ClinVar Miner

List of variants studied for Lynch syndrome by Department of Pathology and Laboratory Medicine, Sinai Health System

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Total variants: 128
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HGVS dbSNP gnomAD frequency
NM_000251.3(MSH2):c.1077-10T>C rs17224360 0.01428
NM_000251.3(MSH2):c.339G>A (p.Lys113=) rs35898375 0.00313
NM_000251.3(MSH2):c.1387-8G>T rs187525243 0.00143
NM_000535.7(PMS2):c.2149G>A (p.Val717Met) rs201671325 0.00072
NM_000179.3(MSH6):c.4001+11_4001+15dup rs587779302 0.00019
NM_000179.3(MSH6):c.3160A>T (p.Ile1054Phe) rs267608075 0.00016
NM_000251.3(MSH2):c.-3G>C rs587779960 0.00013
NM_000179.3(MSH6):c.1081C>T (p.Arg361Cys) rs587782651 0.00012
NM_000251.3(MSH2):c.913G>A (p.Ala305Thr) rs63751454 0.00008
NM_000179.3(MSH6):c.178T>C (p.Leu60=) rs35819209 0.00006
NM_000179.3(MSH6):c.3824G>A (p.Cys1275Tyr) rs150990541 0.00006
NM_000249.4(MLH1):c.69A>G (p.Glu23=) rs63750555 0.00006
NM_000179.3(MSH6):c.2239C>T (p.Leu747=) rs63751305 0.00005
NM_000535.7(PMS2):c.2347G>A (p.Val783Ile) rs553286217 0.00004
NM_000535.7(PMS2):c.705+12C>T rs368486366 0.00004
NM_000179.3(MSH6):c.-2G>T rs374748889 0.00003
NM_000179.3(MSH6):c.1822A>G (p.Ile608Val) rs201613780 0.00003
NM_000179.3(MSH6):c.240A>G (p.Val80=) rs864622281 0.00003
NM_000179.3(MSH6):c.3426G>A (p.Thr1142=) rs747771350 0.00003
NM_000251.3(MSH2):c.14C>A (p.Pro5Gln) rs56170584 0.00003
NM_000251.3(MSH2):c.2801C>A (p.Thr934Lys) rs587779969 0.00003
NM_000179.3(MSH6):c.1501C>T (p.His501Tyr) rs779411998 0.00002
NM_000179.3(MSH6):c.957G>C (p.Thr319=) rs375210430 0.00002
NM_000249.4(MLH1):c.303T>G (p.Gly101=) rs4647220 0.00002
NM_000251.3(MSH2):c.581T>C (p.Ile194Thr) rs730881778 0.00002
NM_000251.3(MSH2):c.894G>C (p.Gln298His) rs587781397 0.00002
NM_000179.3(MSH6):c.*11T>C rs757708396 0.00001
NM_000179.3(MSH6):c.148T>C (p.Trp50Arg) rs374597395 0.00001
NM_000179.3(MSH6):c.2027A>G (p.Lys676Arg) rs143643688 0.00001
NM_000179.3(MSH6):c.2827G>T (p.Asp943Tyr) rs143520357 0.00001
NM_000179.3(MSH6):c.2949G>C (p.Glu983Asp) rs780485157 0.00001
NM_000179.3(MSH6):c.4043A>C (p.Glu1348Ala) rs1449733937 0.00001
NM_000249.4(MLH1):c.1693A>T (p.Ile565Phe) rs63750062 0.00001
NM_000249.4(MLH1):c.298C>T (p.Arg100Ter) rs63751221 0.00001
NM_000249.4(MLH1):c.963_1014dup (p.Ser339fs) rs1553648058 0.00001
NM_000535.7(PMS2):c.114G>A (p.Ala38=) rs558032755 0.00001
NM_000535.7(PMS2):c.1682A>C (p.Lys561Thr) rs876658481 0.00001
NM_000535.7(PMS2):c.1760G>A (p.Ser587Asn) rs762100304 0.00001
NC_000002.12:g.(?_47482779)_(47482949_?)del
NM_000179.2(MSH6):c.3439-?_3556+?del
NM_000179.2(MSH6):c.458-?_3556+?del
NM_000179.2(MSH6):c.458-?_627+?del
NM_000179.3(MSH6):c.1471ATG[1] (p.Met492del) rs587782576
NM_000179.3(MSH6):c.1669G>A (p.Gly557Ser) rs1553413048
NM_000179.3(MSH6):c.189C>T (p.Ser63=) rs917331457
NM_000179.3(MSH6):c.2194C>T (p.Arg732Ter) rs63751127
NM_000179.3(MSH6):c.2238T>C (p.Phe746=) rs1384756767
NM_000179.3(MSH6):c.2966A>T (p.Asn989Ile) rs763146296
NM_000179.3(MSH6):c.3142C>T (p.Gln1048Ter) rs200492211
NM_000179.3(MSH6):c.3173-3C>G rs1060502944
NM_000179.3(MSH6):c.3226C>G (p.Arg1076Gly) rs63750617
NM_000179.3(MSH6):c.3238_3239del (p.Leu1080fs) rs863225406
NM_000179.3(MSH6):c.3261dup (p.Phe1088fs) rs267608078
NM_000179.3(MSH6):c.4002-10del rs59056100
NM_000179.3(MSH6):c.4062_4065dup (p.Leu1356fs) rs1553334056
NM_000179.3(MSH6):c.866_867delinsAA (p.Gly289Glu) rs267608079
NM_000249.3(MLH1):c.1039-?_1558+?del
