ClinVar Miner

List of variants reported as benign for Lynch syndrome

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Total variants: 199
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HGVS dbSNP gnomAD frequency
NM_000251.3(MSH2):c.2210+317G>C rs4638843 0.92052
NM_000535.7(PMS2):c.780C>G (p.Ser260=) rs1805319 0.82058
NM_000179.3(MSH6):c.3173-101G>C rs2072447 0.78513
NM_000179.3(MSH6):c.3802-40C>G rs3136367 0.73398
NM_000179.3(MSH6):c.628-874C>T rs3136329 0.64557
NM_000251.3(MSH2):c.211+9C>G rs2303426 0.55454
NM_000251.3(MSH2):c.211+98T>C rs3815865 0.55408
NM_000179.3(MSH6):c.3556+146G>A rs7562048 0.54192
NM_000251.3(MSH2):c.1276+6765G>A rs3771274 0.53492
NM_000251.3(MSH2):c.1077-80G>A rs2347794 0.53152
NM_014805.4(EPM2AIP1):c.*2570G>T rs9311149 0.53114
NM_000251.3(MSH2):c.1511-1516C>T rs3771281 0.48800
NM_000251.3(MSH2):c.2006-265A>G rs2059520 0.48792
NM_000251.2(MSH2):c.*272+4059G>A rs6720549 0.43302
NM_000249.4(MLH1):c.1668-19A>G rs9876116 0.41821
NM_000251.3(MSH2):c.1511-91G>T rs3732182 0.41551
NM_000249.4(MLH1):c.790+955C>A rs1558528 0.41529
NM_000249.4(MLH1):c.453+79A>G rs4234259 0.41512
NM_000249.4(MLH1):c.1990-121C>T rs2241031 0.41163
NM_000251.3(MSH2):c.1661+12G>A rs3732183 0.40290
NM_000249.4(MLH1):c.207+571C>T rs9852378 0.39684
NM_000249.4(MLH1):c.1038+1005G>T rs3774338 0.39669
NM_000251.3(MSH2):c.1277-212T>A rs1981928 0.39571
NM_000249.4(MLH1):c.1668-885T>C rs748766 0.37254
NM_000535.7(PMS2):c.1408C>T (p.Pro470Ser) rs1805321 0.37107
NM_000249.4(MLH1):c.1039-78A>G rs11129748 0.36570
NM_000249.4(MLH1):c.1558+2204A>C rs3774335 0.36225
NM_000249.4(MLH1):c.1559-3171A>G rs4678925 0.35667
NM_000249.4(MLH1):c.791-1406C>T rs4647269 0.35636
NM_000249.4(MLH1):c.306+416A>C rs4647222 0.35615
NM_000535.7(PMS2):c.705+17A>G rs62456182 0.33782
NM_000179.3(MSH6):c.3438+14A>T rs2020911 0.32279
NM_000535.7(PMS2):c.2570G>C (p.Gly857Ala) rs1802683 0.30966
NM_000179.2(MSH6):c.-557T>G rs3136228 0.29969
NM_000179.3(MSH6):c.457+52T>A rs3136282 0.29585
NM_000179.3(MSH6):c.261-1170G>T rs3136272 0.29018
NM_006303.4(AIMP2):c.-22C>A rs1062372 0.23877
NM_000179.3(MSH6):c.540T>C (p.Asp180=) rs1800935 0.23857
NM_000249.4(MLH1):c.655A>G (p.Ile219Val) rs1799977 0.23048
NM_000249.3(MLH1):c.-93G>A rs1800734 0.22121
NM_000535.7(PMS2):c.538-223A>G rs2345060 0.21434
NM_001406631.1(MSH2):c.2634+4770A>C rs6544991 0.21374
NM_000179.3(MSH6):c.458-52G>T rs1800934 0.20909
NM_000251.3(MSH2):c.2210+274T>G rs4608577 0.19234
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) rs1042821 0.18742
NM_000179.3(MSH6):c.260+2214C>T rs3136245 0.16684
NM_000535.5(PMS2):c.-154C>G rs3735296 0.16495
NM_000535.7(PMS2):c.804-243G>A rs2286680 0.16082
