ClinVar Miner

Variants with conflicting interpretations studied for Lynch syndrome I

Coded as:
Minimum review status of the submission for Lynch syndrome I: Y axis collection method of the submission for Lynch syndrome I:
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 Variants with at least 2 submissions 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 kind of conflict
78 172 34 93 92 0 27 177

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 I pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 15 7 0 0
likely pathogenic 11 0 10 0 0
uncertain significance 5 8 5 49 20
likely benign 0 0 37 0 37
benign 0 1 13 37 29

Condition to condition summary #

Total conditions: 18
Download table as spreadsheet
Condition Variants with only 1 submission Variants with at least 2 submissions 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 kind of conflict
Hereditary cancer-predisposing syndrome 0 212 0 39 53 0 10 97
Lynch syndrome 0 123 27 43 29 0 9 77
Hereditary nonpolyposis colon cancer 0 178 0 35 34 0 8 75
not specified 0 87 0 41 37 0 4 69
not provided 0 145 15 22 26 0 9 66
Lynch syndrome I 381 30 0 7 8 0 1 16
Lynch syndrome II 0 8 0 4 5 0 1 9
Colorectal cancer, non-polyposis 0 3 0 1 5 0 0 6
Hereditary nonpolyposis colorectal cancer type 4 0 7 0 4 1 0 1 6
Hereditary nonpolyposis colorectal cancer type 5 0 7 0 2 3 0 1 6
Adenocarcinoma of stomach 0 0 0 0 0 0 1 1
Breast-ovarian cancer, familial 4 0 0 0 0 0 0 1 1
Colorectal / endometrial cancer 0 0 0 0 1 0 0 1
Colorectal cancer 0 0 0 0 1 0 0 1
Lung adenocarcinoma 0 0 0 0 0 0 1 1
Turcot syndrome 0 0 0 1 0 0 1 1
Turcot syndrome; Hereditary nonpolyposis colorectal cancer type 4 0 2 0 1 0 0 0 1
Turcot syndrome; Muir-Torré syndrome; Lynch syndrome II 0 3 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 177
Download table as spreadsheet
HGVS dbSNP
NM_000179.2(MSH6):c.116G>A (p.Gly39Glu) rs1042821
NM_000179.2(MSH6):c.1186C>G (p.Leu396Val) rs2020908
NM_000179.2(MSH6):c.1487G>A (p.Cys496Tyr) rs764593111
NM_000179.2(MSH6):c.1508C>G (p.Ser503Cys) rs63750897
NM_000179.2(MSH6):c.1526T>C (p.Val509Ala) rs63751005
NM_000179.2(MSH6):c.2300C>T (p.Thr767Ile) rs587781462
NM_000179.2(MSH6):c.2384T>C (p.Ile795Thr) rs202127474
NM_000179.2(MSH6):c.2398G>C (p.Val800Leu) rs61748083
NM_000179.2(MSH6):c.2906A>G (p.Tyr969Cys) rs63749919
NM_000179.2(MSH6):c.3188T>G (p.Leu1063Arg) rs1060502901
NM_000179.2(MSH6):c.3226C>T (p.Arg1076Cys) rs63750617
NM_000179.2(MSH6):c.3246G>T (p.Pro1082=) rs3136351
NM_000179.2(MSH6):c.3557-40T>A rs189436849
NM_000179.2(MSH6):c.3632T>C (p.Leu1211Pro) rs864622041
NM_000179.2(MSH6):c.3G>T (p.Met1Ile) rs876660095
NM_000179.2(MSH6):c.59C>T (p.Ala20Val) rs63750664
NM_000249.3(MLH1):c.-27C>A rs587779001
