ClinVar Miner

Variants with conflicting interpretations studied for Lynch syndrome 5

Coded as:
Minimum review status of the submission for Lynch syndrome 5: Collection method of the submission for Lynch syndrome 5:
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
1090 194 0 103 94 0 5 186

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 5 pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 35 1 0 0
likely pathogenic 35 0 4 0 0
uncertain significance 2 4 0 77 29
likely benign 0 0 76 0 63
benign 0 0 30 66 0

Condition to condition summary #

Total conditions: 2
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 5 1102 188 0 96 91 0 5 180
Lynch syndrome 1 0 17 0 11 8 0 2 17

All variants with conflicting interpretations #

Total variants: 186
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) rs1042821 0.18742
NM_000179.3(MSH6):c.1164C>T (p.His388=) rs55708305 0.01384
NM_000179.3(MSH6):c.2272C>T (p.Leu758=) rs56371757 0.01363
NM_000179.3(MSH6):c.1186C>G (p.Leu396Val) rs2020908 0.00565
NM_000179.3(MSH6):c.2633T>C (p.Val878Ala) rs2020912 0.00448
NM_000179.3(MSH6):c.457+13A>G rs1800933 0.00434
NM_000179.3(MSH6):c.431G>T (p.Ser144Ile) rs3211299 0.00158
NM_000179.3(MSH6):c.3647-6T>A rs182871847 0.00134
NM_000179.3(MSH6):c.984C>T (p.Ser328=) rs138143769 0.00101
NM_000179.3(MSH6):c.1526T>C (p.Val509Ala) rs63751005 0.00067
NM_000179.3(MSH6):c.1665A>G (p.Ala555=) rs146785465 0.00066
NM_000179.3(MSH6):c.1869C>T (p.Pro623=) rs141242295 0.00058
NM_000179.3(MSH6):c.2667G>T (p.Gln889His) rs149945495 0.00048
NM_000179.3(MSH6):c.491A>C (p.His164Pro) rs146469162 0.00045
NM_000179.3(MSH6):c.3960A>G (p.Ala1320=) rs373425206 0.00042
NM_000179.3(MSH6):c.1449G>T (p.Val483=) rs35590297 0.00037
NM_000179.3(MSH6):c.1932G>C (p.Arg644Ser) rs34938432 0.00037
NM_000179.3(MSH6):c.2561A>T (p.Lys854Met) rs34374438 0.00036
NM_000179.3(MSH6):c.4002-10T>A rs545466048 0.00026
NM_000179.3(MSH6):c.3961A>G (p.Arg1321Gly) rs41295278 0.00019
NM_000179.3(MSH6):c.2925C>T (p.Asn975=) rs139026662 0.00016
NM_000179.3(MSH6):c.3160A>T (p.Ile1054Phe) rs267608075 0.00016
NM_000179.3(MSH6):c.2398G>C (p.Val800Leu) rs61748083 0.00014
NM_000179.3(MSH6):c.884A>G (p.Lys295Arg) rs267608051 0.00014
NM_000179.3(MSH6):c.187T>C (p.Ser63Pro) rs763702846 0.00013
NM_000179.3(MSH6):c.59C>T (p.Ala20Val) rs63750664 0.00013
NM_000179.3(MSH6):c.650A>G (p.Asp217Gly) rs554012110 0.00013
NM_000179.3(MSH6):c.124C>T (p.Pro42Ser) rs34014629 0.00011
NM_000179.3(MSH6):c.3674C>T (p.Thr1225Met) rs63750370 0.00011
NM_000179.3(MSH6):c.628-7C>A rs373129248 0.00011
NM_000179.3(MSH6):c.1875C>T (p.Ser625=) rs63749886 0.00010
NM_000179.3(MSH6):c.2417C>G (p.Ser806Cys) rs372990379 0.00010
NM_000179.3(MSH6):c.3788G>A (p.Arg1263His) rs147852216 0.00010
NM_000179.3(MSH6):c.1063G>A (p.Gly355Ser) rs587778531 0.00009
NM_000179.3(MSH6):c.1730G>A (p.Arg577His) rs376220212 0.00009
