ClinVar Miner

List of variants reported as likely benign for Lynch syndrome 1

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ClinVar version:
Total variants: 188
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HGVS dbSNP gnomAD frequency
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) rs17217772 0.02317
NM_000251.3(MSH2):c.573C>T (p.Leu191=) rs1800151 0.01972
NM_000251.3(MSH2):c.965G>A (p.Gly322Asp) rs4987188 0.01714
NM_000251.3(MSH2):c.1077-10T>C rs17224360 0.01428
NM_000251.3(MSH2):c.2766T>C (p.Phe922=) rs55859129 0.01118
NM_000535.7(PMS2):c.1789A>T (p.Thr597Ser) rs1805318 0.01006
NM_000535.7(PMS2):c.52A>G (p.Ile18Val) rs63750123 0.00861
NM_000179.3(MSH6):c.3557-40T>A rs189436849 0.00587
NM_000249.4(MLH1):c.1038+51C>T rs55986674 0.00582
NM_000251.3(MSH2):c.*141T>G rs17225053 0.00526
NM_000251.3(MSH2):c.984C>T (p.Ala328=) rs4987189 0.00495
NM_000534.5(PMS1):c.1643A>G (p.Lys548Arg) rs61736576 0.00477
NM_000251.3(MSH2):c.1666T>C (p.Leu556=) rs61756466 0.00471
NM_000251.3(MSH2):c.1662-9G>A rs17218356 0.00398
NM_000251.3(MSH2):c.339G>A (p.Lys113=) rs35898375 0.00313
NM_000251.2(MSH2):c.-185C>A rs188036046 0.00223
NM_000251.3(MSH2):c.*226A>G rs17225060 0.00201
NM_001040108.2(MLH3):c.2425A>G (p.Met809Val) rs61752722 0.00197
NM_000251.3(MSH2):c.23C>T (p.Thr8Met) rs17217716 0.00184
NM_000251.3(MSH2):c.1277-8T>C rs145400590 0.00159
NM_000251.2(MSH2):c.-161C>T rs17224101 0.00154
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.1526T>C (p.Val509Ala) rs63751005 0.00067
NM_000251.3(MSH2):c.55T>C (p.Phe19Leu) rs141711342 0.00063
NM_000179.3(MSH6):c.1508C>G (p.Ser503Cys) rs63750897 0.00059
NM_000251.2(MSH2):c.-148C>T rs577322036 0.00053
NM_000251.3(MSH2):c.1563T>C (p.Tyr521=) rs63750330 0.00053
NM_000251.3(MSH2):c.1680T>C (p.Asn560=) rs200056411 0.00043
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_000251.3(MSH2):c.1511-41G>C rs202215396 0.00038
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_000251.3(MSH2):c.471C>A (p.Gly157=) rs61756463 0.00029
NM_000251.3(MSH2):c.1277-16T>C rs368653974 0.00024
NM_000251.3(MSH2):c.1787A>G (p.Asn596Ser) rs41295288 0.00022
NM_000251.3(MSH2):c.1255C>A (p.Gln419Lys) rs63750006 0.00019
NM_000251.3(MSH2):c.1276+47T>A rs148018406 0.00019
NM_000251.3(MSH2):c.138C>G (p.His46Gln) rs33946261 0.00019
NM_000251.3(MSH2):c.1276+16G>A rs368120695 0.00016
NM_000251.3(MSH2):c.2537A>G (p.Gln846Arg) rs140754514 0.00015
NM_000179.3(MSH6):c.2398G>C (p.Val800Leu) rs61748083 0.00014
NM_000179.3(MSH6):c.59C>T (p.Ala20Val) rs63750664 0.00013
NM_000251.3(MSH2):c.-3G>C rs587779960 0.00013
NM_000251.3(MSH2):c.505A>G (p.Ile169Val) rs63750716 0.00013