NM_000249.3(MLH1):c.1732-?_1896+?del
NM_000249.3(MLH1):c.307-?_1667+?dup
NM_000249.3(MLH1):c.381-?_677+?del
NM_000249.3(MLH1):c.546-?_1731+?dup
NM_000249.4(MLH1):c.1011del (p.Asn338fs) rs63750677
NM_000249.4(MLH1):c.1325_1346delinsATTTT (p.Ala442fs) rs587778903
NM_000249.4(MLH1):c.1358dup (p.Thr455fs) rs1553651429
NM_000249.4(MLH1):c.1489dup (p.Arg497fs) rs63750855
NM_000249.4(MLH1):c.1559-1G>T rs267607837
NM_000249.4(MLH1):c.1559-2A>G rs267607836
NM_000249.4(MLH1):c.1664T>G (p.Leu555Arg) rs587778937
NM_000249.4(MLH1):c.1667+8A>C rs1553658260
NM_000249.4(MLH1):c.184C>T (p.Gln62Ter) rs63751428
NM_000249.4(MLH1):c.1919C>T (p.Pro640Leu) rs267607875
NM_000249.4(MLH1):c.2040C>A (p.Cys680Ter) rs63749867
NM_000249.4(MLH1):c.2048_2050del (p.Phe683del) rs1553664506
NM_000249.4(MLH1):c.2250C>G (p.Tyr750Ter) rs267607893
NM_000249.4(MLH1):c.230G>A (p.Cys77Tyr) rs63750437
NM_000249.4(MLH1):c.319A>G (p.Ile107Val) rs572906317
NM_000249.4(MLH1):c.453+1G>T rs267607750
NM_000249.4(MLH1):c.456_545+2del rs1553642657
NM_000249.4(MLH1):c.492del (p.Ala165fs) rs1553642698
NM_000249.4(MLH1):c.546-2_589-59del rs2125805231
NM_000249.4(MLH1):c.588+5G>A rs267607768
NM_000249.4(MLH1):c.677+1G>T rs267607778
NM_000249.4(MLH1):c.70del (p.Val24fs) rs63751396
NM_000249.4(MLH1):c.753_755del (p.Tyr251_Ser252delinsTer) rs1553645256
NM_000249.4(MLH1):c.791-1G>A rs267607795
NM_000249.4(MLH1):c.898_908del (p.Pro300fs) rs1553647928
NM_000249.4(MLH1):c.949del (p.Leu317fs) rs1553648029
NM_000251.2(MSH2):c.1662-?_1759+?del
NM_000251.2(MSH2):c.1760-?_2458+?del
NM_000251.2(MSH2):c.2006-?_2210+?del
NM_000251.2(MSH2):c.367-?_1076+?del
NM_000251.2(MSH2):c.367-?_1276+?del
NM_000251.2(MSH2):c.367-?_1386+?del
NM_000251.2(MSH2):c.367-?_645+?del
NM_000251.2(MSH2):c.943-?_1076+?del
NM_000251.3(MSH2):c.1077_1276del rs1553356518
NM_000251.3(MSH2):c.1277-2_1386+1del rs2103751857
NM_000251.3(MSH2):c.1278_1386+1del rs1553361141
NM_000251.3(MSH2):c.1373T>G (p.Leu458Ter) rs63750521
NM_000251.3(MSH2):c.1386+1G>A rs267607957
NM_000251.3(MSH2):c.1418C>G (p.Ser473Ter) rs63751403
NM_000251.3(MSH2):c.163del (p.Arg55fs) rs63750337
NM_000251.3(MSH2):c.1748A>T (p.Asn583Ile) rs201118107
NM_000251.3(MSH2):c.2100del (p.Glu701fs) rs1553369113
NM_000251.3(MSH2):c.213_366+1del rs1553350052
NM_000251.3(MSH2):c.2211-2A>T rs267608001
NM_000251.3(MSH2):c.2375A>G (p.Asn792Ser) rs587782891
NM_000251.3(MSH2):c.2480G>A (p.Gly827Glu) rs2104435371
NM_000251.3(MSH2):c.2525_2526del (p.Glu842fs) rs587779148
NM_000251.3(MSH2):c.2575G>T (p.Glu859Ter) rs63749830
NM_000251.3(MSH2):c.332C>T (p.Ala111Val) rs1672561306
NM_000251.3(MSH2):c.367-2_645+432del rs2104016448
NM_000251.3(MSH2):c.367-2_645+742del
NM_000251.3(MSH2):c.403C>G (p.Leu135Val) rs193096019
NM_000251.3(MSH2):c.448G>T (p.Val150Phe) rs1558459157
NM_000251.3(MSH2):c.459del (p.Ala154fs) rs2104023773
NM_000251.3(MSH2):c.687_688insT (p.Ala230fs) rs63750364
NM_000251.3(MSH2):c.965G>T (p.Gly322Val) rs4987188
NM_000535.7(PMS2):c.1145-982_2006+2del
NM_000535.7(PMS2):c.1356T>G (p.Gly452=) rs786202946
NM_000535.7(PMS2):c.1682A>G (p.Lys561Arg) rs876658481
NM_000535.7(PMS2):c.1771T>C (p.Cys591Arg) rs764252217
NM_000535.7(PMS2):c.1831dup (p.Ile611fs) rs63750250
NM_000535.7(PMS2):c.23+21_23+28del rs1554308880
NM_000535.7(PMS2):c.2458dup (p.Thr820fs) rs1554292880
NM_000535.7(PMS2):c.860dup (p.Gln288fs) rs2128775362
NM_002354.2(EPCAM):c.904-?_945+?del
Single allele

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