NM_000179.3(MSH6):c.3727A>T (p.Thr1243Ser) rs147453999 0.00009
NM_000179.3(MSH6):c.2281A>G (p.Arg761Gly) rs199876321 0.00008
NM_000179.3(MSH6):c.2384T>C (p.Ile795Thr) rs202127474 0.00007
NM_000179.3(MSH6):c.1019T>C (p.Phe340Ser) rs61753793 0.00006
NM_000179.3(MSH6):c.1050C>T (p.Ala350=) rs730881802 0.00006
NM_000179.3(MSH6):c.178T>C (p.Leu60=) rs35819209 0.00006
NM_000179.3(MSH6):c.3283C>T (p.Arg1095Cys) rs376243329 0.00006
NM_000179.3(MSH6):c.3478G>A (p.Val1160Ile) rs376799914 0.00006
NM_000179.3(MSH6):c.3824G>A (p.Cys1275Tyr) rs150990541 0.00006
NM_000179.3(MSH6):c.3986C>T (p.Ser1329Leu) rs199594809 0.00006
NM_000179.3(MSH6):c.643G>A (p.Val215Ile) rs145959653 0.00006
NM_000179.3(MSH6):c.1746T>G (p.Phe582Leu) rs201518545 0.00005
NM_000179.3(MSH6):c.1844G>C (p.Cys615Ser) rs730881793 0.00005
NM_000179.3(MSH6):c.3399T>C (p.Thr1133=) rs61748084 0.00005
NM_000179.3(MSH6):c.3513T>C (p.Asp1171=) rs63749834 0.00005
NM_000179.3(MSH6):c.3762A>T (p.Glu1254Asp) rs375459388 0.00005
NM_000179.3(MSH6):c.3852G>A (p.Thr1284=) rs2229018 0.00005
NM_000179.3(MSH6):c.107C>T (p.Ala36Val) rs61756469 0.00004
NM_000179.3(MSH6):c.1364A>C (p.Asn455Thr) rs200938360 0.00004
NM_000179.3(MSH6):c.2408A>G (p.Asp803Gly) rs63751450 0.00004
NM_000179.3(MSH6):c.242C>T (p.Ala81Val) rs587779924 0.00004
NM_000179.3(MSH6):c.2597A>C (p.Lys866Thr) rs190075874 0.00004
NM_000179.3(MSH6):c.2904C>G (p.Val968=) rs150683226 0.00004
NM_000179.3(MSH6):c.364G>A (p.Glu122Lys) rs143036974 0.00004
NM_000179.3(MSH6):c.3729A>G (p.Thr1243=) rs773807182 0.00004
NM_000179.3(MSH6):c.3801+5G>A rs201080919 0.00004
NM_000179.3(MSH6):c.4004A>C (p.Glu1335Ala) rs564434147 0.00004
NM_000179.3(MSH6):c.749T>C (p.Val250Ala) rs587781275 0.00004
NM_000179.3(MSH6):c.972A>C (p.Lys324Asn) rs876658610 0.00004
NM_000179.3(MSH6):c.-8C>T rs565211544 0.00003
NM_000179.3(MSH6):c.1696G>A (p.Gly566Arg) rs63749973 0.00003
NM_000179.3(MSH6):c.2319C>T (p.Leu773=) rs63749895 0.00003
NM_000179.3(MSH6):c.240A>G (p.Val80=) rs864622281 0.00003
NM_000179.3(MSH6):c.3071G>A (p.Arg1024Gln) rs372705506 0.00003
NM_000179.3(MSH6):c.3284G>A (p.Arg1095His) rs63750253 0.00003
NM_000179.3(MSH6):c.3426G>A (p.Thr1142=) rs747771350 0.00003
NM_000179.3(MSH6):c.3787C>T (p.Arg1263Cys) rs367912290 0.00003
NM_000179.3(MSH6):c.393A>C (p.Val131=) rs752488540 0.00003
NM_000179.3(MSH6):c.4002-14T>C rs587781041 0.00003
NM_000179.3(MSH6):c.10C>T (p.Gln4Ter) rs786201042 0.00002
NM_000179.3(MSH6):c.2241G>A (p.Leu747=) rs377722465 0.00002
NM_000179.3(MSH6):c.2508C>T (p.Asn836=) rs758170249 0.00002
NM_000179.3(MSH6):c.2511C>G (p.His837Gln) rs587779925 0.00002
NM_000179.3(MSH6):c.2664G>C (p.Lys888Asn) rs730881798 0.00002
NM_000179.3(MSH6):c.321T>C (p.Pro107=) rs730881823 0.00002
NM_000179.3(MSH6):c.3244C>T (p.Pro1082Ser) rs186240214 0.00002
NM_000179.3(MSH6):c.3851C>T (p.Thr1284Met) rs63750836 0.00002
NM_000179.3(MSH6):c.4062G>T (p.Leu1354=) rs863224335 0.00002
