ClinVar Miner

List of variants reported as benign for Hereditary cancer-predisposing syndrome by Institute for Biomarker Research, Medical Diagnostic Laboratories, L.L.C.

Minimum submission review status: Collection method:
Minimum conflict level:
ClinVar version:
Total variants: 222
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HGVS dbSNP gnomAD frequency
NM_000038.6(APC):c.5465T>A (p.Val1822Asp) rs459552 0.82099
NM_000038.6(APC):c.5034G>A (p.Gly1678=) rs42427 0.59504
NM_000038.6(APC):c.5880G>A (p.Pro1960=) rs465899 0.59308
NM_000038.6(APC):c.5268T>G (p.Ser1756=) rs866006 0.59230
NM_000038.6(APC):c.4479G>A (p.Thr1493=) rs41115 0.59177
NM_000038.6(APC):c.1635G>A (p.Ala545=) rs351771 0.59150
NM_004655.4(AXIN2):c.1386C>T (p.Pro462=) rs1133683 0.52439
NM_000038.6(APC):c.1458T>C (p.Tyr486=) rs2229992 0.46792
NM_017763.6(RNF43):c.139A>G (p.Ile47Val) rs3744093 0.34051
NM_001048174.2(MUTYH):c.930G>C (p.Gln310His) rs3219489 0.26720
NM_000368.5(TSC1):c.965T>C (p.Met322Thr) rs1073123 0.15387
NM_002691.4(POLD1):c.463+8G>T rs1726802 0.13898
NM_002691.4(POLD1):c.356G>A (p.Arg119His) rs1726801 0.13815
NM_006231.4(POLE):c.4187A>G (p.Asn1396Ser) rs5744934 0.12807
NM_002439.5(MSH3):c.693G>A (p.Pro231=) rs1805355 0.12319
NM_002691.4(POLD1):c.810T>C (p.Ala270=) rs1143666 0.12250
NM_002691.4(POLD1):c.2244T>C (p.Ser748=) rs1274607 0.10634
NM_024642.5(GALNT12):c.356A>T (p.Glu119Val) rs1137654 0.06543
NM_001048174.2(MUTYH):c.22G>A (p.Val8Met) rs3219484 0.04794
NM_002691.4(POLD1):c.1548C>T (p.Ala516=) rs2230247 0.04514
NM_002691.4(POLD1):c.1539G>A (p.Leu513=) rs2230246 0.04513
NM_004329.3(BMPR1A):c.435G>A (p.Pro145=) rs11818239 0.04296
NM_024642.5(GALNT12):c.897A>G (p.Gln299=) rs16917929 0.04000
NM_002691.4(POLD1):c.1860G>A (p.Thr620=) rs1726790 0.03590
NM_002691.4(POLD1):c.234C>G (p.Arg78=) rs2228665 0.03571
NM_002691.4(POLD1):c.518G>A (p.Ser173Asn) rs1726803 0.03166
NM_000038.6(APC):c.7704A>G (p.Gly2568=) rs35043160 0.02992
NM_002691.4(POLD1):c.1173C>T (p.Asp391=) rs2230244 0.02764
NM_006231.4(POLE):c.3379-5T>C rs5744886 0.02670
NM_000535.7(PMS2):c.1532C>T (p.Thr511Met) rs74902811 0.02492
NM_004329.3(BMPR1A):c.1342+6A>G rs55763614 0.02404
NM_000249.4(MLH1):c.2152C>T (p.His718Tyr) rs2020873 0.02345
NM_006231.4(POLE):c.4290+5C>T rs5744936 0.02053
NM_006231.4(POLE):c.2340G>A (p.Ser780=) rs5744822 0.02051
NM_000251.3(MSH2):c.573C>T (p.Leu191=) rs1800151 0.01972
NM_013372.7(GREM1):c.207C>G (p.Pro69=) rs2280738 0.01757
NM_000251.3(MSH2):c.965G>A (p.Gly322Asp) rs4987188 0.01714
NM_000038.6(APC):c.7504G>A (p.Gly2502Ser) rs2229995 0.01693
NM_004329.3(BMPR1A):c.1140C>T (p.Asp380=) rs35572415 0.01512
NM_000251.3(MSH2):c.1077-10T>C rs17224360 0.01428
