ClinVar Miner

Variants with conflicting interpretations studied for Lynch syndrome 1

Coded as:
Minimum review status of the submission for Lynch syndrome 1: Collection method of the submission for Lynch syndrome 1:
Minimum review status of the other submission: Collection method of the other submission:
Minimum conflict level:
ClinVar version:

If a variant has more than two submissions, it may have multiple conflicts and therefore be counted in more than one conflict column. If this is the case, the "Variants with any kind of conflict" cell will be less than the sum of the conflicted variants cells to its left.

Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
1297 264 0 128 127 0 12 241

Significance breakdown #

In the table below, cells that correspond to a term paired with itself represent synonymous conflicts, i.e. variants that have been annotated with different terms that map to the same standard term. To compare the terms that were actually submitted, check the box in the filters section at the top of this page.

All conditions
Lynch syndrome 1 pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 55 5 0 0
likely pathogenic 52 0 3 0 0
uncertain significance 5 3 0 93 38
likely benign 0 0 91 0 55
benign 0 0 38 57 0

Condition to condition summary #

Total conditions: 5
Download table as spreadsheet
Condition Variants with only 1 submission per condition Variants with at least 2 submissions on the same condition and no conflicts Variants with a synonymous conflict
(e.g. benign vs non-pathogenic)
Variants with a confidence conflict
(e.g. benign vs likely benign)
Variants with a benign or likely benign vs uncertain conflict Variants with a category conflict
(e.g. benign vs affects)
Variants with a clinically significant conflict
(e.g. benign vs pathogenic)
Variants with any conflict
Lynch syndrome 1 1420 200 0 91 102 0 3 182
Colorectal cancer, hereditary nonpolyposis, type 2 0 41 0 21 10 0 5 30
Lynch syndrome 5 0 17 0 11 8 0 2 17
Lynch syndrome 4 0 14 0 9 6 0 2 15
Colorectal cancer, hereditary nonpolyposis, type 7 0 0 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 241
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) rs1042821 0.18742
NM_000535.7(PMS2):c.59G>A (p.Arg20Gln) rs10254120 0.07445
NM_000249.4(MLH1):c.1558+14G>A rs41562513 0.05554
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_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_000249.4(MLH1):c.474C>T (p.Asn158=) rs4647256 0.01161
NM_000249.4(MLH1):c.1039-8T>A rs193922367 0.01153
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_000249.4(MLH1):c.1959G>T (p.Leu653=) rs1800146 0.00913
NM_000535.7(PMS2):c.52A>G (p.Ile18Val) rs63750123 0.00861
NM_000249.4(MLH1):c.1038+51C>T rs55986674 0.00582
NM_000179.3(MSH6):c.1186C>G (p.Leu396Val) rs2020908 0.00565
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_001040108.2(MLH3):c.2425A>G (p.Met809Val) rs61752722 0.00197
NM_000251.3(MSH2):c.23C>T (p.Thr8Met) rs17217716 0.00184
NM_000535.7(PMS2):c.383C>T (p.Ser128Leu) rs116373169 0.00177
NM_000251.3(MSH2):c.1387-8G>T rs187525243 0.00143
NM_000251.3(MSH2):c.819A>G (p.Val273=) rs146577635 0.00101
NM_000251.3(MSH2):c.942+2T>A rs587779195 0.00101
NM_000249.4(MLH1):c.1151T>A (p.Val384Asp) rs63750447 0.00077
NM_000251.3(MSH2):c.942+3A>T rs193922376 0.00072
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_000251.3(MSH2):c.1563T>C (p.Tyr521=) rs63750330 0.00053
NM_000251.3(MSH2):c.815C>T (p.Ala272Val) rs34136999 0.00046
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.1511-41G>C rs202215396 0.00038
NM_000249.4(MLH1):c.977T>C (p.Val326Ala) rs63751049 0.00037
NM_000179.3(MSH6):c.2561A>T (p.Lys854Met) rs34374438 0.00036
NM_000249.4(MLH1):c.1321G>A (p.Ala441Thr) rs63750365 0.00034
NM_000251.3(MSH2):c.2154A>G (p.Gln718=) rs63750810 0.00033
