ClinVar Miner

List of variants reported as benign for bone development disease by ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories

Included ClinVar conditions (588):
Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 140
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HGVS dbSNP gnomAD frequency
NM_006371.5(CRTAP):c.1044G>A (p.Ser348=) rs1135128 0.36102
NM_006371.5(CRTAP):c.1032T>G (p.Thr344=) rs1135127 0.36088
NM_203486.3(DLL3):c.515T>G (p.Phe172Cys) rs8107127 0.29570
NM_203486.3(DLL3):c.410-40C>T rs2278440 0.27956
NM_203486.3(DLL3):c.425T>A (p.Leu142Gln) rs55741253 0.06752
NM_022356.4(P3H1):c.1045G>A (p.Gly349Arg) rs6700677 0.06024
NM_003036.4(SKI):c.185C>G (p.Ala62Gly) rs28384811 0.05253
NM_022356.4(P3H1):c.139G>T (p.Ala47Ser) rs55716016 0.04262
NM_001127671.2(LIFR):c.143-60A>G rs62355821 0.04013
NM_014140.4(SMARCAL1):c.1129G>C (p.Glu377Gln) rs2066518 0.03294
NM_001127671.2(LIFR):c.991+80G>T rs6451387 0.03281
NM_006129.5(BMP1):c.2575+14T>C rs28374147 0.03056
NM_003118.4(SPARC):c.55C>T (p.Pro19Ser) rs6874468 0.02536
NM_005032.7(PLS3):c.367+11T>C rs112140311 0.02260
NM_014140.4(SMARCAL1):c.2141+17T>C rs2066516 0.02186
NM_006031.6(PCNT):c.5879G>A (p.Arg1960Gln) rs34813667 0.02167
NM_002615.7(SERPINF1):c.395C>G (p.Pro132Arg) rs1804145 0.02133
NM_006031.6(PCNT):c.7867C>T (p.Leu2623=) rs61735821 0.02105
NM_006031.6(PCNT):c.9014C>T (p.Thr3005Met) rs60078675 0.02025
NM_152281.3(GORAB):c.62-3T>C rs73029138 0.01889
NM_022356.4(P3H1):c.1284C>T (p.Ile428=) rs61746642 0.01592
NM_198239.2(CCN6):c.237C>T (p.Ala79=) rs112665393 0.01588
NM_022356.4(P3H1):c.1026C>T (p.Ala342=) rs61100157 0.01581
NM_022356.4(P3H1):c.1569+3A>G rs76871760 0.01579
NM_022356.4(P3H1):c.1812C>T (p.Pro604=) rs34809608 0.01577
NM_006031.6(PCNT):c.6739C>T (p.His2247Tyr) rs61735812 0.01575
NM_006031.6(PCNT):c.7652C>T (p.Ala2551Val) rs12481791 0.01548
NM_006031.6(PCNT):c.5742G>A (p.Ala1914=) rs61735810 0.01545
NM_001127671.2(LIFR):c.1886-18C>T rs3729743 0.01528
NM_006031.6(PCNT):c.7800G>A (p.Ala2600=) rs61735820 0.01494
NM_014822.4(SEC24D):c.125T>C (p.Met42Thr) rs10029206 0.01448
NM_014140.4(SMARCAL1):c.127G>A (p.Ala43Thr) rs2066524 0.01441
NM_203486.3(DLL3):c.1152G>A (p.Ala384=) rs115456333 0.01391
NM_001127671.2(LIFR):c.2066-74T>G rs113874922 0.01368
NM_003036.4(SKI):c.99C>G (p.Gly33=) rs200019352 0.01364
NM_052854.4(CREB3L1):c.454G>A (p.Ala152Thr) rs199951144 0.01311
NM_005032.7(PLS3):c.321T>A (p.Gly107=) rs140121121 0.01269
NM_001173467.3(SP7):c.993C>T (p.Cys331=) rs116856142 0.01263
NM_022356.4(P3H1):c.978C>T (p.Thr326=) rs74070022 0.01251
NM_006031.6(PCNT):c.4962+10G>A rs114474454 0.01225
NM_003036.4(SKI):c.294C>T (p.Thr98=) rs115746142 0.01188
NM_022356.4(P3H1):c.1233G>A (p.Arg411=) rs61746653 0.01103
NM_000942.5(PPIB):c.324C>T (p.Thr108=) rs2307247 0.01016
