Variants with conflicting interpretations studied for Lynch syndrome 4

Minimum review status of the submission for Lynch syndrome 4:		Collection method of the submission for Lynch syndrome 4:
Minimum review status of the other submission:		Collection method of the other submission:
Minimum conflict level: Report conflict between different conditions
Show significances as they were submitted (without aggregation into standard terms)

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
1593	187	1	117	41	0	11	159

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 4		pathogenic	likely pathogenic	uncertain significance	likely benign	benign
	pathogenic	0	72	3	0	0
	likely pathogenic	72	0	10	0	0
	uncertain significance	3	10	1	35	15
	likely benign	0	0	35	0	45
	benign	0	0	15	45	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 4	1593	187	1	117	41	0	11	159

All variants with conflicting interpretations #

Total variants: 159

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HGVS	dbSNP	gnomAD frequency
NM_000535.7(PMS2):c.59G>A (p.Arg20Gln)	rs10254120	0.07451
NM_000535.7(PMS2):c.1532C>T (p.Thr511Met)	rs74902811	0.02492
NM_000535.7(PMS2):c.1488C>T (p.His496=)	rs1805320	0.02307
NM_000535.7(PMS2):c.1531A>G (p.Thr511Ala)	rs2228007	0.02174
NM_000535.7(PMS2):c.1866G>A (p.Met622Ile)	rs1805324	0.01574
NM_000535.7(PMS2):c.1789A>T (p.Thr597Ser)	rs1805318	0.01006
NM_000535.7(PMS2):c.1557T>C (p.Tyr519=)	rs6972869	0.00992
NM_000535.7(PMS2):c.52A>G (p.Ile18Val)	rs63750123	0.00861
NM_000535.7(PMS2):c.1711C>A (p.Leu571Ile)	rs63750055	0.00784
NM_000535.7(PMS2):c.1569C>G (p.Ser523=)	rs141458772	0.00560
NM_000535.7(PMS2):c.1609G>A (p.Glu537Lys)	rs115052399	0.00370
NM_000535.7(PMS2):c.1266G>A (p.Glu422=)	rs138049175	0.00333
NM_000535.7(PMS2):c.2350G>A (p.Asp784Asn)	rs143340522	0.00192
NM_000535.7(PMS2):c.23+10G>C	rs192027828	0.00182
NM_000535.7(PMS2):c.383C>T (p.Ser128Leu)	rs116373169	0.00177
NM_000535.7(PMS2):c.2523G>A (p.Trp841Ter)	rs587780057	0.00174
NM_000535.7(PMS2):c.353+9A>C	rs139990791	0.00100
NM_000535.7(PMS2):c.2253T>C (p.Phe751=)	rs1805325	0.00094
NM_000535.7(PMS2):c.180C>G (p.Asp60Glu)	rs200313585	0.00085
NM_000535.7(PMS2):c.2187C>G (p.Leu729=)	rs373630535	0.00083
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_000535.7(PMS2):c.1708A>G (p.Asn570Asp)	rs115670442	0.00048
NM_000535.7(PMS2):c.936G>A (p.Met312Ile)	rs139194813	0.00041
NM_000535.7(PMS2):c.1268C>G (p.Ala423Gly)	rs756883400	0.00038
NM_000535.7(PMS2):c.1560G>A (p.Ala520=)	rs201167814	0.00038
