ClinVar Miner

Variants with conflicting interpretations studied for MSH2-related disorder

Minimum review status of the submission for MSH2-related disorder: Collection method of the submission for MSH2-related disorder:
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
11 44 0 32 86 0 2 108

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
MSH2-related disorder pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 1 1 0 0
likely pathogenic 1 0 0 0 0
uncertain significance 1 1 0 47 26
likely benign 0 0 27 0 28
benign 0 0 0 2 0

Condition to condition summary #

Total conditions: 8
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
Hereditary nonpolyposis colorectal neoplasms 0 72 0 15 60 0 1 76
not specified 0 45 0 21 33 0 0 47
not provided 0 82 0 10 32 0 2 43
Breast and/or ovarian cancer 0 18 0 1 4 0 0 5
Hereditary cancer 0 0 0 0 5 0 0 5
Colorectal cancer, non-polyposis 0 1 0 0 3 0 0 3
Inherited ovarian cancer (without breast cancer) 0 0 0 0 2 0 0 2
Inherited MMR deficiency (Lynch syndrome) 0 4 0 0 1 0 0 1

All variants with conflicting interpretations #

Total variants: 108
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000251.3(MSH2):c.1737A>G (p.Lys579=) rs61756467 0.00138
NM_000251.3(MSH2):c.942+4A>G rs749778569 0.00082
NM_000251.3(MSH2):c.55T>C (p.Phe19Leu) rs141711342 0.00063
NM_000251.2(MSH2):c.-73G>A rs552303079 0.00058
NM_000251.3(MSH2):c.1511-41G>C rs202215396 0.00038
NM_000251.3(MSH2):c.815C>T (p.Ala272Val) rs34136999 0.00032
NM_000251.3(MSH2):c.435T>G (p.Ile145Met) rs63750124 0.00031
NM_000251.3(MSH2):c.942+4A>T rs749778569 0.00024
NM_000251.3(MSH2):c.138C>G (p.His46Gln) rs33946261 0.00019
NM_000251.3(MSH2):c.481G>A (p.Val161Ile) rs149511545 0.00019
NM_000251.3(MSH2):c.1730T>C (p.Ile577Thr) rs63749910 0.00018
NM_000251.3(MSH2):c.1662-23A>G rs56404027 0.00017
NM_000251.3(MSH2):c.1275A>G (p.Glu425=) rs63751650 0.00016
NM_000251.3(MSH2):c.-3G>C rs587779960 0.00013
NM_000251.3(MSH2):c.2425G>A (p.Glu809Lys) rs202145681 0.00013
NM_000251.3(MSH2):c.1387-4G>C rs376796243 0.00011
NM_000251.3(MSH2):c.1461C>G (p.Asp487Glu) rs35107951 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.128A>G (p.Tyr43Cys) rs17217723 0.00010
NM_000251.3(MSH2):c.1505A>G (p.Asp502Gly) rs148192104 0.00009
NM_000251.3(MSH2):c.1690A>G (p.Thr564Ala) rs55778204 0.00009
NM_000251.3(MSH2):c.2308A>G (p.Ile770Val) rs63750684 0.00009
NM_000251.3(MSH2):c.2802G>A (p.Thr934=) rs150259097 0.00009
NM_000251.3(MSH2):c.820A>G (p.Ile274Val) rs371944271 0.00008
NM_000251.3(MSH2):c.913G>A (p.Ala305Thr) rs63751454 0.00008
NM_000251.3(MSH2):c.1560A>G (p.Gly520=) rs63750820 0.00007
NM_000251.3(MSH2):c.1638G>A (p.Lys546=) rs372350768 0.00007
NM_000251.3(MSH2):c.4G>A (p.Ala2Thr) rs63750466 0.00007
NM_000251.3(MSH2):c.1077-7A>G rs370807334 0.00006
NM_000251.3(MSH2):c.1321A>C (p.Thr441Pro) rs587779086 0.00006
NM_000251.3(MSH2):c.2271C>T (p.Tyr757=) rs56076152 0.00006
NM_000251.3(MSH2):c.2503A>C (p.Asn835His) rs41295296 0.00006
NM_000251.3(MSH2):c.2732T>G (p.Leu911Arg) rs41295182 0.00006
NM_000251.3(MSH2):c.499G>C (p.Asp167His) rs63750255 0.00006
NM_000251.3(MSH2):c.944G>T (p.Gly315Val) rs202026056 0.00006
NM_000251.3(MSH2):c.2400A>G (p.Leu800=) rs201298777 0.00005
NM_000251.3(MSH2):c.-225G>C rs138068023 0.00004
NM_000251.3(MSH2):c.-76G>A rs34355730 0.00004
NM_000251.3(MSH2):c.1530G>C (p.Gln510His) rs587782355 0.00003
NM_000251.3(MSH2):c.1601G>A (p.Arg534His) rs587778523 0.00003
NM_000251.3(MSH2):c.1847C>G (p.Pro616Arg) rs587779965 0.00003