NM_000251.3(MSH2):c.128A>G (p.Tyr43Cys) rs17217723 0.00011
NM_000251.3(MSH2):c.1790A>C (p.Asp597Ala) rs548407418 0.00011
NM_000251.3(MSH2):c.198C>T (p.Tyr66=) rs730881784 0.00011
NM_000251.3(MSH2):c.2203A>G (p.Ile735Val) rs2229061 0.00011
NM_000251.3(MSH2):c.2308A>G (p.Ile770Val) rs63750684 0.00011
NM_000251.3(MSH2):c.1386+23T>G rs747646424 0.00010
NM_000251.3(MSH2):c.1662-23A>G rs56404027 0.00010
NM_000251.2(MSH2):c.-73G>A rs552303079 0.00009
NM_000251.3(MSH2):c.114C>G (p.Asp38Glu) rs587779074 0.00009
NM_000251.3(MSH2):c.2802G>A (p.Thr934=) rs150259097 0.00009
NM_000251.3(MSH2):c.367-19A>T rs730881783 0.00009
NM_000251.3(MSH2):c.97A>C (p.Thr33Pro) rs63751107 0.00009
NM_000251.3(MSH2):c.1488A>G (p.Leu496=) rs267607960 0.00008
NM_000251.3(MSH2):c.2458+16G>A rs373624698 0.00008
NM_000251.3(MSH2):c.2500G>A (p.Ala834Thr) rs63750757 0.00008
NM_000251.3(MSH2):c.4G>A (p.Ala2Thr) rs63750466 0.00008
NM_000251.3(MSH2):c.820A>G (p.Ile274Val) rs371944271 0.00008
NM_000251.3(MSH2):c.1560A>G (p.Gly520=) rs63750820 0.00007
NM_000251.3(MSH2):c.2732T>G (p.Leu911Arg) rs41295182 0.00007
NM_000251.3(MSH2):c.2400A>G (p.Leu800=) rs201298777 0.00006
NM_000251.3(MSH2):c.499G>C (p.Asp167His) rs63750255 0.00006
NM_000251.3(MSH2):c.1774A>G (p.Met592Val) rs371614039 0.00005
NM_000251.3(MSH2):c.843A>T (p.Ser281=) rs150197753 0.00005
NM_000251.3(MSH2):c.885C>G (p.Asp295Glu) rs201334592 0.00005
NM_000251.3(MSH2):c.1021C>G (p.Leu341Val) rs748115066 0.00004
NM_000251.3(MSH2):c.1530G>C (p.Gln510His) rs587782355 0.00004
NM_000251.3(MSH2):c.1600C>T (p.Arg534Cys) rs63750029 0.00004
NM_000251.3(MSH2):c.1601G>A (p.Arg534His) rs587778523 0.00004
NM_000251.3(MSH2):c.1813G>T (p.Val605Phe) rs730881777 0.00004
NM_000251.3(MSH2):c.2211-6C>A rs267608003 0.00004
NM_000251.3(MSH2):c.2580G>A (p.Ser860=) rs752428475 0.00004
NM_000251.3(MSH2):c.287G>A (p.Arg96His) rs63750002 0.00004
NM_000251.3(MSH2):c.336C>A (p.Ser112=) rs34312619 0.00004
NM_000251.3(MSH2):c.607G>A (p.Gly203Arg) rs587779973 0.00004
NM_000251.3(MSH2):c.1144C>T (p.Arg382Cys) rs752373431 0.00003
NM_000251.3(MSH2):c.14C>A (p.Pro5Gln) rs56170584 0.00003
NM_000251.3(MSH2):c.1760-16T>G rs768370188 0.00003
NM_000251.3(MSH2):c.1963G>A (p.Val655Ile) rs549467183 0.00003
NM_000251.3(MSH2):c.211+8C>T rs267607916 0.00003
NM_000251.3(MSH2):c.2205C>T (p.Ile735=) rs533553381 0.00003
NM_000251.3(MSH2):c.2211-5T>G rs368596736 0.00003
NM_000251.3(MSH2):c.2458+8C>G rs189025757 0.00003
NM_000251.3(MSH2):c.260C>G (p.Ser87Cys) rs587781447 0.00003
NM_000251.3(MSH2):c.2801C>A (p.Thr934Lys) rs587779969 0.00003
NM_000251.3(MSH2):c.835C>G (p.Leu279Val) rs375351205 0.00003