NM_000535.7(PMS2):c.379G>A (p.Ala127Thr)	rs114090343	0.00024
NM_000535.7(PMS2):c.1567T>A (p.Ser523Thr)	rs63751132	0.00021
NM_000535.7(PMS2):c.953A>G (p.Tyr318Cys)	rs139438201	0.00019
NM_000535.7(PMS2):c.137G>T (p.Ser46Ile)	rs121434629	0.00018
NM_000535.7(PMS2):c.2012C>T (p.Thr671Met)	rs587780046	0.00017
NM_000535.7(PMS2):c.53T>C (p.Ile18Thr)	rs201343342	0.00016
NM_000535.7(PMS2):c.255G>A (p.Leu85=)	rs200491279	0.00013
NM_000535.7(PMS2):c.1533G>A (p.Thr511=)	rs542520309	0.00011
NM_000535.7(PMS2):c.1689A>G (p.Arg563=)	rs551226281	0.00011
NM_000535.7(PMS2):c.1714G>A (p.Ala572Thr)	rs63751023	0.00011
NM_000535.7(PMS2):c.2276-10A>G	rs573900018	0.00010
NM_000535.7(PMS2):c.1980C>T (p.Ala660=)	rs368928783	0.00009
NM_000535.7(PMS2):c.857A>G (p.Asp286Gly)	rs116788608	0.00009
NM_000535.7(PMS2):c.2127C>T (p.Phe709=)	rs199943748	0.00008
NM_000535.7(PMS2):c.1490G>A (p.Gly497Asp)	rs199739859	0.00007
NM_000535.7(PMS2):c.384G>A (p.Ser128=)	rs371342884	0.00007
NM_000535.7(PMS2):c.1500C>T (p.Ser500=)	rs116094787	0.00006
NM_000535.7(PMS2):c.353+6A>G	rs376449640	0.00006
NM_000535.7(PMS2):c.475G>A (p.Val159Met)	rs142416537	0.00006
NM_000535.7(PMS2):c.477G>A (p.Val159=)	rs147701251	0.00006
NM_000535.7(PMS2):c.944G>A (p.Arg315Gln)	rs116314131	0.00006
NM_000535.7(PMS2):c.632G>A (p.Arg211Gln)	rs587781934	0.00005
NM_000535.7(PMS2):c.738C>G (p.Pro246=)	rs202094399	0.00005
NM_000535.7(PMS2):c.*17G>C	rs556089649	0.00004
NM_000535.7(PMS2):c.1936A>C (p.Arg646=)	rs369582237	0.00004
NM_000535.7(PMS2):c.1A>G (p.Met1Val)	rs587779333	0.00004
NM_000535.7(PMS2):c.2356C>A (p.Leu786Met)	rs576055272	0.00004
NM_000535.7(PMS2):c.614A>C (p.Gln205Pro)	rs587779342	0.00004
NM_000535.7(PMS2):c.1096G>C (p.Asp366His)	rs141769057	0.00003
NM_000535.7(PMS2):c.2113G>A (p.Glu705Lys)	rs267608161	0.00003
NM_000535.7(PMS2):c.1103A>G (p.Asn368Ser)	rs777814445	0.00002
NM_000535.7(PMS2):c.1170G>A (p.Ala390=)	rs755578413	0.00002
NM_000535.7(PMS2):c.2444C>T (p.Ser815Leu)	rs587779338	0.00002
NM_000535.7(PMS2):c.378C>T (p.His126=)	rs768488890	0.00002
NM_000535.7(PMS2):c.789G>A (p.Leu263=)	rs755394319	0.00002
NM_000535.7(PMS2):c.1144+1G>A	rs373885654	0.00001
NM_000535.7(PMS2):c.1240G>T (p.Asp414Tyr)	rs370752614	0.00001
NM_000535.7(PMS2):c.1261C>T (p.Arg421Ter)	rs587778617	0.00001
NM_000535.7(PMS2):c.142G>A (p.Asp48Asn)	rs755665894	0.00001
NM_000535.7(PMS2):c.1455G>A (p.Thr485=)	rs752665758	0.00001
NM_000535.7(PMS2):c.1471G>T (p.Glu491Ter)	rs1064794577	0.00001