NM_000179.3(MSH6):c.276A>G (p.Pro92=) rs1800932 0.14697
NM_000179.3(MSH6):c.260+2467A>G rs3136247 0.14683
NM_000249.4(MLH1):c.307-1403A>T rs1540354 0.14330
NM_000535.7(PMS2):c.1621= (p.Lys541=) rs2228006 0.13518
NM_000179.3(MSH6):c.260+22C>G rs55927047 0.13136
NM_000179.3(MSH6):c.457+394T>C rs3136284 0.12872
NM_000179.3(MSH6):c.186C>A (p.Arg62=) rs1042820 0.12806
NM_000535.7(PMS2):c.2007-4G>A rs1805326 0.12350
NM_000179.3(MSH6):c.457+1223T>C rs2348244 0.12176
NM_000535.7(PMS2):c.2007-7C>T rs55954143 0.12135
NM_000251.1(MSH2):c.-433T>G rs1863332 0.11834
NM_000179.3(MSH6):c.628-56C>T rs1800936 0.11629
NM_000535.7(PMS2):c.2466T>C (p.Leu822=) rs10000 0.11447
NM_000251.2(MSH2):c.-118T>C rs2303425 0.10354
NM_000251.3(MSH2):c.1076+3400C>T rs4952887 0.10157
NM_000251.3(MSH2):c.1277-6990T>G rs13408008 0.10114
NM_000179.2(MSH6):c.-448G>A rs3136229 0.09540
NM_000251.3(MSH2):c.2635-214T>C rs2042649 0.09372
NM_000251.3(MSH2):c.1759+501A>G rs17036614 0.09371
NM_000251.3(MSH2):c.1511-9A>T rs12998837 0.09123
NM_000251.3(MSH2):c.1277-5849T>C rs17036577 0.08736
NM_000251.3(MSH2):c.2006-6T>C rs2303428 0.08349
NM_000179.3(MSH6):c.3172+171C>T rs3136337 0.08328
NM_000179.3(MSH6):c.627+1200T>C rs3136326 0.07750
NM_000179.2(MSH6):c.-159C>T rs41540312 0.07535
NM_000179.3(MSH6):c.642C>T (p.Tyr214=) rs1800937 0.07457
NM_000535.7(PMS2):c.59G>A (p.Arg20Gln) rs10254120 0.07445
NM_000535.7(PMS2):c.1454C>A (p.Thr485Lys) rs1805323 0.05742
NM_000249.4(MLH1):c.1558+14G>A rs41562513 0.05554
NM_000249.4(MLH1):c.1558+4245A>G rs3774332 0.05535
NM_000535.5(PMS2):c.-195T>C rs2302336 0.04915
NM_006303.4(AIMP2):c.135+2080A>T rs78453798 0.04887
NM_006303.4(AIMP2):c.135+1667G>T rs77199218 0.04878
NM_000249.4(MLH1):c.1410-54C>T rs7633154 0.04850
NM_000535.7(PMS2):c.2006+6G>A rs111905775 0.04390
NM_000251.3(MSH2):c.1387-250G>A rs6741393 0.04348
NM_000535.7(PMS2):c.288C>T (p.Ala96=) rs12532895 0.03944
NM_000179.3(MSH6):c.261-36A>G rs1800931 0.03614
NM_000179.3(MSH6):c.3556+160T>C rs56320267 0.03454
NM_000249.4(MLH1):c.454-51T>C rs4647255 0.03218
NM_000251.3(MSH2):c.1661+90T>C rs10183143 0.03147
NM_000251.3(MSH2):c.1077-2037G>T rs13425206 0.03061
NM_000249.4(MLH1):c.1668-254C>T rs41552415 0.03054
NM_000251.3(MSH2):c.1760-62G>A rs17218439 0.02701
NM_000535.7(PMS2):c.1532C>T (p.Thr511Met) rs74902811 0.02492
NM_000535.7(PMS2):c.251-72A>G rs117831773 0.02449
NM_000249.4(MLH1):c.2152C>T (p.His718Tyr) rs2020873 0.02345
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) rs17217772 0.02317
NM_000535.7(PMS2):c.1488C>T (p.His496=) rs1805320 0.02307
NM_000535.7(PMS2):c.1531A>G (p.Thr511Ala) rs2228007 0.02174