NM_000251.3(MSH2):c.943-25T>C rs775155213 0.00003
NM_000251.3(MSH2):c.968C>G (p.Ser323Cys) rs63750732 0.00003
NM_000251.3(MSH2):c.991A>G (p.Asn331Asp) rs267607938 0.00003
NM_000251.3(MSH2):c.1182T>G (p.Phe394Leu) rs374135434 0.00002
NM_000251.3(MSH2):c.1510+11G>C rs370675562 0.00002
NM_000251.3(MSH2):c.1681G>A (p.Glu561Lys) rs63750328 0.00002
NM_000251.3(MSH2):c.1854A>G (p.Pro618=) rs786203744 0.00002
NM_000251.3(MSH2):c.2061C>G (p.Leu687=) rs63750032 0.00002
NM_000251.3(MSH2):c.2717T>C (p.Ile906Thr) rs587780687 0.00002
NM_000251.3(MSH2):c.2786G>A (p.Arg929Gln) rs587779967 0.00002
NM_000251.3(MSH2):c.304G>A (p.Val102Ile) rs193922373 0.00002
NM_000251.3(MSH2):c.366+24A>G rs200890440 0.00002
NM_000251.3(MSH2):c.42G>A (p.Ala14=) rs374396150 0.00002
NM_000251.3(MSH2):c.438T>C (p.Gly146=) rs587779161 0.00002
NM_000251.3(MSH2):c.762T>C (p.Asn254=) rs587779180 0.00002
NM_000251.3(MSH2):c.80C>T (p.Pro27Leu) rs750746034 0.00002
NM_000179.3(MSH6):c.1487G>A (p.Cys496Tyr) rs764593111 0.00001
NM_000251.3(MSH2):c.-9G>C rs547444746 0.00001
NM_000251.3(MSH2):c.1077-15G>T rs753277524 0.00001
NM_000251.3(MSH2):c.115C>A (p.Arg39=) rs786202334 0.00001
NM_000251.3(MSH2):c.1171G>A (p.Ala391Thr) rs878853798 0.00001
NM_000251.3(MSH2):c.123C>G (p.Asp41Glu) rs761960690 0.00001
NM_000251.3(MSH2):c.1254A>G (p.Ile418Met) rs751431238 0.00001
NM_000251.3(MSH2):c.1311G>T (p.Val437=) rs730881781 0.00001
NM_000251.3(MSH2):c.1344C>T (p.Ser448=) rs1010360604 0.00001
NM_000251.3(MSH2):c.1640A>G (p.Asn547Ser) rs267607967 0.00001
NM_000251.3(MSH2):c.1760-10T>A rs767536391 0.00001
NM_000251.3(MSH2):c.1796T>C (p.Leu599Ser) rs747504492 0.00001
NM_000251.3(MSH2):c.1804C>G (p.Leu602Val) rs748797209 0.00001
NM_000251.3(MSH2):c.186G>A (p.Gly62=) rs750058876 0.00001
NM_000251.3(MSH2):c.2006-26dup rs781614743 0.00001
NM_000251.3(MSH2):c.2048G>T (p.Gly683Val) rs755920849 0.00001
NM_000251.3(MSH2):c.213A>G (p.Gly71=) rs878853808 0.00001
NM_000251.3(MSH2):c.220A>C (p.Asn74His) rs150548839 0.00001
NM_000251.3(MSH2):c.2437A>G (p.Met813Val) rs63749841 0.00001
NM_000251.3(MSH2):c.2439G>A (p.Met813Ile) rs587781678 0.00001
NM_000251.3(MSH2):c.2634+12T>C rs372907481 0.00001
NM_000251.3(MSH2):c.2804G>A (p.Ter935=) rs876658335 0.00001
NM_000251.3(MSH2):c.439G>A (p.Val147Ile) rs773125415 0.00001
NM_000251.3(MSH2):c.459C>T (p.Ser153=) rs63751065 0.00001
NM_000251.3(MSH2):c.589A>C (p.Lys197Gln) rs778573140 0.00001
NM_000251.3(MSH2):c.5C>T (p.Ala2Val) rs587778521 0.00001
NM_000251.3(MSH2):c.610G>A (p.Gly204Arg) rs63750574 0.00001
NM_000251.3(MSH2):c.646-3T>C rs267607930 0.00001
NM_000251.3(MSH2):c.728G>A (p.Arg243Gln) rs63751455 0.00001