NM_006231.4(POLE):c.91G>T (p.Ala31Ser) rs34047482 0.01320
NM_000038.6(APC):c.3732A>G (p.Gln1244=) rs74380081 0.01174
NM_000038.6(APC):c.1695A>G (p.Glu565=) rs77921116 0.01170
NM_000249.4(MLH1):c.474C>T (p.Asn158=) rs4647256 0.01161
NM_006231.4(POLE):c.2174-8G>A rs117409343 0.01137
NM_000038.6(APC):c.7201C>T (p.Leu2401=) rs2229994 0.01134
NM_000251.3(MSH2):c.2766T>C (p.Phe922=) rs55859129 0.01118
NM_002691.4(POLD1):c.2862G>C (p.Thr954=) rs3219440 0.01109
NM_001048174.2(MUTYH):c.1517G>A (p.Arg506Gln) rs3219497 0.01092
NM_002691.4(POLD1):c.849G>T (p.Gln283His) rs113282414 0.01085
NM_000535.7(PMS2):c.1557T>C (p.Tyr519=) rs6972869 0.01065
NM_024642.5(GALNT12):c.781G>A (p.Asp261Asn) rs41306504 0.01010
NM_001048174.2(MUTYH):c.1460C>T (p.Ser487Phe) rs140118273 0.00997
NM_000038.6(APC):c.2608C>T (p.Pro870Ser) rs33974176 0.00917
NM_006231.4(POLE):c.5804G>A (p.Cys1935Tyr) rs5744991 0.00898
NM_000249.4(MLH1):c.637G>A (p.Val213Met) rs2308317 0.00818
NM_002485.5(NBN):c.1489A>G (p.Thr497Ala) rs3026268 0.00711
NM_002691.4(POLD1):c.88C>T (p.Arg30Trp) rs3218772 0.00706
NM_000038.6(APC):c.4326T>A (p.Pro1442=) rs67622085 0.00705
NM_000038.6(APC):c.5265G>A (p.Ala1755=) rs34506289 0.00675
NM_002691.4(POLD1):c.2546G>A (p.Arg849His) rs3218775 0.00670
NM_000455.5(STK11):c.369G>A (p.Gln123=) rs140112347 0.00636
NM_000455.5(STK11):c.*365C>G rs535975204 0.00633
NM_001048174.2(MUTYH):c.1347G>C (p.Thr449=) rs74318065 0.00596
NM_000038.6(APC):c.1959G>A (p.Arg653=) rs72541809 0.00583
NM_000038.6(APC):c.3949G>C (p.Glu1317Gln) rs1801166 0.00570
NM_000179.3(MSH6):c.1186C>G (p.Leu396Val) rs2020908 0.00565
NM_000038.6(APC):c.1958+8T>C rs62626346 0.00510
NM_000038.6(APC):c.5250C>G (p.Val1750=) rs2229997 0.00497
NM_000251.3(MSH2):c.984C>T (p.Ala328=) rs4987189 0.00495
NM_000251.3(MSH2):c.1666T>C (p.Leu556=) rs61756466 0.00471
NM_000465.4(BARD1):c.1738G>A (p.Glu580Lys) rs35306212 0.00455
NM_000179.3(MSH6):c.2633T>C (p.Val878Ala) rs2020912 0.00448
NM_001127511.3(APC):c.166-28452G>C rs115242894 0.00443
NM_000051.4(ATM):c.1810C>T (p.Pro604Ser) rs2227922 0.00431
NM_000179.3(MSH6):c.1345C>T (p.Leu449=) rs3136333 0.00429
NM_000051.4(ATM):c.6437G>C (p.Ser2146Thr) rs56815840 0.00424
NM_000249.4(MLH1):c.1852A>G (p.Lys618Glu) rs35001569 0.00399
NM_000535.7(PMS2):c.1609G>A (p.Glu537Lys) rs115052399 0.00370
NM_000038.6(APC):c.7862C>G (p.Ser2621Cys) rs72541816 0.00358
NM_000251.3(MSH2):c.339G>A (p.Lys113=) rs35898375 0.00313
NM_000038.6(APC):c.3471G>A (p.Glu1157=) rs143927847 0.00308
NM_000249.4(MLH1):c.1963A>G (p.Ile655Val) rs55907433 0.00297
NM_006231.4(POLE):c.846C>T (p.Pro282=) rs5744758 0.00291
NM_000038.6(APC):c.3165A>T (p.Ile1055=) rs61734287 0.00286