NM_000179.3(MSH6):c.1061G>T (p.Gly354Val) rs730881788 0.00001
NM_000179.3(MSH6):c.1106C>T (p.Thr369Ile) rs375974046 0.00001
NM_000179.3(MSH6):c.1170T>C (p.Asp390=) rs55882234 0.00001
NM_000179.3(MSH6):c.1190A>G (p.Tyr397Cys) rs63750065 0.00001
NM_000179.3(MSH6):c.1209C>G (p.Leu403=) rs748603803 0.00001
NM_000179.3(MSH6):c.1346T>C (p.Leu449Pro) rs63750741 0.00001
NM_000179.3(MSH6):c.1599G>C (p.Glu533Asp) rs373726731 0.00001
NM_000179.3(MSH6):c.161G>C (p.Gly54Ala) rs63751098 0.00001
NM_000179.3(MSH6):c.1677C>T (p.Cys559=) rs63749893 0.00001
NM_000179.3(MSH6):c.1740G>A (p.Ser580=) rs762089407 0.00001
NM_000179.3(MSH6):c.1776A>T (p.Val592=) rs56132616 0.00001
NM_000179.3(MSH6):c.1858G>A (p.Gly620Ser) rs876661043 0.00001
NM_000179.3(MSH6):c.1999G>C (p.Asp667His) rs151086192 0.00001
NM_000179.3(MSH6):c.2027A>G (p.Lys676Arg) rs143643688 0.00001
NM_000179.3(MSH6):c.2035T>C (p.Leu679=) rs757741943 0.00001
NM_000179.3(MSH6):c.2057G>A (p.Gly686Asp) rs587779227 0.00001
NM_000179.3(MSH6):c.2154C>T (p.Ser718=) rs771662801 0.00001
NM_000179.3(MSH6):c.2300C>G (p.Thr767Ser) rs587781462 0.00001
NM_000179.3(MSH6):c.2400T>C (p.Val800=) rs267608071 0.00001
NM_000179.3(MSH6):c.2419G>A (p.Glu807Lys) rs587779923 0.00001
NM_000179.3(MSH6):c.2827G>T (p.Asp943Tyr) rs143520357 0.00001
NM_000179.3(MSH6):c.2982C>T (p.Tyr994=) rs367758473 0.00001
NM_000179.3(MSH6):c.3084A>T (p.Ser1028=) rs786201843 0.00001
NM_000179.3(MSH6):c.3198T>C (p.Tyr1066=) rs199643502 0.00001
NM_000179.3(MSH6):c.3233T>C (p.Val1078Ala) rs376452612 0.00001
NM_000179.3(MSH6):c.3255C>G (p.Thr1085=) rs371568610 0.00001
NM_000179.3(MSH6):c.3334G>A (p.Asp1112Asn) rs773955368 0.00001
NM_000179.3(MSH6):c.333C>T (p.Tyr111=) rs786202772 0.00001
NM_000179.3(MSH6):c.3514_3515insAA (p.Arg1172fs) rs63751327 0.00001
NM_000179.3(MSH6):c.363C>T (p.Arg121=) rs587779276 0.00001
NM_000179.3(MSH6):c.3936T>C (p.Val1312=) rs61753796 0.00001
NM_000179.3(MSH6):c.4002-4T>C rs370428032 0.00001
NM_000179.3(MSH6):c.458-17A>G rs554847828 0.00001
NM_000179.3(MSH6):c.533G>A (p.Arg178His) rs786204186 0.00001
NM_000179.3(MSH6):c.87C>G (p.Arg29=) rs778354962 0.00001
NM_000179.3(MSH6):c.1100A>G (p.His367Arg) rs1553412495
NM_000179.3(MSH6):c.125_132dup (p.Gly45fs) rs1553408245
NM_000179.3(MSH6):c.1347G>A (p.Leu449=) rs786201760
NM_000179.3(MSH6):c.1560T>C (p.Gly520=) rs762396230
NM_000179.3(MSH6):c.1634_1635del (p.Lys545fs) rs267608064
NM_000179.3(MSH6):c.1691C>A (p.Ser564Ter) rs864622153
NM_000179.3(MSH6):c.1767del (p.Pro591fs) rs1114167765
NM_000179.3(MSH6):c.1786T>A (p.Phe596Ile) rs587779918
NM_000179.3(MSH6):c.1847C>G (p.Ser616Cys) rs772363120
NM_000179.3(MSH6):c.1866dup (p.Pro623fs) rs2104372581
NM_000179.3(MSH6):c.2092C>T (p.Gln698Ter) rs63750832
NM_000179.3(MSH6):c.215_258del (p.Leu72fs) rs1553408380
NM_000179.3(MSH6):c.2187C>T (p.Ala729=) rs375610656
NM_000179.3(MSH6):c.2194C>A (p.Arg732=) rs63751127