NM_152281.3(GORAB):c.657C>T (p.Tyr219=) rs76365864 0.00986
NM_003036.4(SKI):c.456C>T (p.Arg152=) rs149898447 0.00976
NM_006031.6(PCNT):c.9015G>A (p.Thr3005=) rs79359463 0.00973
NM_203486.3(DLL3):c.1674-10C>T rs116099821 0.00950
NM_003036.4(SKI):c.1211+11G>A rs115186522 0.00934
NM_014822.4(SEC24D):c.653C>G (p.Ala218Gly) rs35392900 0.00928
NM_014822.4(SEC24D):c.1576C>T (p.Leu526Phe) rs141180741 0.00908
NM_004836.7(EIF2AK3):c.1756A>T (p.Ile586Leu) rs75385605 0.00906
NM_014140.4(SMARCAL1):c.423T>C (p.Tyr141=) rs35907255 0.00906
NM_001127671.2(LIFR):c.1937C>A (p.Thr646Asn) rs79040751 0.00875
NM_022356.4(P3H1):c.2055+70G>T rs115690038 0.00864
NM_006031.6(PCNT):c.6616A>G (p.Thr2206Ala) rs9981448 0.00833
NM_006031.6(PCNT):c.3615G>A (p.Ala1205=) rs61735806 0.00816
NM_006031.6(PCNT):c.4572G>A (p.Pro1524=) rs116431741 0.00812
NM_014140.4(SMARCAL1):c.901C>G (p.Pro301Ala) rs146084305 0.00795
NM_006031.6(PCNT):c.4910C>T (p.Pro1637Leu) rs34849154 0.00771
NM_006031.6(PCNT):c.7159G>A (p.Val2387Met) rs75024419 0.00771
NM_006031.6(PCNT):c.7353G>A (p.Gly2451=) rs61735816 0.00767
NM_006031.6(PCNT):c.7914-4G>A rs76287849 0.00764
NM_006031.6(PCNT):c.7404G>C (p.Gln2468His) rs77075366 0.00759
NM_022356.4(P3H1):c.611C>A (p.Pro204His) rs77208721 0.00751
NM_006031.6(PCNT):c.8065-19G>A rs78561636 0.00750
NM_006031.6(PCNT):c.8671G>A (p.Ala2891Thr) rs33956783 0.00733
NM_203486.3(DLL3):c.674G>A (p.Ser225Asn) rs35380611 0.00724
NM_006031.6(PCNT):c.2575G>A (p.Asp859Asn) rs115369710 0.00703
NM_001127671.2(LIFR):c.1899A>G (p.Ile633Met) rs2303743 0.00702
NM_006031.6(PCNT):c.7398G>A (p.Glu2466=) rs114739559 0.00679
NM_006031.6(PCNT):c.7914-5C>T rs114120845 0.00679
NM_203486.3(DLL3):c.1562C>T (p.Ser521Phe) rs191149379 0.00662
NM_006031.6(PCNT):c.8924T>C (p.Leu2975Pro) rs35881595 0.00647
NM_006031.6(PCNT):c.7656C>T (p.Arg2552=) rs61735819 0.00644
NM_001127671.2(LIFR):c.1991C>T (p.Ser664Leu) rs3729744 0.00642
NM_006031.6(PCNT):c.6986C>G (p.Pro2329Arg) rs35848602 0.00640
NM_022356.4(P3H1):c.2055+193G>A rs116577636 0.00625
NM_003036.4(SKI):c.1974C>T (p.Arg658=) rs201895384 0.00623
NM_006031.6(PCNT):c.5771C>T (p.Ala1924Val) rs184420466 0.00604
NM_006031.6(PCNT):c.8646G>C (p.Leu2882Phe) rs141771795 0.00596
NM_006031.6(PCNT):c.5954C>T (p.Ser1985Phe) rs140398533 0.00585
NM_006031.6(PCNT):c.8752-5A>C rs149444205 0.00573
NM_003036.4(SKI):c.1446G>A (p.Ala482=) rs114345135 0.00570
NM_022356.4(P3H1):c.1716C>T (p.Ile572=) rs35500164 0.00563
NM_203486.3(DLL3):c.543T>C (p.Pro181=) rs115194365 0.00553
NM_182943.3(PLOD2):c.1171G>C (p.Val391Leu) rs150981193 0.00532
NM_006129.5(BMP1):c.879C>T (p.Asn293=) rs35120584 0.00529
NM_006371.5(CRTAP):c.888C>T (p.Thr296=) rs13637 0.00524
NM_006031.6(PCNT):c.6634C>T (p.Arg2212Trp) rs144471022 0.00516
NM_001127671.2(LIFR):c.2766T>C (p.Asp922=) rs61027880 0.00501
NM_000942.5(PPIB):c.249+19G>T rs150590633 0.00489
