ClinVar Miner

List of variants reported as likely benign for Lynch syndrome by Mendelics

Included ClinVar conditions (26):
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ClinVar version:
Total variants: 118
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HGVS dbSNP gnomAD frequency
NM_000249.4(MLH1):c.1039-8T>A rs193922367 0.01153
NM_000249.4(MLH1):c.1732-19T>A rs77120160 0.00923
NM_000535.7(PMS2):c.52A>G (p.Ile18Val) rs63750123 0.00861
NM_000179.3(MSH6):c.3557-40T>A rs189436849 0.00587
NM_000179.3(MSH6):c.1186C>G (p.Leu396Val) rs2020908 0.00565
NM_014805.3(EPM2AIP1):c.-202G>C rs35032294 0.00539
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.457+13A>G rs1800933 0.00434
NM_000249.4(MLH1):c.1852A>G (p.Lys618Glu) rs35001569 0.00399
NM_000251.3(MSH2):c.339G>A (p.Lys113=) rs35898375 0.00313
NM_000179.3(MSH6):c.3911G>A (p.Arg1304Lys) rs34625968 0.00253
NM_000251.3(MSH2):c.*226A>G rs17225060 0.00201
NM_000249.4(MLH1):c.790+10A>G rs182733777 0.00188
NM_000535.7(PMS2):c.383C>T (p.Ser128Leu) rs116373169 0.00177
NM_000179.3(MSH6):c.3801+17T>C rs3136365 0.00159
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_000179.3(MSH6):c.3802-22G>A rs373409282 0.00097
NM_000535.7(PMS2):c.180C>G (p.Asp60Glu) rs200313585 0.00088
NM_000249.4(MLH1):c.1217G>A (p.Ser406Asn) rs41294980 0.00087
NM_000249.4(MLH1):c.2104-11G>A rs147984696 0.00072
NM_000179.3(MSH6):c.3173-35C>T rs186475107 0.00070
NM_000249.4(MLH1):c.375A>G (p.Ala125=) rs1800144 0.00062
NM_000179.3(MSH6):c.1508C>G (p.Ser503Cys) rs63750897 0.00059
NM_000251.3(MSH2):c.1680T>C (p.Asn560=) rs200056411 0.00043
NM_000249.4(MLH1):c.702G>A (p.Glu234=) rs35908749 0.00041
NM_000535.7(PMS2):c.936G>A (p.Met312Ile) rs139194813 0.00041
NM_000249.4(MLH1):c.198C>T (p.Thr66=) rs61751642 0.00040
NM_000249.4(MLH1):c.977T>C (p.Val326Ala) rs63751049 0.00037
NM_000251.3(MSH2):c.2154A>G (p.Gln718=) rs63750810 0.00033
NM_000535.7(PMS2):c.706-3C>T rs1229860023 0.00030
NM_000249.4(MLH1):c.1897-17C>G rs2308316 0.00029
NM_000249.4(MLH1):c.307-19A>G rs121909451 0.00022
NM_000251.3(MSH2):c.138C>G (p.His46Gln) rs33946261 0.00019
NM_000179.3(MSH6):c.3160A>T (p.Ile1054Phe) rs267608075 0.00016
NM_000249.4(MLH1):c.1820T>A (p.Leu607His) rs41295284 0.00015
NM_000535.7(PMS2):c.255G>A (p.Leu85=) rs200491279 0.00013
NM_000249.4(MLH1):c.1050A>G (p.Pro350=) rs137937003 0.00012
NM_000179.3(MSH6):c.124C>T (p.Pro42Ser) rs34014629 0.00011
NM_000179.3(MSH6):c.1875C>T (p.Ser625=) rs63749886 0.00010
NM_000251.3(MSH2):c.1386+23T>G rs747646424 0.00010
NM_000179.3(MSH6):c.660A>C (p.Glu220Asp) rs1800938 0.00009
NM_000249.4(MLH1):c.1808C>G (p.Pro603Arg) rs63750876 0.00009
NM_000251.3(MSH2):c.2802G>A (p.Thr934=) rs150259097 0.00009
NR_136154.1(PMS2):n.13T>C rs746329908 0.00009
NM_000535.7(PMS2):c.1280G>A (p.Arg427His) rs112902065 0.00007
NM_000535.7(PMS2):c.384G>A (p.Ser128=) rs371342884 0.00007
NM_000179.3(MSH6):c.1050C>T (p.Ala350=) rs730881802 0.00006
NM_000249.4(MLH1):c.1989+37T>C rs374195343 0.00006
NM_000249.4(MLH1):c.207+523G>A rs760066426 0.00006
NM_000179.3(MSH6):c.2173A>G (p.Ile725Val) rs148898662 0.00005
NM_000179.3(MSH6):c.3513T>C (p.Asp1171=) rs63749834 0.00005
NM_000251.3(MSH2):c.843A>T (p.Ser281=) rs150197753 0.00005
