ClinVar Miner

Variants with conflicting interpretations studied for Lynch syndrome

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

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
4858 549 0 90 55 0 10 153

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 pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 66 4 0 0
likely pathogenic 66 0 6 0 0
uncertain significance 4 6 0 50 7
likely benign 0 0 50 0 24
benign 0 0 7 24 0

Condition to condition summary #

Total conditions: 1
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 4858 549 0 90 55 0 10 153

All variants with conflicting interpretations #

Total variants: 153
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000535.7(PMS2):c.2466T>C (p.Leu822=) rs10000 0.11353
NM_000249.4(MLH1):c.2152C>T (p.His718Tyr) rs2020873 0.02345
NM_000249.4(MLH1):c.589-15C>T rs55658850 0.00548
NM_000251.3(MSH2):c.339G>A (p.Lys113=) rs35898375 0.00313
NM_000249.4(MLH1):c.1963A>G (p.Ile655Val) rs55907433 0.00297
NM_000535.7(PMS2):c.383C>T (p.Ser128Leu) rs116373169 0.00177
NM_000179.3(MSH6):c.431G>T (p.Ser144Ile) rs3211299 0.00158
NM_000251.3(MSH2):c.1737A>G (p.Lys579=) rs61756467 0.00138
NM_000249.4(MLH1):c.1217G>A (p.Ser406Asn) rs41294980 0.00081
NM_000535.7(PMS2):c.2149G>A (p.Val717Met) rs201671325 0.00072
NM_000535.7(PMS2):c.86G>C (p.Gly29Ala) rs146176004 0.00059
NM_000179.3(MSH6):c.1508C>G (p.Ser503Cys) rs63750897 0.00056
NM_000249.4(MLH1):c.198C>T (p.Thr66=) rs61751642 0.00040
NM_000249.4(MLH1):c.977T>C (p.Val326Ala) rs63751049 0.00037
NM_000251.3(MSH2):c.1680T>C (p.Asn560=) rs200056411 0.00032
NM_000251.3(MSH2):c.815C>T (p.Ala272Val) rs34136999 0.00032
NM_000179.3(MSH6):c.3217C>T (p.Pro1073Ser) rs142254875 0.00027
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) rs17420802 0.00025
NM_000535.7(PMS2):c.379G>A (p.Ala127Thr) rs114090343 0.00024
NM_000249.4(MLH1):c.2101C>A (p.Gln701Lys) rs63750114 0.00021
NM_000179.3(MSH6):c.73G>T (p.Ala25Ser) rs267608026 0.00019
NM_000535.7(PMS2):c.137G>T (p.Ser46Ile) rs121434629 0.00018
NM_000179.3(MSH6):c.2398G>C (p.Val800Leu) rs61748083 0.00014
NM_000179.3(MSH6):c.1081C>T (p.Arg361Cys) rs587782651 0.00012
NM_000251.3(MSH2):c.2785C>T (p.Arg929Ter) rs551060742 0.00011
NM_000179.3(MSH6):c.942C>G (p.Ser314Arg) rs150440246 0.00009
NM_000535.7(PMS2):c.857A>G (p.Asp286Gly) rs116788608 0.00009
NM_000251.3(MSH2):c.2500G>A (p.Ala834Thr) rs63750757 0.00008
NM_000535.7(PMS2):c.993C>T (p.Cys331=) rs186577215 0.00008
NM_000535.7(PMS2):c.384G>A (p.Ser128=) rs371342884 0.00007
NM_000249.4(MLH1):c.1733A>G (p.Glu578Gly) rs63751612 0.00006
NM_000249.4(MLH1):c.1128T>C (p.Asp376=) rs267607824 0.00005
NM_000535.7(PMS2):c.-4A>G rs544503598 0.00005
NM_000179.3(MSH6):c.1974G>A (p.Val658=) rs372916347 0.00004
NM_000249.4(MLH1):c.1474G>A (p.Ala492Thr) rs63751145 0.00004
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_000249.4(MLH1):c.116+5G>A rs267607710 0.00003
NM_000249.4(MLH1):c.94A>G (p.Ile32Val) rs2020872 0.00003