NM_018112.3(TMEM38B):c.113-7A>G rs186864213 0.00484
NC_000005.10:g.38594967T>A rs186528221 0.00479
NM_182943.3(PLOD2):c.2229T>C (p.Pro743=) rs78976445 0.00458
NM_182943.3(PLOD2):c.1647T>C (p.Asn549=) rs141850775 0.00428
NM_014822.4(SEC24D):c.2959-16G>T rs58916284 0.00425
NM_001127671.2(LIFR):c.954C>T (p.Thr318=) rs61748202 0.00421
NM_003036.4(SKI):c.1834C>T (p.Leu612=) rs35833638 0.00418
NM_003036.4(SKI):c.1163C>T (p.Ala388Val) rs75280988 0.00410
NM_022356.4(P3H1):c.2115C>T (p.Leu705=) rs199887811 0.00409
NM_006031.6(PCNT):c.9623+8C>T rs75758339 0.00388
NM_006031.6(PCNT):c.4345C>G (p.Gln1449Glu) rs139432601 0.00379
NM_022356.4(P3H1):c.1322A>G (p.Asp441Gly) rs113593896 0.00341
NM_001025295.3(IFITM5):c.278C>T (p.Thr93Met) rs141240817 0.00334
NM_000493.4(COL10A1):c.1851T>C (p.Asn617=) rs61745148 0.00330
NM_003036.4(SKI):c.1410C>T (p.Pro470=) rs150985728 0.00322
NM_001127671.2(LIFR):c.789A>G (p.Val263=) rs141925289 0.00321
NM_001127671.2(LIFR):c.2498-7G>A rs113078097 0.00306
NM_006031.6(PCNT):c.6933C>T (p.Val2311=) rs148444313 0.00289
NM_203486.3(DLL3):c.160C>A (p.Leu54Ile) rs200673897 0.00285
NM_003036.4(SKI):c.1527C>T (p.Ser509=) rs111935632 0.00270
NM_006371.5(CRTAP):c.622-16T>C rs147610884 0.00250
NM_006031.6(PCNT):c.9274-3C>T rs200348425 0.00242
NM_203486.3(DLL3):c.390G>A (p.Glu130=) rs113780398 0.00200
NM_006129.5(BMP1):c.1443+12G>C rs181328614 0.00140
NM_022356.4(P3H1):c.33A>G (p.Thr11=) rs144378478 0.00140
NM_006031.6(PCNT):c.6957T>G (p.Phe2319Leu) rs61735813 0.00115
NM_003036.4(SKI):c.798C>T (p.Ala266=) rs149642284 0.00097
NM_003036.4(SKI):c.417C>T (p.Ile139=) rs144874401 0.00076
NM_004836.7(EIF2AK3):c.2014G>A (p.Glu672Lys) rs35226268 0.00071
NM_001127671.2(LIFR):c.2578C>T (p.Arg860Trp) rs146205670 0.00066
NM_006031.6(PCNT):c.6579G>A (p.Pro2193=) rs150756913 0.00051
NM_003118.4(SPARC):c.120+8G>T rs199756185 0.00040
NM_006031.6(PCNT):c.6822G>A (p.Pro2274=) rs375741970 0.00009
NM_022356.4(P3H1):c.1626G>A (p.Thr542=) rs577059613 0.00007
NM_052854.4(CREB3L1):c.1325T>G (p.Leu442Arg) rs544539212 0.00004
NM_003036.4(SKI):c.1272G>A (p.Pro424=) rs552946737 0.00003
NM_001025295.3(IFITM5):c.120G>T (p.Ser40=) rs79625057
NM_001127671.2(LIFR):c.143-37GT[11] rs10637374
NM_001127671.2(LIFR):c.143-37GT[13] rs10637374
NM_001127671.2(LIFR):c.143-37GT[16] rs10637374
NM_001127671.2(LIFR):c.3288C>T (p.Asn1096=) rs3729751
NM_001127671.2(LIFR):c.397+17_397+20del rs139143276
NM_003036.4(SKI):c.1311C>T (p.Ala437=) rs140889128
NM_006031.6(PCNT):c.467_505dup (p.His156_Gln168dup) rs587784306
NM_006031.6(PCNT):c.6150+11G>C rs10222116
NM_006371.5(CRTAP):c.558A>G (p.Ala186=) rs35357409
NM_022356.4(P3H1):c.2055+13C>G rs76628300
NM_152281.3(GORAB):c.61+17A>C rs76513879
NM_203486.3(DLL3):c.546C>G (p.Ala182=) rs8106337

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