NM_006231.4(POLE):c.6820C>G (p.Leu2274Val) rs148788180 0.00284
NM_000038.6(APC):c.4893T>C (p.Ser1631=) rs35634377 0.00268
NM_000179.3(MSH6):c.3911G>A (p.Arg1304Lys) rs34625968 0.00253
NM_002691.4(POLD1):c.433G>A (p.Ala145Thr) rs137953986 0.00253
NM_000038.6(APC):c.3386T>C (p.Leu1129Ser) rs143638171 0.00250
NM_001042492.3(NF1):c.1994C>T (p.Ser665Phe) rs145891889 0.00220
NM_000038.6(APC):c.705A>G (p.Leu235=) rs147036141 0.00213
NM_000535.7(PMS2):c.2182A>G (p.Thr728Ala) rs141893001 0.00203
NM_032043.3(BRIP1):c.584T>C (p.Leu195Pro) rs4988347 0.00197
NM_032043.3(BRIP1):c.2937A>G (p.Lys979=) rs75091137 0.00194
NM_001042492.3(NF1):c.2553C>T (p.Cys851=) rs2230852 0.00190
NM_001042492.3(NF1):c.7531G>C (p.Val2511Leu) rs2230850 0.00189
NM_000249.4(MLH1):c.790+10A>G rs182733777 0.00188
NM_002691.4(POLD1):c.378C>T (p.Arg126=) rs145324823 0.00188
NM_000251.3(MSH2):c.23C>T (p.Thr8Met) rs17217716 0.00184
NM_000535.7(PMS2):c.23+10G>C rs192027828 0.00182
NM_000038.6(APC):c.120G>A (p.Glu40=) rs142720069 0.00161
NM_000251.3(MSH2):c.1277-8T>C rs145400590 0.00159
NM_001048174.2(MUTYH):c.1501C>A (p.Leu501Met) rs3219496 0.00154
NM_000465.4(BARD1):c.2282G>A (p.Ser761Asn) rs142155101 0.00153
NM_000038.6(APC):c.8068G>A (p.Ala2690Thr) rs140868933 0.00146
NM_000051.4(ATM):c.2608A>G (p.Asn870Asp) rs61734354 0.00146
NM_000038.6(APC):c.6921G>A (p.Ser2307=) rs2229993 0.00143
NM_000249.4(MLH1):c.2146G>A (p.Val716Met) rs35831931 0.00143
NM_000251.3(MSH2):c.1387-8G>T rs187525243 0.00143
NM_000251.3(MSH2):c.1737A>G (p.Lys579=) rs61756467 0.00138
NM_000179.3(MSH6):c.3647-6T>A rs182871847 0.00134
NM_000546.6(TP53):c.139C>T (p.Pro47Ser) rs1800371 0.00123
NM_000455.5(STK11):c.894C>A (p.Phe298Leu) rs199681533 0.00100
NM_000038.6(APC):c.7514G>A (p.Arg2505Gln) rs147549623 0.00093
NM_001042492.3(NF1):c.3867C>T (p.Phe1289=) rs138186428 0.00089
NM_000038.6(APC):c.6821C>T (p.Ala2274Val) rs34919187 0.00088
NM_000535.7(PMS2):c.180C>G (p.Asp60Glu) rs200313585 0.00088
NM_002691.4(POLD1):c.2628C>T (p.Ile876=) rs75874199 0.00088
NM_000249.4(MLH1):c.1217G>A (p.Ser406Asn) rs41294980 0.00087
NM_001042492.3(NF1):c.3468C>T (p.Asn1156=) rs147955381 0.00083
NM_000051.4(ATM):c.1073A>G (p.Asn358Ser) rs149636614 0.00079
NM_000051.4(ATM):c.3517T>C (p.Leu1173=) rs141460670 0.00079
NM_000051.4(ATM):c.7928-10T>C rs188404773 0.00079
NM_000535.7(PMS2):c.2187C>G (p.Leu729=) rs373630535 0.00077
NM_032043.3(BRIP1):c.3378A>C (p.Glu1126Asp) rs145855459 0.00076
NM_000051.4(ATM):c.6988C>G (p.Leu2330Val) rs148432863 0.00075
NM_000535.7(PMS2):c.2149G>A (p.Val717Met) rs201671325 0.00072
NM_000038.6(APC):c.1604C>T (p.Ser535Phe) rs75870842 0.00071
NM_000051.4(ATM):c.1744T>C (p.Phe582Leu) rs2235006 0.00071
NM_007194.4(CHEK2):c.320-5T>A rs121908700 0.00070