NM_000535.7(PMS2):c.1587G>A (p.Ser529=)	rs786201709	0.00001
NM_000535.7(PMS2):c.164-1G>A	rs763308607	0.00001
NM_000535.7(PMS2):c.1926A>G (p.Glu642=)	rs765262682	0.00001
NM_000535.7(PMS2):c.1929G>T (p.Gln643His)	rs786203379	0.00001
NM_000535.7(PMS2):c.2174+1G>A	rs267608172	0.00001
NM_000535.7(PMS2):c.2382dup (p.Gly795fs)	rs1231406078	0.00001
NM_000535.7(PMS2):c.2438G>T (p.Arg813Leu)	rs587782665	0.00001
NM_000535.7(PMS2):c.2445+1G>T	rs876661113	0.00001
NM_000535.7(PMS2):c.251-2A>T	rs587779340	0.00001
NM_000535.7(PMS2):c.2T>C (p.Met1Thr)	rs587780059	0.00001
NM_000535.7(PMS2):c.354C>T (p.Ser118=)	rs760615315	0.00001
NM_000535.7(PMS2):c.506G>A (p.Arg169His)	rs730881917	0.00001
NM_000535.7(PMS2):c.538-1G>C	rs988423880	0.00001
NM_000535.7(PMS2):c.538-2A>G	rs758304323	0.00001
NM_000535.7(PMS2):c.555C>T (p.Val185=)	rs759078497	0.00001
NM_000535.7(PMS2):c.598G>A (p.Val200Ile)	rs587778620	0.00001
NM_000535.7(PMS2):c.709C>T (p.Gln237Ter)	rs1458321358	0.00001
NM_000535.7(PMS2):c.713G>A (p.Ser238Asn)	rs1060503111	0.00001
NM_000535.7(PMS2):c.750C>T (p.Ser250=)	rs200439295	0.00001
NM_000535.7(PMS2):c.825A>G (p.Gln275=)	rs876659736	0.00001
NM_000535.7(PMS2):c.983A>G (p.Asp328Gly)	rs587782852	0.00001
NM_000535.7(PMS2):c.1111_1112del (p.Asn371fs)	rs1583334346
NM_000535.7(PMS2):c.1144+2T>A	rs267608158
NM_000535.7(PMS2):c.123_131del (p.Leu42_Glu44del)	rs863224676
NM_000535.7(PMS2):c.1245G>A (p.Val415=)	rs370701800
NM_000535.7(PMS2):c.1254del (p.Arg419fs)	rs2535825476
NM_000535.7(PMS2):c.1281del (p.His428fs)	rs1783147885
NM_000535.7(PMS2):c.1344A>G (p.Gly448=)	rs759192470
NM_000535.7(PMS2):c.1437C>G (p.His479Gln)	rs63750685
NM_000535.7(PMS2):c.1552G>T (p.Glu518Ter)	rs376142390
NM_000535.7(PMS2):c.1579_1580del (p.Arg527fs)	rs1064793234
NM_000535.7(PMS2):c.1588C>T (p.Gln530Ter)	rs751261543
NM_000535.7(PMS2):c.162_163insAATT (p.Asp55delinsAsnTer)	rs1554306288
NM_000535.7(PMS2):c.163+1G>T	rs1064795705
NM_000535.7(PMS2):c.163+5G>C	rs2128843551
NM_000535.7(PMS2):c.1638_1639del (p.Ser547fs)	rs863224498
NM_000535.7(PMS2):c.164-1G>C	rs763308607
NM_000535.7(PMS2):c.1675G>T (p.Gly559Ter)	rs751153838
NM_000535.7(PMS2):c.1688G>A (p.Arg563Gln)	rs63750668
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu)	rs63750668
NM_000535.7(PMS2):c.1721del (p.Pro574fs)	rs1583316404
NM_000535.7(PMS2):c.1731_1732delinsAGT (p.Arg578fs)	rs1057515572
NM_000535.7(PMS2):c.1802C>G (p.Ser601Ter)	rs63750456
NM_000535.7(PMS2):c.1810C>T (p.Gln604Ter)	rs1064793426
