A>T (p.Ile1811=) rs200029926 0.00022
NM_018451.5(CPAP):c.2852A>G (p.Gln951Arg) rs138675304 0.00021
NM_144508.5(KNL1):c.4000C>T (p.Pro1334Ser) rs148070447 0.00021
NM_006031.6(PCNT):c.6277G>A (p.Asp2093Asn) rs200303861 0.00020
NM_018136.5(ASPM):c.5224T>C (p.Tyr1742His) rs143733126 0.00019
NM_006031.6(PCNT):c.1040A>G (p.Lys347Arg) rs80166001 0.00017
NM_001194998.2(CEP152):c.2804A>G (p.Gln935Arg) rs74245641 0.00016
NM_006031.6(PCNT):c.6150+3G>A rs760779996 0.00016
NM_000702.4(ATP1A2):c.1092G>A (p.Thr364=) rs55741021 0.00015
NM_001126121.2(SLC25A19):c.642T>C (p.Asn214=) rs147091827 0.00015
NM_001194998.2(CEP152):c.2777A>T (p.Glu926Val) rs117557829 0.00014
NM_006031.6(PCNT):c.7459C>G (p.Leu2487Val) rs201185279 0.00014
NM_018451.5(CPAP):c.1430C>T (p.Thr477Met) rs193181742 0.00014
NM_006031.6(PCNT):c.5826G>A (p.Arg1942=) rs536281306 0.00012
NM_006031.6(PCNT):c.7413G>A (p.Glu2471=) rs191561981 0.00012
NM_001365536.1(SCN9A):c.2875-5del rs774840081 0.00011
NM_018451.5(CENPJ):c.*890T>C rs17480581 0.00011
NM_001194998.2(CEP152):c.5078C>T (p.Pro1693Leu) rs368764302 0.00010
NM_018136.5(ASPM):c.9539A>C (p.Gln3180Pro) rs193251130 0.00009
NM_000702.4(ATP1A2):c.1821C>T (p.Gly607=) rs771085157 0.00006
NM_006031.6(PCNT):c.5724G>A (p.Gln1908=) rs199519762 0.00006
NM_006031.6(PCNT):c.9279G>A (p.Ser3093=) rs199596313 0.00006
NM_000702.4(ATP1A2):c.627T>C (p.Cys209=) rs139229302 0.00005
NM_001048166.1(STIL):c.3515C>T (p.Ser1172Phe) rs550062989 0.00005
NM_152296.5(ATP1A3):c.1924G>A (p.Val642Ile) rs201391210 0.00005
NM_152296.5(ATP1A3):c.786C>T (p.Thr262=) rs74581050 0.00005
NM_152296.5(ATP1A3):c.994-4C>G rs373698149 0.00005
NM_007254.4(PNKP):c.1322C>G (p.Ala441Gly) rs549000007 0.00003
NM_152296.5(ATP1A3):c.1714A>G (p.Asn572Asp) rs782415633 0.00003
NM_152296.5(ATP1A3):c.1806+14T>C rs377372631 0.00003
NM_000702.4(ATP1A2):c.1578G>A (p.Pro526=) rs376128790 0.00002
NM_000817.3(GAD1):c.-170G>A rs561714411 0.00002
NM_006031.6(PCNT):c.2865C>T (p.Ala955=) rs540548340 0.00002
NM_018136.5(ASPM):c.8203T>G (p.Phe2735Val) rs372416792 0.00002
NM_000702.4(ATP1A2):c.1674A>G (p.Pro558=) rs769798147 0.00001
NM_000702.4(ATP1A2):c.2015C>T (p.Ser672Leu) rs145701604 0.00001
NM_000702.4(ATP1A2):c.2115+8C>T rs768746868 0.00001
NM_001083961.2(WDR62):c.4033C>T (p.Arg1345Cys) rs201363122 0.00001
NM_006031.6(PCNT):c.3698A>C (p.Glu1233Ala) rs199787861 0.00001
NM_152296.5(ATP1A3):c.1905C>T (p.Ala635=) rs781822752 0.00001
NM_152296.5(ATP1A3):c.2688+11C>A rs782430886 0.00001
NM_001083961.2(WDR62):c.1233+15C>A rs554017479
NM_001126121.2(SLC25A19):c.-173AG[2] rs796850773
NM_001365536.1(SCN9A):c.*1605_*1606del rs200091138
NM_001365536.1(SCN9A):c.*1960_*1962dup rs202073550
NM_001365536.1(SCN9A):c.1975-3del rs35888674
NM_002474.3(MYH11):c.4116+29A>G rs138543179
NM_006031.6(PCNT):c.*101T>G rs138450666
NM_006031.6(PCNT):c.*343_*346del rs145379994
NM_006031.6(PCNT):c.4571C>G (p.Pro1524Arg) rs35513449
NM_006031.6(PCNT):c.5982C>G (p.Val1994=) rs552463011
NM_006031.6(PCNT):c.9394-3T>C rs545618955
NM_021734.4(SLC25A19):c.-201T>A rs576181366
NM_024596.5(MCPH1):c.1351G>A (p.Glu451Lys) rs202004426
NM_152296.5(ATP1A3):c.909C>T (p.Leu303=) rs782266448

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