NM_000251.3(MSH2):c.435T>G (p.Ile145Met) rs63750124 0.00031
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.138C>G (p.His46Gln) rs33946261 0.00019
NM_000535.7(PMS2):c.137G>T (p.Ser46Ile) rs121434629 0.00018
NM_000535.7(PMS2):c.2253T>C (p.Phe751=) rs1805325 0.00018
NM_000249.4(MLH1):c.2101C>A (p.Gln701Lys) rs63750114 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_000251.3(MSH2):c.766G>A (p.Ala256Thr) rs377403073 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.557A>G (p.Asn186Ser) rs151129360 0.00011
NM_000535.7(PMS2):c.857A>G (p.Asp286Gly) rs116788608 0.00011
NM_000535.7(PMS2):c.379G>A (p.Ala127Thr) rs114090343 0.00010
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.1217G>A (p.Arg406Gln) rs146567853 0.00008
NM_000251.3(MSH2):c.1488A>G (p.Leu496=) rs267607960 0.00008
NM_000251.3(MSH2):c.1690A>G (p.Thr564Ala) rs55778204 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_000179.3(MSH6):c.2384T>C (p.Ile795Thr) rs202127474 0.00007
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_000249.4(MLH1):c.955G>A (p.Glu319Lys) rs63750796 0.00006
NM_000251.3(MSH2):c.2400A>G (p.Leu800=) rs201298777 0.00006
NM_000251.3(MSH2):c.2503A>C (p.Asn835His) rs41295296 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.336C>A (p.Ser112=) rs34312619 0.00004
NM_000251.3(MSH2):c.607G>A (p.Gly203Arg) rs587779973 0.00004
NM_000535.7(PMS2):c.1A>G (p.Met1Val) rs587779333 0.00004
NM_000249.4(MLH1):c.191A>G (p.Asn64Ser) rs63750952 0.00003
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.1847C>G (p.Pro616Arg) rs587779965 0.00003
NM_000251.3(MSH2):c.1963G>A (p.Val655Ile) rs549467183 0.00003
NM_000251.3(MSH2):c.2006-26dup rs781614743 0.00003
NM_000251.3(MSH2):c.211+8C>T rs267607916 0.00003
NM_000251.3(MSH2):c.2120G>A (p.Cys707Tyr) rs373226409 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.2558A>C (p.Glu853Ala) rs63750797 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.399C>T (p.Asp133=) rs61756462 0.00003
NM_000251.3(MSH2):c.835C>G (p.Leu279Val) rs375351205 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_000535.7(PMS2):c.2113G>A (p.Glu705Lys) rs267608161 0.00003
NM_000251.3(MSH2):c.1182T>G (p.Phe394Leu) rs374135434 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.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.1106C>T (p.Thr369Ile) rs375974046 0.00001
NM_000249.4(MLH1):c.2059C>T (p.Arg687Trp) rs63751275 0.00001
NM_000249.4(MLH1):c.2080G>T (p.Glu694Ter) rs147542208 0.00001
NM_000249.4(MLH1):c.244A>G (p.Thr82Ala) rs587778998 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.1462T>G (p.Leu488Val) rs587781314 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.1862G>A (p.Arg621Gln) rs759263820 0.00001
NM_000251.3(MSH2):c.2006-4G>A rs369853630 0.00001
NM_000251.3(MSH2):c.2048G>T (p.Gly683Val) rs755920849 0.00001
NM_000251.3(MSH2):c.2131C>T (p.Arg711Ter) rs63750636 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.459C>T (p.Ser153=) rs63751065 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.972G>A (p.Gln324=) rs63750505 0.00001
NM_000179.3(MSH6):c.1100A>G (p.His367Arg) rs1553412495
NM_000179.3(MSH6):c.2092C>T (p.Gln698Ter) rs63750832
NM_000179.3(MSH6):c.2300C>T (p.Thr767Ile) rs587781462
NM_000179.3(MSH6):c.3188T>G (p.Leu1063Arg) rs1060502901
NM_000179.3(MSH6):c.3246G>T (p.Pro1082=) rs3136351
NM_000179.3(MSH6):c.3439-1G>T rs587779263
NM_000179.3(MSH6):c.4001+2TAAC[2] rs267608132
NM_000179.3(MSH6):c.4068_4071dup (p.Lys1358delinsAspTer) rs55740729
NM_000179.3(MSH6):c.718C>T (p.Arg240Ter) rs63750019
NM_000249.4(MLH1):c.1038+1G>C rs267607816
NM_000249.4(MLH1):c.116G>A (p.Cys39Tyr) rs63751701
NM_000249.4(MLH1):c.1649T>C (p.Leu550Pro) rs63750193
NM_000249.4(MLH1):c.1667G>A (p.Ser556Asn) rs63751596
NM_000249.4(MLH1):c.1846AAG[2] (p.Lys618del) rs63751247