NM_000249.3(MLH1):c.1038+51C>T rs55986674
NM_000249.3(MLH1):c.1039-8T>A rs193922367
NM_000249.3(MLH1):c.1151T>A (p.Val384Asp) rs63750447
NM_000249.3(MLH1):c.116G>A (p.Cys39Tyr) rs63751701
NM_000249.3(MLH1):c.1321G>A (p.Ala441Thr) rs63750365
NM_000249.3(MLH1):c.1327A>C (p.Lys443Gln) rs34213726
NM_000249.3(MLH1):c.1558+14G>A rs41562513
NM_000249.3(MLH1):c.1649T>C (p.Leu550Pro) rs63750193
NM_000249.3(MLH1):c.1852_1853delAAinsGC (p.Lys618Ala) rs35502531
NM_000249.3(MLH1):c.1853A>C (p.Lys618Thr) rs63750449
NM_000249.3(MLH1):c.1855G>C (p.Ala619Pro) rs267607866
NM_000249.3(MLH1):c.191A>G (p.Asn64Ser) rs63750952
NM_000249.3(MLH1):c.1943C>T (p.Pro648Leu) rs63750610
NM_000249.3(MLH1):c.1959G>T (p.Leu653=) rs1800146
NM_000249.3(MLH1):c.1989G>A (p.Glu663=) rs63751662
NM_000249.3(MLH1):c.2038T>C (p.Cys680Arg) rs63750809
NM_000249.3(MLH1):c.2048T>C (p.Phe683Ser) rs587778972
NM_000249.3(MLH1):c.2074T>C (p.Ser692Pro) rs587779957
NM_000249.3(MLH1):c.2103G>A (p.Gln701=) rs63750603
NM_000249.3(MLH1):c.2152C>T (p.His718Tyr) rs2020873
NM_000249.3(MLH1):c.2197C>T (p.His733Tyr) rs1553665846
NM_000249.3(MLH1):c.2252_2253delAA (p.Lys751Serfs) rs267607901
NM_000249.3(MLH1):c.244A>G (p.Thr82Ala) rs587778998
NM_000249.3(MLH1):c.301G>A (p.Gly101Ser) rs267607726
NM_000249.3(MLH1):c.304G>A (p.Glu102Lys) rs63750453
NM_000249.3(MLH1):c.306G>A (p.Glu102=) rs63751665
NM_000249.3(MLH1):c.350C>G (p.Thr117Arg) rs63750781
NM_000249.3(MLH1):c.3G>A (p.Met1Ile) rs72481822
NM_000249.3(MLH1):c.474C>T (p.Asn158=) rs4647256
NM_000249.3(MLH1):c.55A>T (p.Ile19Phe) rs63750648
NM_000249.3(MLH1):c.588+11G>C rs4647258
NM_000249.3(MLH1):c.655A>G (p.Ile219Val) rs1799977
NM_000249.3(MLH1):c.85G>T (p.Ala29Ser) rs63750656
NM_000249.3(MLH1):c.918T>A (p.Asn306Lys) rs587779054
NM_000249.3(MLH1):c.931A>G (p.Lys311Glu) rs876658657
NM_000249.3(MLH1):c.955G>A (p.Glu319Lys) rs63750796
NM_000249.3(MLH1):c.977T>C (p.Val326Ala) rs63751049
NM_000251.2(MSH2):c.-68-111C>T rs17224094
NM_000251.2(MSH2):c.-68-157G>C rs138068023
NM_000251.2(MSH2):c.-9G>C rs547444746
NM_000251.2(MSH2):c.1046C>G (p.Pro349Arg) rs587779067
NM_000251.2(MSH2):c.1077-10T>C rs17224360
NM_000251.2(MSH2):c.115C>A (p.Arg39=) rs786202334
NM_000251.2(MSH2):c.1217G>A (p.Arg406Gln) rs146567853
NM_000251.2(MSH2):c.1271A>G (p.His424Arg) rs200429136
NM_000251.2(MSH2):c.1276+11A>G rs189015988
NM_000251.2(MSH2):c.1276+16G>A rs368120695
NM_000251.2(MSH2):c.1276+2T>C rs267607953
NM_000251.2(MSH2):c.1277-16T>C rs368653974
NM_000251.2(MSH2):c.128A>G (p.Tyr43Cys) rs17217723
NM_000251.2(MSH2):c.1311G>T (p.Val437=) rs730881781
NM_000251.2(MSH2):c.1316_1318delCTC (p.Pro439del) rs587779082
NM_000251.2(MSH2):c.1387-8G>T rs187525243
NM_000251.2(MSH2):c.1461C>G (p.Asp487Glu) rs35107951