NM_000249.4(MLH1):c.2252A>G (p.Lys751Arg) rs140195825 0.00004
NM_000249.4(MLH1):c.381-43C>G rs368847278 0.00004
NM_000251.3(MSH2):c.287G>A (p.Arg96His) rs63750002 0.00004
NM_000179.3(MSH6):c.627+9C>T rs373155872 0.00003
NM_000249.4(MLH1):c.884+15A>G rs372817491 0.00003
NM_000179.3(MSH6):c.204G>A (p.Lys68=) rs864622565 0.00002
NM_000179.3(MSH6):c.4002-28del rs1572749250 0.00002
NM_000251.3(MSH2):c.2061C>G (p.Leu687=) rs63750032 0.00002
NM_000179.3(MSH6):c.1623C>T (p.Ser541=) rs777678406 0.00001
NM_000179.3(MSH6):c.2641G>A (p.Gly881Ser) rs998186339 0.00001
NM_000179.3(MSH6):c.2982C>T (p.Tyr994=) rs367758473 0.00001
NM_000179.3(MSH6):c.3300G>A (p.Thr1100=) rs540252208 0.00001
NM_000249.4(MLH1):c.1896+7C>T rs863224339 0.00001
NM_000249.4(MLH1):c.1990-6G>A rs117221851 0.00001
NM_000249.4(MLH1):c.2104-22T>G rs267607890 0.00001
NM_000249.4(MLH1):c.351G>A (p.Thr117=) rs61751643 0.00001
NM_000249.4(MLH1):c.885-5G>T rs267607802 0.00001
NM_000535.7(PMS2):c.1047G>A (p.Lys349=) rs1422380612 0.00001
NM_000535.7(PMS2):c.1352G>A (p.Arg451Lys) rs876660834 0.00001
NM_000535.7(PMS2):c.713G>A (p.Ser238Asn) rs1060503111 0.00001
NM_000535.7(PMS2):c.750C>T (p.Ser250=) rs200439295 0.00001
NM_000179.3(MSH6):c.-46T>G rs748339592
NM_000179.3(MSH6):c.183G>C (p.Ala61=) rs1060504757
NM_000179.3(MSH6):c.3151G>A (p.Val1051Ile) rs576269342
NM_000179.3(MSH6):c.3153A>G (p.Val1051=) rs1057521587
NM_000179.3(MSH6):c.3172+230_3172+231dup rs10666222
NM_000179.3(MSH6):c.3246G>T (p.Pro1082=) rs3136351
NM_000179.3(MSH6):c.3557-16T>A rs1259754363
NM_000179.3(MSH6):c.3557-2del rs587779271
NM_000179.3(MSH6):c.3557-4del rs267608102
NM_000179.3(MSH6):c.3636G>T (p.Val1212=) rs1363247790
NM_000179.3(MSH6):c.378A>G (p.Ser126=) rs1572708845
NM_000179.3(MSH6):c.4001+2TAAC[2] rs267608132
NM_000179.3(MSH6):c.4001+2TAAC[4] rs267608132
NM_000179.3(MSH6):c.4001+4_4001+8dup rs587782853
NM_000179.3(MSH6):c.4002-11_4002-10del rs59056100
NM_000179.3(MSH6):c.4002-36C>A rs983280767
NM_000179.3(MSH6):c.423C>G (p.Gly141=) rs777587467
NM_000179.3(MSH6):c.457+32TG[12] rs397839804
NM_000179.3(MSH6):c.520A>C (p.Arg174=) rs1405000889
NM_000249.4(MLH1):c.1038+8C>T rs751872237
NM_000249.4(MLH1):c.116+27C>T rs1575377948
NM_000249.4(MLH1):c.1281del (p.Asp428fs) rs1575536988
NM_000249.4(MLH1):c.1559-16A>T rs769709911
NM_000249.4(MLH1):c.1587C>T (p.Ser529=) rs767089159
NM_000249.4(MLH1):c.253C>T (p.Leu85=) rs63750659
NM_000249.4(MLH1):c.885-21TC[2] rs267607804
NM_000251.2(MSH2):c.-68G>A rs576303132
NM_000251.3(MSH2):c.-21A>T rs776559145
NM_000251.3(MSH2):c.1389G>T (p.Val463=) rs1553365702
NM_000251.3(MSH2):c.1746C>T (p.Val582=) rs786201486
NM_000251.3(MSH2):c.2005+8dup rs267607992
NM_000251.3(MSH2):c.2210+8C>T rs778020437
NM_000251.3(MSH2):c.2459-46G>A rs1573578232
NM_000251.3(MSH2):c.2801C>T (p.Thr934Met) rs587779969
NM_000251.3(MSH2):c.942+25_942+29del rs11309117
NM_000251.3(MSH2):c.942+28_942+29del rs11309117
NM_000535.7(PMS2):c.1437C>G (p.His479Gln) rs63750685
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu) rs63750668
NM_000535.7(PMS2):c.353+7C>G rs1057520512
NM_000535.7(PMS2):c.538-8T>C rs922948916
NM_022055.2(KCNK12):c.*8388G>T rs1573613933

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