ClinVar Miner

List of variants reported as likely benign for bone remodeling disease by Illumina Laboratory Services, Illumina

Included ClinVar conditions (104):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 205
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HGVS dbSNP gnomAD frequency
NM_003839.4(TNFRSF11A):c.933A>G (p.Thr311=) rs8092336 0.95903
NM_003839.4(TNFRSF11A):c.575C>T (p.Ala192Val) rs1805034 0.56701
NM_003839.4(TNFRSF11A):c.-9T>C rs1805033 0.28610
NM_003839.4(TNFRSF11A):c.-39G>A rs7238731 0.28496
NM_003839.4(TNFRSF11A):c.421C>T (p.His141Tyr) rs35211496 0.12362
NM_001287.6(CLCN7):c.1252G>A (p.Val418Met) rs12926089 0.11417
NM_000376.3(VDR):c.*437C>G rs11574119 0.03464
NM_000376.3(VDR):c.*562A>C rs3858733 0.03190
NM_000376.3(VDR):c.*2974A>T rs11574139 0.03175
NM_006208.3(ENPP1):c.2320C>T (p.Arg774Cys) rs28933977 0.02826
NM_000067.3(CA2):c.754A>G (p.Asn252Asp) rs2228063 0.02817
NM_006208.3(ENPP1):c.-10C>T rs750410843 0.02463
NM_003839.4(TNFRSF11A):c.75+5G>A rs146553439 0.02406
NM_002496.4(NDUFS8):c.*40A>G rs61329983 0.02403
NM_000376.3(VDR):c.*1281G>A rs7967673 0.02377
NM_000376.3(VDR):c.*1242A>G rs7954412 0.02375
NM_000376.3(VDR):c.*2827A>G rs11574138 0.02365
NM_003052.5(SLC34A1):c.1702C>T (p.His568Tyr) rs34225933 0.02221
NM_003701.4(TNFSF11):c.107C>G (p.Pro36Arg) rs138818878 0.02149
NM_000785.4(CYP27B1):c.942G>A (p.Leu314=) rs8176345 0.02124
NM_000376.3(VDR):c.*408T>C rs112308011 0.01929
NM_003839.4(TNFRSF11A):c.*668G>T rs78622775 0.01625
NM_003900.5(SQSTM1):c.822G>C (p.Glu274Asp) rs55793208 0.01529
NM_000376.3(VDR):c.*2593A>G rs11168263 0.01497
NM_006208.3(ENPP1):c.2002G>A (p.Glu668Lys) rs115371819 0.01496
NM_000376.3(VDR):c.*409G>A rs11574118 0.01495
NM_000785.4(CYP27B1):c.*415G>A rs8176351 0.01487
NM_207122.2(EXT2):c.124A>G (p.Met42Val) rs4755779 0.01478
NM_006208.3(ENPP1):c.1831C>G (p.Leu611Val) rs79079368 0.01455
NM_207122.2(EXT2):c.1761G>A (p.Thr587=) rs16937864 0.01303
NM_016175.4(MRNIP):c.*12C>T rs73334055 0.01186
NM_016175.4(MRNIP):c.729C>T (p.Asp243=) rs61742526 0.01155
NM_006208.3(ENPP1):c.*2076C>T rs117531639 0.01090
NM_003839.4(TNFRSF11A):c.1397G>A (p.Arg466His) rs35993683 0.01070
NM_003900.5(SQSTM1):c.961C>T (p.Arg321Cys) rs140226523 0.00943
NM_207122.2(EXT2):c.1017T>C (p.Cys339=) rs11828047 0.00930
NM_000088.4(COL1A1):c.1615-4C>A rs41316657 0.00846
NM_000088.4(COL1A1):c.1803C>T (p.Pro601=) rs148275339 0.00788
NM_002546.4(TNFRSF11B):c.*545T>C rs11573947 0.00754
NM_000088.4(COL1A1):c.1821C>T (p.Val607=) rs41316667 0.00750
NM_000444.6(PHEX):c.537T>A (p.Val179=) rs137961493 0.00746
NM_020638.3(FGF23):c.*388G>A rs13312795 0.00731
NM_003839.4(TNFRSF11A):c.*1738C>T rs6567277 0.00718
NM_000088.4(COL1A1):c.904-9G>T rs141726413 0.00680
NM_000505.4(F12):c.1342C>T (p.Arg448Cys) rs115119084 0.00679
NM_000376.3(VDR):c.444C>T (p.Ser148=) rs2229828 0.00638
NM_003839.4(TNFRSF11A):c.1519G>A (p.Ala507Thr) rs61751992 0.00618