NM_000251.2(MSH2):c.1462T>G (p.Leu488Val) rs587781314
NM_000251.2(MSH2):c.1488A>G (p.Leu496=) rs267607960
NM_000251.2(MSH2):c.1511-41G>C rs202215396
NM_000251.2(MSH2):c.1511-9A>T rs12998837
NM_000251.2(MSH2):c.1560A>G (p.Gly520=) rs63750820
NM_000251.2(MSH2):c.1563T>C (p.Tyr521=) rs63750330
NM_000251.2(MSH2):c.1571G>C (p.Arg524Pro) rs63751207
NM_000251.2(MSH2):c.1661+12G>A rs3732183
NM_000251.2(MSH2):c.1661+17T>G rs377461923
NM_000251.2(MSH2):c.1662-18T>C rs376235435
NM_000251.2(MSH2):c.1662-9G>A rs17218356
NM_000251.2(MSH2):c.1666T>C (p.Leu556=) rs61756466
NM_000251.2(MSH2):c.1690A>G (p.Thr564Ala) rs55778204
NM_000251.2(MSH2):c.1730T>C (p.Ile577Thr) rs63749910
NM_000251.2(MSH2):c.1737A>G (p.Lys579=) rs61756467
NM_000251.2(MSH2):c.1760-16T>G rs768370188
NM_000251.2(MSH2):c.1774A>G (p.Met592Val) rs371614039
NM_000251.2(MSH2):c.1787A>G (p.Asn596Ser) rs41295288
NM_000251.2(MSH2):c.182A>C (p.Gln61Pro) rs587779113
NM_000251.2(MSH2):c.1854A>G (p.Pro618=) rs786203744
NM_000251.2(MSH2):c.1886A>G (p.Gln629Arg) rs61756468
NM_000251.2(MSH2):c.1915C>T (p.His639Tyr) rs28929484
NM_000251.2(MSH2):c.1963G>A (p.Val655Ile) rs549467183
NM_000251.2(MSH2):c.1979A>G (p.Asp660Gly) rs1085308057
NM_000251.2(MSH2):c.198C>T (p.Tyr66=) rs730881784
NM_000251.2(MSH2):c.1A>C (p.Met1Leu) rs267607911
NM_000251.2(MSH2):c.2005+8dupA rs267607992
NM_000251.2(MSH2):c.2006-4G>A rs369853630
NM_000251.2(MSH2):c.2006-6T>C rs2303428
NM_000251.2(MSH2):c.2074G>T (p.Gly692Trp) rs63750232
NM_000251.2(MSH2):c.211+8C>T rs267607916
NM_000251.2(MSH2):c.211+9C>G rs2303426
NM_000251.2(MSH2):c.212-4delT rs746333570
NM_000251.2(MSH2):c.2120G>A (p.Cys707Tyr) rs373226409
NM_000251.2(MSH2):c.2139G>T (p.Gly713=) rs63750003
NM_000251.2(MSH2):c.213A>G (p.Gly71=) rs878853808
NM_000251.2(MSH2):c.2205C>T (p.Ile735=) rs533553381
NM_000251.2(MSH2):c.2210+11_2210+22delCTCCTAGTCCCT rs730881782
NM_000251.2(MSH2):c.2211-5T>G rs368596736
NM_000251.2(MSH2):c.2211-6C>A rs267608003
NM_000251.2(MSH2):c.2308A>G (p.Ile770Val) rs63750684
NM_000251.2(MSH2):c.23C>T (p.Thr8Met) rs17217716
NM_000251.2(MSH2):c.2400A>G (p.Leu800=) rs201298777
NM_000251.2(MSH2):c.2437A>G (p.Met813Val) rs63749841
NM_000251.2(MSH2):c.2458+8C>G rs189025757
NM_000251.2(MSH2):c.2500G>A (p.Ala834Thr) rs63750757
NM_000251.2(MSH2):c.2503A>C (p.Asn835His) rs41295296
NM_000251.2(MSH2):c.2576_2584delAATCGCAAG (p.Glu859_Gln861del) rs587781278
NM_000251.2(MSH2):c.2615A>G (p.Lys872Arg) rs587780686
NM_000251.2(MSH2):c.2714C>G (p.Thr905Arg) rs267608022
NM_000251.2(MSH2):c.2732T>G (p.Leu911Arg) rs41295182
NM_000251.2(MSH2):c.274C>G (p.Leu92Val) rs587779154
NM_000251.2(MSH2):c.2766T>C (p.Phe922=) rs55859129
NM_000251.2(MSH2):c.2785C>T (p.Arg929Ter) rs551060742