NM_000249.4(MLH1):c.9C>G (p.Phe3Leu) rs779759678 0.00003
NM_000535.7(PMS2):c.1616C>T (p.Ala539Val) rs138222146 0.00003
NM_000535.7(PMS2):c.2113G>A (p.Glu705Lys) rs267608161 0.00003
NM_000179.3(MSH6):c.3226C>T (p.Arg1076Cys) rs63750617 0.00002
NM_000179.3(MSH6):c.3801+4T>C rs758830540 0.00002
NM_000179.3(MSH6):c.3832C>A (p.Pro1278Thr) rs587782109 0.00002
NM_000249.4(MLH1):c.303T>G (p.Gly101=) rs4647220 0.00002
NM_000251.3(MSH2):c.304G>A (p.Val102Ile) rs193922373 0.00002
NM_000179.3(MSH6):c.1168G>A (p.Asp390Asn) rs147737737 0.00001
NM_000179.3(MSH6):c.1347G>A (p.Leu449=) rs786201760 0.00001
NM_000179.3(MSH6):c.1403G>A (p.Arg468His) rs41295268 0.00001
NM_000179.3(MSH6):c.148T>C (p.Trp50Arg) rs374597395 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.3563G>A (p.Ser1188Asn) rs587779272 0.00001
NM_000179.3(MSH6):c.3605T>C (p.Met1202Thr) rs587779273 0.00001
NM_000179.3(MSH6):c.3647-7T>G rs780269667 0.00001
NM_000179.3(MSH6):c.4002-4T>C rs370428032 0.00001
NM_000179.3(MSH6):c.892C>T (p.Arg298Ter) rs146816935 0.00001
NM_000249.4(MLH1):c.1103C>T (p.Ser368Leu) rs201673334 0.00001
NM_000249.4(MLH1):c.1652A>G (p.Asn551Ser) rs63750271 0.00001
NM_000251.3(MSH2):c.1270C>T (p.His424Tyr) rs587782278 0.00001
NM_000251.3(MSH2):c.164G>A (p.Arg55Gln) rs748196422 0.00001
NM_000251.3(MSH2):c.212-3A>T rs879255341 0.00001
NM_000251.3(MSH2):c.763A>G (p.Ser255Gly) rs761529282 0.00001
NM_000535.7(PMS2):c.1144+1G>A rs373885654 0.00001
NM_000535.7(PMS2):c.1398C>T (p.Gly466=) rs752666485 0.00001
NM_000535.7(PMS2):c.1420G>T (p.Ala474Ser) rs373114291 0.00001
NM_000535.7(PMS2):c.1765G>C (p.Asp589His) rs749727182 0.00001
NM_000535.7(PMS2):c.2404C>T (p.Arg802Ter) rs63751466 0.00001
NM_000535.7(PMS2):c.248T>G (p.Leu83Ter) rs1064794083 0.00001
NM_000535.7(PMS2):c.251-2A>T rs587779340 0.00001
NM_000535.7(PMS2):c.33T>A (p.Pro11=) rs780178572 0.00001
MSH6:c.3647-51_3647-35del17 rs267607687
NC_000002.12:g.(?_47482779)_(47482949_?)del
NM_000179.3(MSH6):c.1109T>C (p.Leu370Ser) rs587779204
NM_000179.3(MSH6):c.1352del (p.Phe451fs) rs869312769
NM_000179.3(MSH6):c.1615CTT[1] (p.Leu540del) rs1064793600
NM_000179.3(MSH6):c.1740G>T (p.Ser580=) rs762089407
NM_000179.3(MSH6):c.184C>A (p.Arg62Ser) rs876659508
NM_000179.3(MSH6):c.2161A>C (p.Arg721=) rs537604099
NM_000179.3(MSH6):c.2314C>T (p.Arg772Trp) rs63750138
NM_000179.3(MSH6):c.2419G>T (p.Glu807Ter) rs587779923
NM_000179.3(MSH6):c.2535dup (p.Glu846Ter) rs587779241
NM_000179.3(MSH6):c.2983G>T (p.Glu995Ter) rs63750258
NM_000179.3(MSH6):c.3029C>T (p.Thr1010Ile) rs768925694
NM_000179.3(MSH6):c.3108_3109del (p.Phe1037fs) rs1553414519
NM_000179.3(MSH6):c.3172+1G>T rs587779255
NM_000179.3(MSH6):c.3173-1G>C rs397515875
NM_000179.3(MSH6):c.3227G>A (p.Arg1076His) rs779617676
NM_000179.3(MSH6):c.3238_3239del (p.Leu1080fs) rs863225406
NM_000179.3(MSH6):c.3246G>C (p.Pro1082=) rs3136351
NM_000179.3(MSH6):c.3261dup (p.Phe1088fs) rs267608078
NM_000179.3(MSH6):c.3439-2A>G rs267608098