NM_000251.3(MSH2):c.759G>A (p.Met253Ile) rs1060502021 0.00001
NM_000251.3(MSH2):c.972G>A (p.Gln324=) rs63750505 0.00001
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.2197C>T (p.His733Tyr) rs1553665846
NM_000251.2(MSH2):c.-68G>A rs576303132
NM_000251.3(MSH2):c.-21A>T rs776559145
NM_000251.3(MSH2):c.1076+23C>G rs377417056
NM_000251.3(MSH2):c.108T>C (p.Leu36=) rs876659034
NM_000251.3(MSH2):c.114C>A (p.Asp38Glu) rs587779074
NM_000251.3(MSH2):c.1251T>C (p.Val417=) rs1553356731
NM_000251.3(MSH2):c.1276+10G>A rs374061707
NM_000251.3(MSH2):c.1389G>T (p.Val463=) rs1553365702
NM_000251.3(MSH2):c.1530G>T (p.Gln510His) rs587782355
NM_000251.3(MSH2):c.160G>T (p.Ala54Ser) rs749212640
NM_000251.3(MSH2):c.1661+17T>G rs377461923
NM_000251.3(MSH2):c.1661+25del rs1553366691
NM_000251.3(MSH2):c.1662-18T>C rs376235435
NM_000251.3(MSH2):c.1706A>G (p.Glu569Gly) rs786201077
NM_000251.3(MSH2):c.1746C>T (p.Val582=) rs786201486
NM_000251.3(MSH2):c.1759+16C>G rs1057517573
NM_000251.3(MSH2):c.182A>C (p.Gln61Pro) rs587779113
NM_000251.3(MSH2):c.1884A>T (p.Gly628=) rs786202663
NM_000251.3(MSH2):c.2005+8dup rs267607992
NM_000251.3(MSH2):c.2028A>C (p.Ser676=) rs1057522032
NM_000251.3(MSH2):c.2210+8C>T rs778020437
NM_000251.3(MSH2):c.2260A>T (p.Thr754Ser) rs757268664
NM_000251.3(MSH2):c.2288C>T (p.Ala763Val) rs144412585
NM_000251.3(MSH2):c.2439G>C (p.Met813Ile) rs587781678
NM_000251.3(MSH2):c.2458+12T>C rs1553369841
NM_000251.3(MSH2):c.2459-20C>A rs1553370283
NM_000251.3(MSH2):c.2459-46G>A rs1573578232
NM_000251.3(MSH2):c.2576_2584del (p.Glu859_Gln861del) rs587781278
NM_000251.3(MSH2):c.2714C>G (p.Thr905Arg) rs267608022
NM_000251.3(MSH2):c.2726A>T (p.Lys909Ile) rs34319539
NM_000251.3(MSH2):c.276T>G (p.Leu92=) rs1060504425
NM_000251.3(MSH2):c.2801C>T (p.Thr934Met) rs587779969
NM_000251.3(MSH2):c.366+25C>T rs764158568
NM_000251.3(MSH2):c.383T>G (p.Leu128Arg) rs730881768
NM_000251.3(MSH2):c.403C>T (p.Leu135Phe) rs193096019
NM_000251.3(MSH2):c.507A>G (p.Ile169Met) rs748762580
NM_000251.3(MSH2):c.606C>T (p.Pro202=) rs63750600
NM_000251.3(MSH2):c.6G>T (p.Ala2=) rs368270856
NM_000251.3(MSH2):c.759G>C (p.Met253Ile)
NM_000251.3(MSH2):c.888C>G (p.Phe296Leu) rs876659918
NM_000251.3(MSH2):c.89C>T (p.Pro30Leu) rs757892928
NM_000251.3(MSH2):c.942+25_942+29del rs11309117
NM_000251.3(MSH2):c.942+27_942+29del rs11309117
NM_000251.3(MSH2):c.942+28_942+29del rs11309117
NM_000251.3(MSH2):c.965G>T (p.Gly322Val) rs4987188
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu) rs63750668
NM_022055.2(KCNK12):c.*8388G>T rs1573613933

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