NM_000179.3(MSH6):c.1526T>C (p.Val509Ala) rs63751005 0.00067
NM_000179.3(MSH6):c.663A>C (p.Glu221Asp) rs41557217 0.00064
NM_004360.5(CDH1):c.2520C>T (p.Ser840=) rs140328601 0.00064
NM_000251.3(MSH2):c.55T>C (p.Phe19Leu) rs141711342 0.00063
NM_000455.5(STK11):c.945G>A (p.Pro315=) rs376329042 0.00060
NM_000179.3(MSH6):c.1869C>T (p.Pro623=) rs141242295 0.00058
NM_024675.4(PALB2):c.2851T>C (p.Ser951Pro) rs149522412 0.00058
NM_000038.6(APC):c.3173A>G (p.Asp1058Gly) rs148725540 0.00056
NM_000038.6(APC):c.1240C>T (p.Arg414Cys) rs137854567 0.00053
NM_000251.3(MSH2):c.1563T>C (p.Tyr521=) rs63750330 0.00053
NM_001042492.3(NF1):c.7461A>G (p.Thr2487=) rs149924365 0.00052
NM_000179.3(MSH6):c.2667G>T (p.Gln889His) rs149945495 0.00048
NM_000535.7(PMS2):c.1708A>G (p.Asn570Asp) rs115670442 0.00048
NM_032043.3(BRIP1):c.317G>A (p.Arg106His) rs143615668 0.00048
NM_000051.4(ATM):c.4709T>C (p.Val1570Ala) rs140856217 0.00046
NM_002691.4(POLD1):c.2052G>C (p.Gln684His) rs144143245 0.00045
NM_004360.5(CDH1):c.1138-3C>T rs36103202 0.00042
NM_000038.6(APC):c.2322C>T (p.Asp774=) rs145792879 0.00041
NM_000249.4(MLH1):c.702G>A (p.Glu234=) rs35908749 0.00041
NM_004360.5(CDH1):c.1239C>T (p.Tyr413=) rs36074916 0.00041
NM_000249.4(MLH1):c.977T>C (p.Val326Ala) rs63751049 0.00037
NM_000179.3(MSH6):c.2561A>T (p.Lys854Met) rs34374438 0.00036
NM_000051.4(ATM):c.6919C>T (p.Leu2307Phe) rs56009889 0.00035
NM_000535.7(PMS2):c.1864A>G (p.Met622Val) rs370853512 0.00035
NM_000249.4(MLH1):c.1321G>A (p.Ala441Thr) rs63750365 0.00034
NM_006231.4(POLE):c.4246G>A (p.Ala1416Thr) rs146711942 0.00034
NM_000179.3(MSH6):c.1867C>G (p.Pro623Ala) rs3136334 0.00033
NM_001042492.3(NF1):c.4851A>G (p.Gln1617=) rs150309802 0.00032
NM_000038.6(APC):c.2593C>T (p.Pro865Ser) rs192620988 0.00028
NM_000038.6(APC):c.3511C>T (p.Arg1171Cys) rs201830995 0.00028
NM_000051.4(ATM):c.3014A>G (p.Asn1005Ser) rs146531614 0.00028
NM_000465.4(BARD1):c.1491A>G (p.Pro497=) rs61754117 0.00027
NM_007194.4(CHEK2):c.1604G>A (p.Arg535His) rs544216926 0.00027
NM_000051.4(ATM):c.5975A>C (p.Lys1992Thr) rs150757822 0.00025
NM_002691.4(POLD1):c.624G>A (p.Pro208=) rs78996304 0.00025
NM_000038.6(APC):c.6526T>C (p.Leu2176=) rs183468041 0.00023
NM_000535.7(PMS2):c.953A>G (p.Tyr318Cys) rs139438201 0.00022
NM_024675.4(PALB2):c.298C>T (p.Leu100Phe) rs61756147 0.00021
NM_001042492.3(NF1):c.8499T>C (p.Asn2833=) rs142636150 0.00020
NM_000546.6(TP53):c.1079G>C (p.Gly360Ala) rs35993958 0.00019
NM_001042492.3(NF1):c.4749A>G (p.Glu1583=) rs144091165 0.00019
NM_004360.5(CDH1):c.2412C>T (p.Pro804=) rs202075199 0.00018
NM_000051.4(ATM):c.7381C>T (p.Arg2461Cys) rs201314561 0.00017
NM_000249.4(MLH1):c.2101C>A (p.Gln701Lys) rs63750114 0.00016