NM_003701.4(TNFSF11):c.*745T>C rs12721444 0.00615
NM_003900.5(SQSTM1):c.*83G>A rs155790 0.00589
NM_000088.4(COL1A1):c.3897C>T (p.Cys1299=) rs34940368 0.00563
NM_006208.3(ENPP1):c.*1122A>G rs148507889 0.00539
NM_006019.4(TCIRG1):c.*68G>A rs139720520 0.00538
NM_006208.3(ENPP1):c.*3176T>A rs114333444 0.00525
NM_000088.4(COL1A1):c.*1233G>A rs73987442 0.00516
NM_003052.5(SLC34A1):c.*485G>A rs143160780 0.00504
NM_006208.3(ENPP1):c.*1038T>A rs79214335 0.00496
NM_003900.5(SQSTM1):c.183C>T (p.Gly61=) rs767340839 0.00487
NM_000505.4(F12):c.1272G>C (p.Thr424=) rs61737766 0.00486
NM_006019.4(TCIRG1):c.1515C>T (p.Thr505=) rs34211419 0.00473
NM_000088.4(COL1A1):c.750+12G>T rs79480112 0.00434
NM_002546.4(TNFRSF11B):c.885T>A (p.Leu295=) rs11573942 0.00387
NM_207122.2(EXT2):c.*56G>A rs77554103 0.00371
NM_025237.3(SOST):c.*222A>G rs544576964 0.00346
NM_207122.2(EXT2):c.*101G>C rs117755165 0.00332
NM_003839.4(TNFRSF11A):c.570C>T (p.Ser190=) rs12721430 0.00322
NM_025237.3(SOST):c.-21T>G rs202008449 0.00319
NM_003701.4(TNFSF11):c.45G>A (p.Ser15=) rs200121871 0.00316
NM_006208.3(ENPP1):c.2657G>C (p.Arg886Thr) rs8192683 0.00299
NM_003052.5(SLC34A1):c.398C>T (p.Ala133Val) rs148976897 0.00298
NM_000396.4(CTSK):c.675A>G (p.Arg225=) rs41271965 0.00297
NM_000088.4(COL1A1):c.4179C>T (p.Ser1393=) rs1800219 0.00281
NM_003839.4(TNFRSF11A):c.*2077G>T rs75853662 0.00278
NM_000088.4(COL1A1):c.*1088G>A rs191326459 0.00264
NM_001287.6(CLCN7):c.*1572C>T rs539134149 0.00264
NM_025237.3(SOST):c.-10G>A rs190743758 0.00262
NM_025237.3(SOST):c.*1391G>C rs144304911 0.00249
NM_003839.4(TNFRSF11A):c.1348C>T (p.Arg450Trp) rs34945627 0.00239
NM_003052.5(SLC34A1):c.*179G>A rs141664220 0.00237
NM_207122.2(EXT2):c.710C>T (p.Ser237Leu) rs139525250 0.00236
NM_003900.5(SQSTM1):c.712A>G (p.Lys238Glu) rs11548633 0.00229
NM_014028.4(OSTM1):c.615+8A>G rs144204437 0.00220
NM_004407.4(DMP1):c.639G>A (p.Glu213=) rs116732769 0.00193
NM_006208.3(ENPP1):c.2757A>T (p.Pro919=) rs73541508 0.00178
NM_003701.4(TNFSF11):c.214G>A (p.Ala72Thr) rs142756983 0.00164
NM_006019.4(TCIRG1):c.630+14G>A rs201531306 0.00161
NM_006208.3(ENPP1):c.*3528C>T rs557822175 0.00161
NM_006019.4(TCIRG1):c.482C>T (p.Pro161Leu) rs34227834 0.00144
NM_014028.4(OSTM1):c.*2366A>G rs564822548 0.00143
NM_000785.4(CYP27B1):c.*77G>A rs8176350 0.00137
NM_000088.4(COL1A1):c.1873G>A (p.Ala625Thr) rs149561221 0.00134
NM_003839.4(TNFRSF11A):c.284-5C>T rs371545302 0.00130
NM_003900.5(SQSTM1):c.350C>T (p.Ala117Val) rs147810437 0.00126
NM_006208.3(ENPP1):c.*1307T>G rs189263683 0.00117
NM_006208.3(ENPP1):c.*4015G>A rs531152298 0.00116
NM_207122.2(EXT2):c.1178G>A (p.Arg393Gln) rs138187791 0.00113
NM_014028.4(OSTM1):c.495A>G (p.Thr165=) rs137974384 0.00110
NM_003839.4(TNFRSF11A):c.*1060C>T rs572639953 0.00100
NM_006208.3(ENPP1):c.*804A>G rs114078048 0.00098
NM_003052.5(SLC34A1):c.*361T>C rs539754545 0.00096
NM_000505.4(F12):c.1299C>T (p.Asn433=) rs17876033 0.00093