NM_000179.3(MSH6):c.2230dup (p.Glu744fs) rs786201050
NM_000179.3(MSH6):c.2300C>T (p.Thr767Ile) rs587781462
NM_000179.3(MSH6):c.249T>G (p.Ala83=) rs876658308
NM_000179.3(MSH6):c.255C>A (p.Pro85=) rs587779242
NM_000179.3(MSH6):c.2759del (p.Lys920fs) rs1114167794
NM_000179.3(MSH6):c.3013C>T (p.Arg1005Ter) rs63750563
NM_000179.3(MSH6):c.3018C>A (p.Tyr1006Ter) rs1553414395
NM_000179.3(MSH6):c.3037AAG[1] (p.Lys1014del) rs267608073
NM_000179.3(MSH6):c.309C>A (p.Tyr103Ter) rs1553410230
NM_000179.3(MSH6):c.3104G>A (p.Arg1035Gln) rs730881801
NM_000179.3(MSH6):c.3111C>A (p.Phe1037Leu) rs587781673
NM_000179.3(MSH6):c.3151G>A (p.Val1051Ile) rs576269342
NM_000179.3(MSH6):c.3173-10_3173-6del rs781520783
NM_000179.3(MSH6):c.3173-18T>C rs189672273
NM_000179.3(MSH6):c.3188T>G (p.Leu1063Arg) rs1060502901
NM_000179.3(MSH6):c.3215_3222del (p.Gly1072fs) rs1057517552
NM_000179.3(MSH6):c.3246G>A (p.Pro1082=) rs3136351
NM_000179.3(MSH6):c.3246G>C (p.Pro1082=) rs3136351
NM_000179.3(MSH6):c.3246G>T (p.Pro1082=) rs3136351
NM_000179.3(MSH6):c.3259C>A (p.Pro1087Thr) rs63750998
NM_000179.3(MSH6):c.3259C>G (p.Pro1087Ala) rs63750998
NM_000179.3(MSH6):c.3261C>T (p.Pro1087=) rs370226185
NM_000179.3(MSH6):c.3261dup (p.Phe1088fs) rs267608078
NM_000179.3(MSH6):c.3354G>A (p.Glu1118=) rs35642130
NM_000179.3(MSH6):c.3371dup (p.Asn1124fs) rs1553331659
NM_000179.3(MSH6):c.3416G>A (p.Gly1139Asp) rs1316409501
NM_000179.3(MSH6):c.3439-1G>T rs587779263
NM_000179.3(MSH6):c.3439-2A>G rs267608098
NM_000179.3(MSH6):c.3478G>T (p.Val1160Phe) rs376799914
NM_000179.3(MSH6):c.3640G>T (p.Glu1214Ter)
NM_000179.3(MSH6):c.3646+1G>A rs1553332772
NM_000179.3(MSH6):c.3647-1G>A rs587779279
NM_000179.3(MSH6):c.3753_3756dup (p.Val1253fs) rs876661222
NM_000179.3(MSH6):c.3758T>C (p.Val1253Ala) rs202066386
NM_000179.3(MSH6):c.3792A>C (p.Leu1264=) rs786202051
NM_000179.3(MSH6):c.3802-8T>G rs864622195
NM_000179.3(MSH6):c.3836G>A (p.Ser1279Asn) rs864622400
NM_000179.3(MSH6):c.3840_3846del (p.Glu1281fs) rs63751319
NM_000179.3(MSH6):c.3852G>T (p.Thr1284=) rs2229018
NM_000179.3(MSH6):c.3922_3938dup (p.Gln1314fs) rs1670123011
NM_000179.3(MSH6):c.3980_3983dup (p.Leu1330fs) rs1553333738
NM_000179.3(MSH6):c.3996_3999dup (p.Arg1334fs) rs1553333753
NM_000179.3(MSH6):c.4001+2TAAC[2] rs267608132
NM_000179.3(MSH6):c.4001+4_4001+8dup rs587782853
NM_000179.3(MSH6):c.4001G>A (p.Arg1334Gln) rs267608122
NM_000179.3(MSH6):c.4002-11_4002-10delinsA rs1553333946
NM_000179.3(MSH6):c.4068_4071dup (p.Lys1358delinsAspTer) rs55740729
NM_000179.3(MSH6):c.457+32TG[12] rs397839804
NM_000179.3(MSH6):c.578del (p.Leu193fs) rs587782281
NM_000179.3(MSH6):c.718C>T (p.Arg240Ter) rs63750019
NM_000179.3(MSH6):c.741dup (p.Arg248fs) rs267608041
NM_000179.3(MSH6):c.843_844insAC (p.Val282fs)
NM_000179.3(MSH6):c.905G>C (p.Arg302Thr) rs587781510
NM_000179.3(MSH6):c.908dup (p.Met303fs) rs1057517551

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