NM_000314.8(PTEN):c.234C>T (p.Thr78=) rs35917308 0.00016
NM_032043.3(BRIP1):c.2440C>T (p.Arg814Cys) rs201869624 0.00016
NM_000038.6(APC):c.6985A>G (p.Ile2329Val) rs146048493 0.00015
NM_001042492.3(NF1):c.107C>G (p.Thr36Ser) rs199966218 0.00015
NM_000249.4(MLH1):c.1050A>G (p.Pro350=) rs137937003 0.00012
NM_000535.7(PMS2):c.1689A>G (p.Arg563=) rs551226281 0.00011
NM_000314.8(PTEN):c.579G>A (p.Leu193=) rs568851024 0.00010
NM_000051.4(ATM):c.4167A>G (p.Thr1389=) rs183214437 0.00009
NM_000179.3(MSH6):c.3727A>T (p.Thr1243Ser) rs147453999 0.00009
NM_000465.4(BARD1):c.1694G>A (p.Arg565His) rs146946984 0.00009
NM_000038.6(APC):c.573T>C (p.Tyr191=) rs185154886 0.00008
NM_000051.4(ATM):c.6503C>T (p.Ser2168Leu) rs200431631 0.00008
NM_000179.3(MSH6):c.2384T>C (p.Ile795Thr) rs202127474 0.00007
NM_000051.4(ATM):c.198A>G (p.Lys66=) rs540920248 0.00006
NM_032043.3(BRIP1):c.689C>T (p.Ser230Leu) rs759031349 0.00006
NM_000179.3(MSH6):c.3762A>T (p.Glu1254Asp) rs375459388 0.00005
NM_000535.7(PMS2):c.2356C>A (p.Leu786Met) rs576055272 0.00004
NM_004360.5(CDH1):c.1174G>A (p.Val392Ile) rs141864044 0.00004
NM_000251.3(MSH2):c.2205C>T (p.Ile735=) rs533553381 0.00003
NM_001042492.3(NF1):c.*4T>C rs201044568 0.00003
NM_032043.3(BRIP1):c.2830C>G (p.Gln944Glu) rs140233356 0.00003
NM_000038.6(APC):c.7821C>T (p.Ser2607=) rs532235331 0.00002
NM_002485.5(NBN):c.995-17A>G rs372875251 0.00002
NM_000251.3(MSH2):c.1221C>G (p.Leu407=) rs63750813 0.00001
NM_000546.6(TP53):c.145G>A (p.Asp49Asn) rs587780728 0.00001
NM_004360.5(CDH1):c.604G>A (p.Val202Ile) rs546716073 0.00001
NM_024675.4(PALB2):c.734C>T (p.Ala245Val) rs571063157 0.00001
NM_000038.6(APC):c.3462AGA[2] (p.Glu1157del) rs386833391
NM_000051.4(ATM):c.1020C>A (p.Ala340=) rs546927781
NM_000051.4(ATM):c.1380G>C (p.Thr460=) rs145333518
NM_000051.4(ATM):c.2805G>C (p.Thr935=) rs55934812
NM_000179.3(MSH6):c.3151G>A (p.Val1051Ile) rs576269342
NM_000179.3(MSH6):c.3246G>T (p.Pro1082=) rs3136351
NM_000179.3(MSH6):c.4001+2TAAC[2] rs267608132
NM_000179.3(MSH6):c.4001+2TAAC[4] rs267608132
NM_000249.4(MLH1):c.1853A>C (p.Lys618Thr) rs63750449
NM_000251.3(MSH2):c.273TCT[2] (p.Leu94del) rs267607919
NM_000251.3(MSH2):c.67T>C (p.Phe23Leu) rs372619120
NM_000251.3(MSH2):c.942+17_942+29del rs11309117
NM_000251.3(MSH2):c.942+25_942+29del rs11309117
NM_000535.7(PMS2):c.706-6_706-4del rs60794673
NM_000535.7(PMS2):c.830C>A (p.Thr277Lys) rs1805322
NM_001048174.2(MUTYH):c.-25T>C
NM_001048174.2(MUTYH):c.-7+5C>G rs3219468
NM_002691.4(POLD1):c.324G>A (p.Ala108=) rs20582
NM_024642.5(GALNT12):c.1707G>C (p.Ser569=) rs2273846
NM_032043.3(BRIP1):c.370A>G (p.Thr124Ala) rs45617634

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