NM_000535.7(PMS2):c.1831dup (p.Ile611fs)	rs63750250
NM_000535.7(PMS2):c.1859_1860insAT (p.Phe620fs)	rs756358866
NM_000535.7(PMS2):c.1909C>T (p.Gln637Ter)	rs1554297125
NM_000535.7(PMS2):c.1938del (p.Lys647fs)	rs2128720948
NM_000535.7(PMS2):c.1A>T (p.Met1Leu)	rs587779333
NM_000535.7(PMS2):c.2007-2A>G	rs587782336
NM_000535.7(PMS2):c.2007-6C>G	rs376018314
NM_000535.7(PMS2):c.2040T>G (p.Gly680=)
NM_000535.7(PMS2):c.2095G>C (p.Asp699His)	rs587781317
NM_000535.7(PMS2):c.211_214del (p.Asn71fs)	rs1562695294
NM_000535.7(PMS2):c.2137C>T (p.Gln713Ter)	rs876659900
NM_000535.7(PMS2):c.2186_2187del (p.Leu729fs)	rs587779335
NM_000535.7(PMS2):c.221G>A (p.Gly74Glu)	rs876661272
NM_000535.7(PMS2):c.2247T>A (p.Asn749Lys)	rs200824831
NM_000535.7(PMS2):c.2275+1G>C	rs1554294393
NM_000535.7(PMS2):c.2397_2400dup (p.Ser801fs)	rs2128672594
NM_000535.7(PMS2):c.24-12_107delinsAAAT	rs1554306445
NM_000535.7(PMS2):c.241G>T (p.Glu81Ter)	rs730881919
NM_000535.7(PMS2):c.2506del (p.Glu836fs)	rs2128658092
NM_000535.7(PMS2):c.2531C>A (p.Pro844His)	rs587782787
NM_000535.7(PMS2):c.269_270dup (p.Lys91fs)	rs1554304745
NM_000535.7(PMS2):c.2T>A (p.Met1Lys)	rs587780059
NM_000535.7(PMS2):c.353+1G>A	rs113517055
NM_000535.7(PMS2):c.354-1G>A	rs786203954
NM_000535.7(PMS2):c.354-2A>G	rs786202098
NM_000535.7(PMS2):c.485T>A (p.Leu162Ter)	rs1785199575
NM_000535.7(PMS2):c.503dup (p.Arg169fs)	rs2536435681
NM_000535.7(PMS2):c.520C>T (p.Gln174Ter)	rs1221485925
NM_000535.7(PMS2):c.538-8T>C	rs922948916
NM_000535.7(PMS2):c.573C>A (p.Tyr191Ter)	rs761134229
NM_000535.7(PMS2):c.636G>A (p.Gln212=)	rs1784804225
NM_000535.7(PMS2):c.641_644dup (p.Cys216fs)	rs1784802468
NM_000535.7(PMS2):c.706-4del	rs60794673
NM_000535.7(PMS2):c.706-4dup	rs60794673
NM_000535.7(PMS2):c.741del (p.Ser248fs)	rs1583374709
NM_000535.7(PMS2):c.746_753del (p.Asp249fs)	rs587782710
NM_000535.7(PMS2):c.756_757del (p.Cys252_Glu253delinsTer)	rs1064794905
NM_000535.7(PMS2):c.79del (p.Cys27fs)	rs2536588880
NM_000535.7(PMS2):c.803+1G>A	rs1562669585
NM_000535.7(PMS2):c.804-2A>G	rs1307026290
NM_000535.7(PMS2):c.841G>T (p.Gly281Ter)	rs1784309424
NM_000535.7(PMS2):c.873del (p.Phe291fs)	rs1261282733
NM_000535.7(PMS2):c.903+1G>C	rs1554300689
NM_000535.7(PMS2):c.903G>A (p.Lys301=)	rs267608153
NM_000535.7(PMS2):c.903G>T (p.Lys301Asn)	rs267608153
NM_000535.7(PMS2):c.904-2A>G	rs587781339
NM_000535.7(PMS2):c.917T>A (p.Val306Glu)	rs786201878
NM_000535.7(PMS2):c.939T>A (p.Tyr313Ter)	rs1562651617

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