ClinVar Miner

List of variants reported as likely benign for Lynch syndrome by International Society for Gastrointestinal Hereditary Tumours (InSiGHT)

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Total variants: 89
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HGVS dbSNP gnomAD frequency
NM_000535.7(PMS2):c.1711C>A (p.Leu571Ile) rs63750055 0.00784
NM_000249.4(MLH1):c.589-15C>T rs55658850 0.00582
NM_000535.7(PMS2):c.1569C>G (p.Ser523=) rs141458772 0.00560
NM_014805.3(EPM2AIP1):c.-202G>C rs35032294 0.00539
NM_000251.3(MSH2):c.984C>T (p.Ala328=) rs4987189 0.00495
NM_000179.3(MSH6):c.457+13A>G rs1800933 0.00434
NM_000249.4(MLH1):c.1963A>G (p.Ile655Val) rs55907433 0.00297
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.885-24T>A rs201594027 0.00164
NM_000251.3(MSH2):c.1737A>G (p.Lys579=) rs61756467 0.00138
NM_000535.7(PMS2):c.180C>G (p.Asp60Glu) rs200313585 0.00088
NM_000179.3(MSH6):c.1526T>C (p.Val509Ala) rs63751005 0.00067
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_000249.4(MLH1):c.198C>T (p.Thr66=) rs61751642 0.00040
NM_000251.3(MSH2):c.2154A>G (p.Gln718=) rs63750810 0.00033
NM_000179.3(MSH6):c.3488A>T (p.Glu1163Val) rs63750252 0.00032
NM_000251.3(MSH2):c.471C>A (p.Gly157=) rs61756463 0.00029
NM_000179.3(MSH6):c.3217C>T (p.Pro1073Ser) rs142254875 0.00028
NM_000251.3(MSH2):c.*221G>T rs587779060 0.00024
NM_000249.4(MLH1):c.307-19A>G rs121909451 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.1730T>C (p.Ile577Thr) rs63749910 0.00018
NM_000179.3(MSH6):c.3160A>T (p.Ile1054Phe) rs267608075 0.00016
NM_000249.4(MLH1):c.2101C>A (p.Gln701Lys) rs63750114 0.00016
NM_000249.4(MLH1):c.1820T>A (p.Leu607His) rs41295284 0.00015
NM_000251.3(MSH2):c.505A>G (p.Ile169Val) rs63750716 0.00013
NM_000179.3(MSH6):c.1875C>T (p.Ser625=) rs63749886 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_000249.4(MLH1):c.1742C>T (p.Pro581Leu) rs63751684 0.00008
NM_000251.3(MSH2):c.1488A>G (p.Leu496=) rs267607960 0.00008
NM_000251.3(MSH2):c.2500G>A (p.Ala834Thr) rs63750757 0.00008
NM_000249.4(MLH1):c.545+43C>G rs267607761 0.00007
NM_000535.7(PMS2):c.384G>A (p.Ser128=) rs371342884 0.00007
NM_000179.3(MSH6):c.1019T>C (p.Phe340Ser) rs61753793 0.00006
NM_000179.3(MSH6):c.3986C>T (p.Ser1329Leu) rs199594809 0.00006
NM_000251.3(MSH2):c.944G>T (p.Gly315Val) rs202026056 0.00006
NM_000249.4(MLH1):c.438A>G (p.Gln146=) rs377279035 0.00005
NM_000249.4(MLH1):c.2252A>G (p.Lys751Arg) rs140195825 0.00004
NM_000251.3(MSH2):c.287G>A (p.Arg96His) rs63750002 0.00004
NM_000179.3(MSH6):c.2319C>T (p.Leu773=) rs63749895 0.00003
NM_000249.4(MLH1):c.303T>G (p.Gly101=) rs4647220 0.00002
NM_000249.4(MLH1):c.974G>A (p.Arg325Gln) rs63750268 0.00002
NM_000251.3(MSH2):c.304G>A (p.Val102Ile) rs193922373 0.00002
NM_000179.3(MSH6):c.1403G>A (p.Arg468His) rs41295268 0.00001
NM_000179.3(MSH6):c.161G>C (p.Gly54Ala) rs63751098 0.00001
NM_000179.3(MSH6):c.194C>T (p.Ser65Leu) rs41294984 0.00001
NM_000179.3(MSH6):c.241G>A (p.Ala81Thr) rs587779239 0.00001
NM_000179.3(MSH6):c.2661T>G (p.Leu887=) rs267608069 0.00001
NM_000179.3(MSH6):c.2765G>A (p.Arg922Gln) rs752839086 0.00001
NM_000249.4(MLH1):c.845C>G (p.Ala282Gly) rs63750360 0.00001
NM_000249.4(MLH1):c.885-5G>T rs267607802 0.00001
NM_000251.3(MSH2):c.164G>A (p.Arg55Gln) rs748196422 0.00001
NM_000251.3(MSH2):c.2579C>T (p.Ser860Leu) rs63750849 0.00001
NM_000251.3(MSH2):c.972G>A (p.Gln324=) rs63750505 0.00001
MSH6:c.3647-51_3647-35del17 rs267607687
NM_000179.3(MSH6):c.1667A>T (p.Tyr556Phe) rs63751312
NM_000179.3(MSH6):c.1770C>T (p.Pro590=) rs267608070
NM_000179.3(MSH6):c.2319C>A (p.Leu773=) rs63749895
NM_000179.3(MSH6):c.3207G>T (p.Gly1069=) rs267608074
NM_000179.3(MSH6):c.4001+2TAAC[2] rs267608132
NM_000179.3(MSH6):c.4002-10del rs59056100
NM_000179.3(MSH6):c.4068_4071dup (p.Lys1358delinsAspTer) rs55740729
NM_000249.3(MLH1):c.-107C>G rs587778886
NM_000249.3(MLH1):c.1558+3232_1558+3692delins2
NM_000249.4(MLH1):c.1003C>T (p.Leu335=) rs267607812
NM_000249.4(MLH1):c.1136A>G (p.Tyr379Cys) rs143009528
NM_000249.4(MLH1):c.117-43_117-39del rs587778895
NM_000249.4(MLH1):c.1653C>T (p.Asn551=) rs587778936
NM_000249.4(MLH1):c.1732-9T>C rs267607857
NM_000249.4(MLH1):c.1853A>G (p.Lys618Arg) rs63750449
NM_000249.4(MLH1):c.791-23del rs267607797
NM_000249.4(MLH1):c.885-21TC[2] rs267607804
NM_000251.3(MSH2):c.1602T>A (p.Arg534=) rs267607965
NM_000251.3(MSH2):c.1661+6C>T rs267607973
NM_000251.3(MSH2):c.1755T>C (p.Ser585=) rs63750112
NM_000251.3(MSH2):c.1760-110_1760-108dup rs587779109
NM_000251.3(MSH2):c.2005+8dup rs267607992
NM_000251.3(MSH2):c.2139G>C (p.Gly713=) rs63750003
NM_000251.3(MSH2):c.2583A>G (p.Gln861=) rs63751093
NM_000251.3(MSH2):c.2681T>G (p.Met894Arg) rs1558526026
NM_000251.3(MSH2):c.6G>T (p.Ala2=) rs368270856
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu) rs63750668

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