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.199G>A (p.Gly67Arg) rs63750206
NM_000249.4(MLH1):c.299G>C (p.Arg100Pro) rs63750266
NM_000249.4(MLH1):c.2T>C (p.Met1Thr) rs111052004
NM_000249.4(MLH1):c.304G>A (p.Glu102Lys) rs63750453
NM_000249.4(MLH1):c.350C>T (p.Thr117Met) rs63750781
NM_000249.4(MLH1):c.62C>T (p.Ala21Val) rs63750706
NM_000249.4(MLH1):c.793C>T (p.Arg265Cys) rs63751194
NM_000249.4(MLH1):c.931A>G (p.Lys311Glu) rs876658657
NM_000251.2(MSH2):c.-68G>A rs576303132
NM_000251.3(MSH2):c.1012G>A (p.Gly338Arg) rs63751004
NM_000251.3(MSH2):c.1015C>T (p.Gln339Ter) rs1558466577
NM_000251.3(MSH2):c.1023del (p.Val342fs) rs864622340
NM_000251.3(MSH2):c.1042del (p.Gln348fs) rs1553353233
NM_000251.3(MSH2):c.1046C>G (p.Pro349Arg) rs587779067
NM_000251.3(MSH2):c.1046C>T (p.Pro349Leu) rs587779067
NM_000251.3(MSH2):c.108T>C (p.Leu36=) rs876659034
NM_000251.3(MSH2):c.1139T>G (p.Leu380Ter) rs730881755
NM_000251.3(MSH2):c.1276+1G>A rs267607950
NM_000251.3(MSH2):c.1276+2T>C rs267607953
NM_000251.3(MSH2):c.1339_1340del (p.Phe447fs) rs1553361231
NM_000251.3(MSH2):c.1401del (p.Glu467fs) rs1553365711
NM_000251.3(MSH2):c.1465G>A (p.Glu489Lys) rs876658187
NM_000251.3(MSH2):c.1510+2T>C rs1060502023
NM_000251.3(MSH2):c.1511-2A>G rs267607962
NM_000251.3(MSH2):c.1563T>A (p.Tyr521Ter) rs63750330
NM_000251.3(MSH2):c.1571G>C (p.Arg524Pro) rs63751207
NM_000251.3(MSH2):c.160G>T (p.Ala54Ser) rs749212640
NM_000251.3(MSH2):c.1613dup (p.Asn538fs)
NM_000251.3(MSH2):c.1661+1G>A rs267607969
NM_000251.3(MSH2):c.1661+1G>T rs267607969
NM_000251.3(MSH2):c.1661G>A (p.Ser554Asn) rs63750597
NM_000251.3(MSH2):c.1706A>G (p.Glu569Gly) rs786201077
NM_000251.3(MSH2):c.182A>C (p.Gln61Pro) rs587779113
NM_000251.3(MSH2):c.2005+8dup rs267607992
NM_000251.3(MSH2):c.2006-2A>G rs267607991
NM_000251.3(MSH2):c.2027C>A (p.Ser676Ter)
NM_000251.3(MSH2):c.211G>C (p.Gly71Arg) rs587782659
NM_000251.3(MSH2):c.2139G>T (p.Gly713=) rs63750003
NM_000251.3(MSH2):c.2168C>T (p.Ser723Phe) rs63750794
NM_000251.3(MSH2):c.2251G>A (p.Gly751Arg) rs63751119
NM_000251.3(MSH2):c.2287G>C (p.Ala763Pro) rs1318630651
NM_000251.3(MSH2):c.2288C>T (p.Ala763Val) rs144412585
NM_000251.3(MSH2):c.2342del (p.Ala781fs)
NM_000251.3(MSH2):c.2365del (p.Ala789fs)
NM_000251.3(MSH2):c.2425G>T (p.Glu809Ter) rs202145681
NM_000251.3(MSH2):c.2562del (p.Gln855fs) rs1114167836
NM_000251.3(MSH2):c.2576_2584del (p.Glu859_Gln861del) rs587781278
NM_000251.3(MSH2):c.2634+5G>C rs267608017
NM_000251.3(MSH2):c.2635-1G>A rs267608020
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.354T>G (p.Tyr118Ter) rs1553350250
NM_000251.3(MSH2):c.383T>G (p.Leu128Arg) rs730881768
NM_000251.3(MSH2):c.388C>T (p.Gln130Ter) rs1060501989
NM_000251.3(MSH2):c.403C>T (p.Leu135Phe) rs193096019
NM_000251.3(MSH2):c.448_449del (p.Gly149_Val150insTer)
NM_000251.3(MSH2):c.482T>A (p.Val161Asp) rs63750126
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.67T>C (p.Phe23Leu) rs372619120
NM_000251.3(MSH2):c.6G>T (p.Ala2=) rs368270856
NM_000251.3(MSH2):c.748G>T (p.Gly250Ter) rs864622183
NM_000251.3(MSH2):c.806C>A (p.Ser269Ter) rs63750058
NM_000251.3(MSH2):c.870_874del (p.Glu290fs) rs1114167848
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+28_942+29del rs11309117
NM_000251.3(MSH2):c.942+29del rs11309117
NM_000251.3(MSH2):c.942+3A>C rs193922376
NM_000251.3(MSH2):c.943-2A>G rs587779198
NM_000251.3(MSH2):c.965G>T (p.Gly322Val) rs4987188
NM_000251.3(MSH2):c.998G>T (p.Cys333Phe) rs63750828
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu) rs63750668
NM_000535.7(PMS2):c.1831dup (p.Ile611fs) rs63750250
NM_000535.7(PMS2):c.2186_2187del (p.Leu729fs) rs587779335
NM_000535.7(PMS2):c.241G>T (p.Glu81Ter) rs730881919
NM_000535.7(PMS2):c.706-4dup rs60794673

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