NM_000088.4(COL1A1):c.4181A>G (p.Asn1394Ser) rs147266928 0.00087
NM_001287.6(CLCN7):c.*1452G>A rs578092313 0.00080
NM_004407.4(DMP1):c.724T>C (p.Ser242Pro) rs147552663 0.00080
NM_014028.4(OSTM1):c.134A>G (p.Asp45Gly) rs202093691 0.00068
NM_207122.2(EXT2):c.1760C>T (p.Thr587Met) rs138495222 0.00063
NM_014028.4(OSTM1):c.*3192A>C rs185905869 0.00058
NM_003900.5(SQSTM1):c.1245G>A (p.Arg415=) rs148278350 0.00057
NM_003900.5(SQSTM1):c.1176G>A (p.Pro392=) rs75700262 0.00052
NM_006019.4(TCIRG1):c.274C>T (p.Arg92Trp) rs371907380 0.00052
NM_003701.4(TNFSF11):c.-141C>T rs45468495 0.00046
NM_207122.2(EXT2):c.1087G>A (p.Val363Met) rs138943091 0.00046
NM_054027.6(ANKH):c.*2243C>T rs531980160 0.00045
NM_207122.2(EXT2):c.1022C>T (p.Pro341Leu) rs141035971 0.00044
NM_000127.3(EXT1):c.1536+7G>A rs200128437 0.00041
NM_000444.6(PHEX):c.2214G>A (p.Thr738=) rs140742016 0.00035
NM_001287.6(CLCN7):c.*89C>T rs372232215 0.00035
NM_000127.3(EXT1):c.-642G>A rs534171475 0.00032
NM_000444.6(PHEX):c.10G>C (p.Glu4Gln) rs147859619 0.00030
NM_000088.4(COL1A1):c.1983+9G>C rs201091992 0.00029
NM_207122.2(EXT2):c.1806+11G>A rs372517964 0.00029
NM_014028.4(OSTM1):c.49T>G (p.Trp17Gly) rs546399681 0.00028
NM_003900.5(SQSTM1):c.819A>G (p.Pro273=) rs200388590 0.00026
NM_006019.4(TCIRG1):c.2193C>T (p.Thr731=) rs141601593 0.00025
NM_000127.3(EXT1):c.1066G>A (p.Val356Ile) rs61753260 0.00024
NM_006208.3(ENPP1):c.*2698G>A rs146550172 0.00023
NM_001287.6(CLCN7):c.*1685G>A rs376387077 0.00021
NM_006208.3(ENPP1):c.2336C>A (p.Thr779Asn) rs200239821 0.00021
NM_000088.4(COL1A1):c.957+10C>A rs376179885 0.00020
NM_000444.6(PHEX):c.1483-7T>C rs369175587 0.00020
NM_207122.2(EXT2):c.896G>A (p.Arg299His) rs76901081 0.00020
NM_000444.6(PHEX):c.631G>A (p.Asp211Asn) rs370610267 0.00019
NM_020638.3(FGF23):c.*1398T>A rs531815578 0.00019
NM_020638.3(FGF23):c.*998C>G rs71583766 0.00017
NM_003900.5(SQSTM1):c.*66A>C rs140407570 0.00016
NM_014028.4(OSTM1):c.198A>G (p.Gly66=) rs565610194 0.00015
NM_000127.3(EXT1):c.1749G>C (p.Gln583His) rs575895733 0.00014
NM_000376.3(VDR):c.1206C>A (p.Arg402=) rs2229829 0.00014
NM_000444.6(PHEX):c.2068C>A (p.His690Asn) rs200733697 0.00014
NM_001287.6(CLCN7):c.350C>T (p.Thr117Met) rs201003681 0.00014
NM_002546.4(TNFRSF11B):c.21C>T (p.Cys7=) rs373330021 0.00014
NM_014028.4(OSTM1):c.300G>T (p.Gly100=) rs199570880 0.00014
NM_001287.6(CLCN7):c.286-9G>T rs200321142 0.00013
NM_003052.5(SLC34A1):c.1719A>G (p.Leu573=) rs148575220 0.00012
NM_000088.4(COL1A1):c.2613+13C>T rs368380161 0.00011
NM_003839.4(TNFRSF11A):c.1567+7G>A rs35332936 0.00011
NM_025237.3(SOST):c.56G>A (p.Arg19His) rs199514554 0.00011
NM_207122.2(EXT2):c.*129C>G rs141864253 0.00011
NM_207122.2(EXT2):c.*139C>G rs191451519 0.00011
NM_003052.5(SLC34A1):c.1483C>T (p.Arg495Cys) rs199565633 0.00010
NM_207122.2(EXT2):c.1916C>T (p.Thr639Met) rs138722406 0.00010
NM_006019.4(TCIRG1):c.826C>T (p.Arg276Trp) rs543099977 0.00008