NM_000179.3(MSH6):c.3463C>T (p.Gln1155Ter) rs1553332166
NM_000179.3(MSH6):c.3619_3620del (p.His1207fs) rs1572741984
NM_000179.3(MSH6):c.3632T>C (p.Leu1211Pro) rs864622041
NM_000179.3(MSH6):c.3724_3726del (p.Arg1242del) rs63749942
NM_000179.3(MSH6):c.3920_3923dup (p.Pro1309fs) rs1572747278
NM_000179.3(MSH6):c.3939_3940dup (p.Gln1314fs) rs730881830
NM_000179.3(MSH6):c.4001+2T>C rs267608131
NM_000179.3(MSH6):c.4001G>A (p.Arg1334Gln) rs267608122
NM_000179.3(MSH6):c.4001G>C (p.Arg1334Pro) rs267608122
NM_000179.3(MSH6):c.4002-10del rs59056100
NM_000179.3(MSH6):c.4002-8dup rs267608139
NM_000249.3(MLH1):c.2104_2105delAG rs63751651
NM_000249.4(MLH1):c.1011dup (p.Asn338fs) rs63750677
NM_000249.4(MLH1):c.1039-2A>G rs267607815
NM_000249.4(MLH1):c.1136A>G (p.Tyr379Cys) rs143009528
NM_000249.4(MLH1):c.116+1G>A rs267607709
NM_000249.4(MLH1):c.1409+1G>A rs267607825
NM_000249.4(MLH1):c.1410-2_1410-1delinsCC rs1559558071
NM_000249.4(MLH1):c.1558+1G>A rs267607832
NM_000249.4(MLH1):c.1559-1G>C rs267607837
NM_000249.4(MLH1):c.156del (p.Glu53fs) rs63750028
NM_000249.4(MLH1):c.1668-1G>A rs267607845
NM_000249.4(MLH1):c.1731+1G>C rs267607853
NM_000249.4(MLH1):c.1897-2A>G rs267607871
NM_000249.4(MLH1):c.1989+1G>T rs267607879
NM_000249.4(MLH1):c.2250C>G (p.Tyr750Ter) rs267607893
NM_000249.4(MLH1):c.2262del (p.Arg755fs) rs267607904
NM_000249.4(MLH1):c.306G>T (p.Glu102Asp) rs63751665
NM_000249.4(MLH1):c.453+1G>T rs267607750
NM_000249.4(MLH1):c.791-2A>G rs267607794
NM_000249.4(MLH1):c.793C>A (p.Arg265Ser) rs63751194
NM_000249.4(MLH1):c.836T>G (p.Val279Gly) rs1553646683
NM_000249.4(MLH1):c.860del (p.Asn287fs) rs63750034
NM_000249.4(MLH1):c.885-2A>G rs267607805
NM_000251.2(MSH2):c.646-?_792+?del
NM_000251.3(MSH2):c.1077-1G>T rs267607944
NM_000251.3(MSH2):c.1251_1268delinsAGTT (p.Ile418fs) rs863225388
NM_000251.3(MSH2):c.1276+1G>A rs267607950
NM_000251.3(MSH2):c.1277-1G>A rs267607948
NM_000251.3(MSH2):c.1386+1G>A rs267607957
NM_000251.3(MSH2):c.1511-1G>A rs267607964
NM_000251.3(MSH2):c.1587del (p.Glu530fs) rs63750845
NM_000251.3(MSH2):c.1661+1G>T rs267607969
NM_000251.3(MSH2):c.2021G>A (p.Gly674Asp) rs267607996
NM_000251.3(MSH2):c.2210+1G>A rs267608002
NM_000251.3(MSH2):c.2211-2A>T rs267608001
NM_000251.3(MSH2):c.2335dup (p.Met779fs) rs63750149
NM_000251.3(MSH2):c.2634+1G>A rs267608019
NM_000251.3(MSH2):c.2634+1G>T rs267608019
NM_000251.3(MSH2):c.301_306del (p.Glu101_Val102del) rs587779157
NM_000251.3(MSH2):c.366+1G>T rs267607924
NM_000251.3(MSH2):c.403C>G (p.Leu135Val) rs193096019
NM_000251.3(MSH2):c.593A>G (p.Glu198Gly) rs63750327
NM_000251.3(MSH2):c.793-2A>C rs267607933
NM_000251.3(MSH2):c.943-1G>T rs12476364
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu) rs63750668
NM_000535.7(PMS2):c.1778del (p.Lys593fs) rs766389591
NM_000535.7(PMS2):c.299A>G (p.Gln100Arg) rs747771951
NM_000535.7(PMS2):c.830C>A (p.Thr277Lys) rs1805322
Single allele

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