NM_000249.4(MLH1):c.885-81G>C rs104894999 0.02021
NM_000179.3(MSH6):c.2253T>C (p.Asn751=) rs2020913 0.02003
NM_000251.3(MSH2):c.573C>T (p.Leu191=) rs1800151 0.01972
NM_000251.3(MSH2):c.1276+51C>A rs17217961 0.01831
NM_000249.4(MLH1):c.381-41A>G rs4647245 0.01794
NM_000251.3(MSH2):c.965G>A (p.Gly322Asp) rs4987188 0.01714
NM_000535.7(PMS2):c.1866G>A (p.Met622Ile) rs1805324 0.01651
NM_000251.3(MSH2):c.1077-10T>C rs17224360 0.01428
NM_000179.3(MSH6):c.1164C>T (p.His388=) rs55708305 0.01384
NM_000179.3(MSH6):c.2272C>T (p.Leu758=) rs56371757 0.01363
NM_000249.4(MLH1):c.1039-8T>A rs193922367 0.01153
NM_000249.4(MLH1):c.588+11G>C rs4647258 0.00993
NM_000249.4(MLH1):c.1732-19T>A rs77120160 0.00923
NM_000249.4(MLH1):c.1959G>T (p.Leu653=) rs1800146 0.00913
NM_000179.3(MSH6):c.3306T>A (p.Thr1102=) rs2020910 0.00869
NM_000535.7(PMS2):c.52A>G (p.Ile18Val) rs63750123 0.00861
NM_000249.4(MLH1):c.637G>A (p.Val213Met) rs2308317 0.00818
NM_000249.4(MLH1):c.589-15C>T rs55658850 0.00582
NM_000179.3(MSH6):c.1186C>G (p.Leu396Val) rs2020908 0.00565
NM_000179.2(MSH6):c.-210C>T rs181096360 0.00543
NM_000251.3(MSH2):c.1666T>C (p.Leu556=) rs61756466 0.00471
NM_000179.3(MSH6):c.2633T>C (p.Val878Ala) rs2020912 0.00448
NM_000179.3(MSH6):c.1345C>T (p.Leu449=) rs3136333 0.00429
NM_000249.4(MLH1):c.545+20A>T rs121909453 0.00424
NM_000249.4(MLH1):c.453+25A>G rs4647246 0.00414
NM_000249.4(MLH1):c.307-29C>A rs139620056 0.00398
NM_000251.3(MSH2):c.1662-9G>A rs17218356 0.00398
NM_000251.3(MSH2):c.339G>A (p.Lys113=) rs35898375 0.00313
NM_000179.3(MSH6):c.3439-16C>T rs192614006 0.00237
NM_000249.4(MLH1):c.790+10A>G rs182733777 0.00188
NM_000251.3(MSH2):c.23C>T (p.Thr8Met) rs17217716 0.00184
NM_000179.3(MSH6):c.431G>T (p.Ser144Ile) rs3211299 0.00158
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_000535.7(PMS2):c.2340C>T (p.Pro780=) rs142230276 0.00117
NM_000249.4(MLH1):c.1217G>A (p.Ser406Asn) rs41294980 0.00087
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) rs63750447 0.00077
NM_000251.3(MSH2):c.815C>T (p.Ala272Val) rs34136999 0.00046
NM_000251.3(MSH2):c.*129T>C rs587779059 0.00042
NM_000251.3(MSH2):c.1886A>G (p.Gln629Arg) rs61756468 0.00042
NM_000251.3(MSH2):c.1168C>T (p.Leu390Phe) rs17224367 0.00039
NM_000249.4(MLH1):c.977T>C (p.Val326Ala) rs63751049 0.00037
NM_000249.4(MLH1):c.1321G>A (p.Ala441Thr) rs63750365 0.00034
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) rs17420802 0.00025
NM_000249.4(MLH1):c.2066A>G (p.Gln689Arg) rs63750702 0.00022
NM_000249.4(MLH1):c.394G>C (p.Asp132His) rs28930073 0.00019
NM_000535.7(PMS2):c.2253T>C (p.Phe751=) rs1805325 0.00018
NM_000249.4(MLH1):c.1040C>A (p.Thr347Asn) rs201541505 0.00017