NM_000127.3(EXT1):c.1659C>T (p.Tyr553=) rs757115396 0.00006
NM_000127.3(EXT1):c.214G>A (p.Glu72Lys) rs150818931 0.00006
NM_003052.5(SLC34A1):c.1443C>T (p.Asn481=) rs137867155 0.00005
NM_003052.5(SLC34A1):c.644G>A (p.Arg215Gln) rs1163121743 0.00005
NM_207122.2(EXT2):c.284G>A (p.Arg95His) rs143703574 0.00005
NM_207122.2(EXT2):c.8C>T (p.Ala3Val) rs201185639 0.00005
NM_003052.5(SLC34A1):c.883T>A (p.Ser295Thr) rs763096294 0.00004
NM_207122.2(EXT2):c.849C>T (p.Leu283=) rs749093709 0.00004
NM_000067.3(CA2):c.648C>T (p.Ser216=) rs376387073 0.00003
NM_000088.4(COL1A1):c.*1265C>T rs567249120 0.00003
NM_000127.3(EXT1):c.1781C>G (p.Ala594Gly) rs374887549 0.00003
NM_003900.5(SQSTM1):c.301+12C>G rs141530539 0.00003
NM_207122.2(EXT2):c.1023G>A (p.Pro341=) rs757323768 0.00003
NM_207122.2(EXT2):c.1935+11C>G rs764143899 0.00003
NM_207122.2(EXT2):c.383G>A (p.Arg128Gln) rs771039412 0.00003
NM_000127.3(EXT1):c.1360G>A (p.Val454Ile) rs201504622 0.00002
NM_000127.3(EXT1):c.66T>C (p.Tyr22=) rs764093488 0.00002
NM_000444.6(PHEX):c.*48G>A rs765479131 0.00002
NM_003052.5(SLC34A1):c.123C>T (p.Ile41=) rs759907707 0.00002
NM_003052.5(SLC34A1):c.1469C>T (p.Pro490Leu) rs372577906 0.00002
NM_020638.3(FGF23):c.249G>A (p.Val83=) rs753676774 0.00002
NM_207122.2(EXT2):c.11C>T (p.Ser4Leu) rs527624522 0.00002
NM_001287.6(CLCN7):c.*1589G>C rs532736933 0.00001
NM_003052.5(SLC34A1):c.397G>A (p.Ala133Thr) rs771178295 0.00001
NM_003839.4(TNFRSF11A):c.*2086G>A rs528958493 0.00001
NM_006208.3(ENPP1):c.1791T>C (p.Asn597=) rs548504035 0.00001
NM_016175.4(MRNIP):c.719C>G (p.Ser240Ter) rs199887787 0.00001
NM_020638.3(FGF23):c.138A>G (p.Thr46=) rs368115734 0.00001
NM_054027.6(ANKH):c.39G>C (p.Leu13=) rs748751320 0.00001
NM_207122.2(EXT2):c.1208T>C (p.Ile403Thr) rs530523884 0.00001
NM_000088.4(COL1A1):c.*243_*244dup rs56302025
NM_000088.4(COL1A1):c.*681_*682insAGCA rs3840870
NM_000088.4(COL1A1):c.*88T>A rs1061237
NM_000088.4(COL1A1):c.-98G>A rs574683904
NM_000088.4(COL1A1):c.1983+9G>T rs201091992
NM_000444.6(PHEX):c.653A>G (p.His218Arg) rs774907553
NM_000505.4(F12):c.1251-7C>T rs375340260
NM_001287.6(CLCN7):c.*1144dup rs146690487
NM_001287.6(CLCN7):c.*1619GGT[1] rs143409179
NM_003052.5(SLC34A1):c.1174+9C>T rs752762105
NM_003052.5(SLC34A1):c.654G>A (p.Ala218=) rs150592440
NM_003839.4(TNFRSF11A):c.*1251dup rs150401931
NM_003839.4(TNFRSF11A):c.*320del rs552069161
NM_003839.4(TNFRSF11A):c.*633C>G rs184568614
NM_003839.4(TNFRSF11A):c.*634_*635dup rs142942284
NM_003839.4(TNFRSF11A):c.*938T>C rs565315471
NM_003900.4(SQSTM1):c.-35G>C rs189132632
NM_003900.5(SQSTM1):c.*175TG[8] rs10688915
NM_004407.4(DMP1):c.844C>A (p.Leu282Ile) rs141979823
NM_006019.4(TCIRG1):c.2279TGGGCC[3] (p.760LG[3]) rs199973759
NM_006208.3(ENPP1):c.*150G>A rs571779819
NM_014028.4(OSTM1):c.*2276C>A rs546976371
NM_020638.3(FGF23):c.555G>C (p.Ser185=) rs115283398
NM_207122.2(EXT2):c.245A>C (p.Asp82Ala) rs534539796

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