NM_000251.3(MSH2):c.211+8C>T rs267607916 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.399C>T (p.Asp133=) rs61756462 0.00003
NM_000251.3(MSH2):c.409G>C (p.Gly137Arg) rs587781795 0.00003
NM_000251.3(MSH2):c.594A>G (p.Glu198=) rs369685768 0.00003
NM_000251.3(MSH2):c.1200C>G (p.Asn400Lys) rs1301023135 0.00002
NM_000251.3(MSH2):c.1254A>G (p.Ile418Met) rs751431238 0.00002
NM_000251.3(MSH2):c.2009C>T (p.Pro670Leu) rs41294982 0.00002
NM_000251.3(MSH2):c.2158A>G (p.Lys720Glu) rs747265823 0.00002
NM_000251.3(MSH2):c.2178G>C (p.Met726Ile) rs587782396 0.00002
NM_000251.3(MSH2):c.220A>C (p.Asn74His) rs150548839 0.00002
NM_000251.3(MSH2):c.2621A>G (p.Tyr874Cys) rs775390721 0.00002
NM_000251.3(MSH2):c.2650A>T (p.Ile884Phe) rs774732579 0.00002
NM_000251.3(MSH2):c.2717T>C (p.Ile906Thr) rs587780687 0.00002
NM_000251.3(MSH2):c.304G>A (p.Val102Ile) rs193922373 0.00002
NM_000251.3(MSH2):c.-9G>C rs547444746 0.00001
NM_000251.3(MSH2):c.1148G>A (p.Arg383Gln) rs376934727 0.00001
NM_000251.3(MSH2):c.118G>A (p.Gly40Ser) rs63751260 0.00001
NM_000251.3(MSH2):c.1622C>T (p.Thr541Ile) rs864622079 0.00001
NM_000251.3(MSH2):c.1760-7T>C rs972129356 0.00001
NM_000251.3(MSH2):c.1796T>C (p.Leu599Ser) rs747504492 0.00001
NM_000251.3(MSH2):c.1825G>T (p.Ala609Ser) rs150980616 0.00001
NM_000251.3(MSH2):c.1927G>A (p.Glu643Lys) rs374840361 0.00001
NM_000251.3(MSH2):c.1967A>G (p.Tyr656Cys) rs185356145 0.00001
NM_000251.3(MSH2):c.2110A>G (p.Ile704Val) rs730881764 0.00001
NM_000251.3(MSH2):c.2122A>G (p.Ile708Val) rs750084297 0.00001
NM_000251.3(MSH2):c.2123T>C (p.Ile708Thr) rs63750108 0.00001
NM_000251.3(MSH2):c.2141C>T (p.Ala714Val) rs63751224 0.00001
NM_000251.3(MSH2):c.2164G>A (p.Val722Ile) rs587781996 0.00001
NM_000251.3(MSH2):c.2197G>A (p.Ala733Thr) rs772662439 0.00001
NM_000251.3(MSH2):c.2439G>A (p.Met813Ile) rs587781678 0.00001
NM_000251.3(MSH2):c.2542G>T (p.Ala848Ser) rs746972142 0.00001
NM_000251.3(MSH2):c.2579C>T (p.Ser860Leu) rs63750849 0.00001
NM_000251.3(MSH2):c.440T>G (p.Val147Gly) rs760851623 0.00001
NM_000251.3(MSH2):c.646-3T>C rs267607930 0.00001
NM_000251.3(MSH2):c.775C>T (p.Pro259Ser) rs587781294 0.00001
NM_000251.3(MSH2):c.972G>A (p.Gln324=) rs63750505 0.00001
NM_000251.3(MSH2):c.-7T>A rs1216867699
NM_000251.3(MSH2):c.-8G>T rs1064795641
NM_000251.3(MSH2):c.1077-2A>G rs267607943
NM_000251.3(MSH2):c.1147C>T (p.Arg383Ter) rs63749849
NM_000251.3(MSH2):c.1405C>G (p.Leu469Val) rs780702096
NM_000251.3(MSH2):c.1798G>T (p.Ala600Ser) rs587778526
NM_000251.3(MSH2):c.183G>C (p.Gln61His) rs751082926
NM_000251.3(MSH2):c.1844C>T (p.Ala615Val) rs765493709
NM_000251.3(MSH2):c.1946C>T (p.Ala649Val) rs876659816
NM_000251.3(MSH2):c.1A>C (p.Met1Leu) rs267607911
NM_000251.3(MSH2):c.2005+8dup rs267607992
NM_000251.3(MSH2):c.208G>A (p.Ala70Thr) rs587778522
NM_000251.3(MSH2):c.2354A>C (p.His785Pro) rs200252727
NM_000251.3(MSH2):c.2354A>G (p.His785Arg) rs200252727
NM_000251.3(MSH2):c.2680dup (p.Met894fs) rs876658211
NM_000251.3(MSH2):c.2714C>T (p.Thr905Ile) rs267608022
NM_000251.3(MSH2):c.403C>T (p.Leu135Phe) rs193096019
NM_000251.3(MSH2):c.645+1G>T rs267607689
NM_000251.3(MSH2):c.6G>C (p.Ala2=) rs368270856
NM_000251.3(MSH2):c.743A>G (p.Lys248Arg) rs1064794704
NM_000251.3(MSH2):c.79C>T (p.Pro27Ser) rs878853826
NM_000251.3(MSH2):c.911T>C (p.Ile304Thr) rs1021303606
NM_000251.3(MSH2):c.942+24_942+29del rs11309117
NM_000251.3(MSH2):c.942+28_942+29del rs11309117
NM_000251.3(MSH2):c.942+6A>G rs777429168
NM_000251.3(MSH2):c.965G>T (p.Gly322Val) rs4987188
NM_000251.3(MSH2):c.968C>T (p.Ser323Phe) rs63750732

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