NM_000249.4(MLH1):c.65G>C (p.Gly22Ala) rs41295280 0.00016
NM_000249.4(MLH1):c.803A>G (p.Glu268Gly) rs63750650 0.00014
NM_000251.3(MSH2):c.317G>A (p.Arg106Lys) rs41295286 0.00009
NM_000535.7(PMS2):c.993C>T (p.Cys331=) rs186577215 0.00009
NM_000251.3(MSH2):c.1690A>G (p.Thr564Ala) rs55778204 0.00008
NM_000249.4(MLH1):c.1733A>G (p.Glu578Gly) rs63751612 0.00006
NM_000249.4(MLH1):c.1128T>C (p.Asp376=) rs267607824 0.00005
NM_000179.3(MSH6):c.3557-3A>T rs41295274 0.00004
NM_000535.7(PMS2):c.*17G>C rs556089649 0.00004
NM_000249.4(MLH1):c.1039-33_1039-29del rs148615368 0.00003
NM_000249.4(MLH1):c.303T>G (p.Gly101=) rs4647220 0.00002
NM_000179.3(MSH6):c.1809G>A (p.Lys603=) rs876660790 0.00001
NM_000249.4(MLH1):c.1652A>G (p.Asn551Ser) rs63750271 0.00001
NM_000535.7(PMS2):c.1398C>T (p.Gly466=) rs752666485 0.00001
MSH6:c.3647-51_3647-35del17 rs267607687
NM_000179.2(MSH6):c.*4247G>A
NM_000179.3(MSH6):c.3557-4dup rs267608102
NM_000179.3(MSH6):c.3646+29CTAT[3] rs1805181
NM_000179.3(MSH6):c.3646+35_3646+38del rs1805181
NM_000179.3(MSH6):c.3646+91T>C rs3136359
NM_000179.3(MSH6):c.3647-35_3647-34insTTTGTTCTAATTCCTTT rs397515292
NM_000179.3(MSH6):c.3802-43dup rs34154602
NM_000179.3(MSH6):c.3852G>T (p.Thr1284=) rs2229018
NM_000179.3(MSH6):c.4002-10del rs59056100
NM_000179.3(MSH6):c.4002-11_4002-10dup rs59056100
NM_000179.3(MSH6):c.4002-12_4002-10dup rs59056100
NM_000179.3(MSH6):c.4002-13_4002-10dup rs59056100
NM_000249.4(MLH1):c.*32CTT[1] rs193922366
NM_000249.4(MLH1):c.1038+86T>C rs2286939
NM_000249.4(MLH1):c.1799A>G (p.Glu600Gly) rs267607861
NM_000249.4(MLH1):c.1852_1853delinsGC (p.Lys618Ala) rs35502531
NM_000249.4(MLH1):c.1853A>C (p.Lys618Thr) rs63750449
NM_000249.4(MLH1):c.453+554C>T rs267607748
NM_000249.4(MLH1):c.655A>C (p.Ile219Leu) rs1799977
NM_000251.3(MSH2):c.1277-118G>A rs1981929
NM_000251.3(MSH2):c.1277-945A>C rs7607312
NM_000251.3(MSH2):c.2355T>C (p.His785=) rs1114167840
NM_000251.3(MSH2):c.273TCT[2] (p.Leu94del) rs267607919
NM_000251.3(MSH2):c.593A>G (p.Glu198Gly) rs63750327
NM_000251.3(MSH2):c.7G>T (p.Val3Leu) rs1257347271
NM_000251.3(MSH2):c.942+17_942+29del rs11309117
NM_000251.3(MSH2):c.942+25_942+29del rs11309117
NM_000535.5(PMS2):c.-93G>A rs6976537
NM_000535.7(PMS2):c.*92dup rs267608145
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu) rs63750668
NM_000535.7(PMS2):c.250+8G>A rs1057520511
NM_000535.7(PMS2):c.299A>G (p.Gln100Arg) rs747771951
NM_000535.7(PMS2):c.706-4del rs60794673
NM_000535.7(PMS2):c.706-4dup rs60794673
NM_000535.7(PMS2):c.706-5_706-4del rs60794673
NM_001190274.2(FBXO11):c.2227+1329A>G rs2537742
NM_006309.4(LRRFIP2):c.*272G>A rs10849

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