NM_000251.2(MSH2):c.2802G>A (p.Thr934=) rs150259097
NM_000251.2(MSH2):c.301_306delGAAGTT (p.Glu101_Val102del) rs587779157
NM_000251.2(MSH2):c.304G>A (p.Val102Ile) rs193922373
NM_000251.2(MSH2):c.317G>A (p.Arg106Lys) rs41295286
NM_000251.2(MSH2):c.336C>A (p.Ser112=) rs34312619
NM_000251.2(MSH2):c.339G>A (p.Lys113=) rs35898375
NM_000251.2(MSH2):c.367-19A>T rs730881783
NM_000251.2(MSH2):c.380A>G (p.Asn127Ser) rs17217772
NM_000251.2(MSH2):c.399C>T (p.Asp133=) rs61756462
NM_000251.2(MSH2):c.435T>G (p.Ile145Met) rs63750124
NM_000251.2(MSH2):c.438T>C (p.Gly146=) rs587779161
NM_000251.2(MSH2):c.459C>T (p.Ser153=) rs63751065
NM_000251.2(MSH2):c.471C>A (p.Gly157=) rs61756463
NM_000251.2(MSH2):c.482T>A (p.Val161Asp) rs63750126
NM_000251.2(MSH2):c.484G>A (p.Gly162Arg) rs63750624
NM_000251.2(MSH2):c.499G>C (p.Asp167His) rs63750255
NM_000251.2(MSH2):c.4G>A (p.Ala2Thr) rs63750466
NM_000251.2(MSH2):c.505A>G (p.Ile169Val) rs63750716
NM_000251.2(MSH2):c.557A>G (p.Asn186Ser) rs151129360
NM_000251.2(MSH2):c.55T>C (p.Phe19Leu) rs141711342
NM_000251.2(MSH2):c.573C>T (p.Leu191=) rs1800151
NM_000251.2(MSH2):c.646-3T>C rs267607930
NM_000251.2(MSH2):c.6G>T (p.Ala2=) rs368270856
NM_000251.2(MSH2):c.762T>C (p.Asn254=) rs587779180
NM_000251.2(MSH2):c.766G>A (p.Ala256Thr) rs377403073
NM_000251.2(MSH2):c.792+5A>G rs267607935
NM_000251.2(MSH2):c.815C>T (p.Ala272Val) rs34136999
NM_000251.2(MSH2):c.885C>G (p.Asp295Glu) rs201334592
NM_000251.2(MSH2):c.888C>G (p.Phe296Leu) rs876659918
NM_000251.2(MSH2):c.943-2A>G rs587779198
NM_000251.2(MSH2):c.965G>A (p.Gly322Asp) rs4987188
NM_000251.2(MSH2):c.972G>A (p.Gln324=) rs63750505
NM_000251.2(MSH2):c.984C>T (p.Ala328=) rs4987189
NM_000251.2(MSH2):c.991A>G (p.Asn331Asp) rs267607938
NM_000251.2(MSH2):c.998G>A (p.Cys333Tyr) rs63750828
NM_000535.5(PMS2):c.2182A>G (p.Thr728Ala) rs141893001
NM_000535.5(PMS2):c.2186_2187delTC (p.Leu729Glnfs) rs587779335
NM_000535.6(PMS2):c.1408C>T (p.Pro470Ser) rs1805321
NM_000535.6(PMS2):c.1688G>T (p.Arg563Leu) rs63750668
NM_000535.6(PMS2):c.1789A>T (p.Thr597Ser) rs1805318
NM_000535.6(PMS2):c.1831dup (p.Ile611Asnfs) rs63750250
NM_000535.6(PMS2):c.1A>G (p.Met1Val) rs587779333
NM_000535.6(PMS2):c.2007-4G>A rs1805326
NM_000535.6(PMS2):c.2012C>T (p.Thr671Met) rs587780046
NM_000535.6(PMS2):c.2113G>A (p.Glu705Lys) rs267608161
NM_000535.6(PMS2):c.2253T>C (p.Phe751=) rs1805325
NM_000535.6(PMS2):c.2324A>G (p.Asn775Ser) rs17420802
NM_000535.6(PMS2):c.2570G>C (p.Gly857Ala) rs1802683
NM_000535.6(PMS2):c.52A>G (p.Ile18Val) rs63750123
NM_000535.6(PMS2):c.59G>A (p.Arg20Gln) rs10254120
NM_002354.2(EPCAM):c.344T>C (p.Met115Thr) rs1126497
NM_002878.3(RAD51D):c.493C>T (p.Arg165Trp) rs544654228

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