ClinVar Miner

Variants with conflicting interpretations studied for Lynch syndrome II

Coded as:
Minimum review status of the submission for Lynch syndrome II: Y axis collection method of the submission for Lynch syndrome II:
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
21 101 14 49 57 0 11 94

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 II pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 9 4 0 0
likely pathogenic 12 0 4 0 0
uncertain significance 2 3 3 34 15
likely benign 0 0 23 0 19
benign 0 1 7 12 11

Condition to condition summary #

Total conditions: 12
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 0 110 0 20 30 0 4 50
Lynch syndrome 0 79 12 21 23 0 3 46
Hereditary nonpolyposis colon cancer 0 104 0 21 20 0 3 41
not specified 0 46 0 19 27 0 2 40
not provided 0 85 5 15 13 0 3 31
Lynch syndrome II 202 4 0 3 6 0 1 10
Lynch syndrome I 0 8 0 4 5 0 1 9
Colorectal cancer, non-polyposis 0 2 0 1 3 0 0 4
Turcot syndrome; Muir-Torré syndrome; Lynch syndrome II 0 18 0 3 0 0 0 3
Adenocarcinoma of stomach 0 0 0 0 0 0 1 1
Hereditary breast and ovarian cancer syndrome 0 0 0 0 0 0 1 1
Lung adenocarcinoma 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 94
Download table as spreadsheet
HGVS dbSNP
NM_000249.3(MLH1):c.*3A>G rs587778880
NM_000249.3(MLH1):c.-27C>A rs587779001
NM_000249.3(MLH1):c.-28A>G rs56198082
NM_000249.3(MLH1):c.-42C>T rs41285097
NM_000249.3(MLH1):c.-93G>A rs1800734
NM_000249.3(MLH1):c.1011dupC (p.Asn338Glnfs) rs63750677
NM_000249.3(MLH1):c.1038+51C>T rs55986674
NM_000249.3(MLH1):c.1039-4A>G rs368618417
NM_000249.3(MLH1):c.1039-5T>C rs587782626
NM_000249.3(MLH1):c.1039-8T>A rs193922367
NM_000249.3(MLH1):c.1104G>A (p.Ser368=) rs769364808
NM_000249.3(MLH1):c.1128T>C (p.Asp376=) rs267607824
NM_000249.3(MLH1):c.1136A>G (p.Tyr379Cys) rs143009528
NM_000249.3(MLH1):c.1151T>A (p.Val384Asp) rs63750447
NM_000249.3(MLH1):c.116+1G>A rs267607709
NM_000249.3(MLH1):c.116+5G>A rs267607710
NM_000249.3(MLH1):c.1166G>A (p.Arg389Gln) rs63750361
NM_000249.3(MLH1):c.1219C>T (p.Gln407Ter) rs1057517541
NM_000249.3(MLH1):c.1266C>T (p.Gly422=) rs63750791
NM_000249.3(MLH1):c.1268G>A (p.Arg423Lys) rs370687064
NM_000249.3(MLH1):c.1269G>A (p.Arg423=) rs373076967
NM_000249.3(MLH1):c.1297G>T (p.Glu433Ter) rs63750443
NM_000249.3(MLH1):c.1321G>A (p.Ala441Thr) rs63750365
NM_000249.3(MLH1):c.1360G>C (p.Gly454Arg) rs63750527
NM_000249.3(MLH1):c.1379A>C (p.Glu460Ala) rs202038499
NM_000249.3(MLH1):c.1410-2_1410-1delinsCC
NM_000249.3(MLH1):c.1410-8C>T rs1057521668
NM_000249.3(MLH1):c.1420C>G (p.Arg474Gly) rs147939838
NM_000249.3(MLH1):c.1421G>A (p.Arg474Gln) rs63751083
NM_000249.3(MLH1):c.1500_1502delCAT (p.Ile501del) rs587778920
NM_000249.3(MLH1):c.1558+14G>A rs41562513
NM_000249.3(MLH1):c.1558+5G>A rs199935667
NM_000249.3(MLH1):c.1559-11T>C rs730881750
NM_000249.3(MLH1):c.1565G>A (p.Arg522Gln) rs63751630
NM_000249.3(MLH1):c.1637A>G (p.Lys546Arg) rs587779954
NM_000249.3(MLH1):c.1668-19A>G rs9876116
NM_000249.3(MLH1):c.1731+8T>C rs370108219
NM_000249.3(MLH1):c.1733A>G (p.Glu578Gly) rs63751612
NM_000249.3(MLH1):c.1852A>G (p.Lys618Glu) rs35001569
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.1853A>G (p.Lys618Arg) rs63750449
NM_000249.3(MLH1):c.1897-2A>G rs267607871
NM_000249.3(MLH1):c.1937A>G (p.Tyr646Cys) rs35045067
NM_000249.3(MLH1):c.1959G>T (p.Leu653=) rs1800146
NM_000249.3(MLH1):c.1963A>G (p.Ile655Val) rs55907433
NM_000249.3(MLH1):c.1964T>C (p.Ile655Thr) rs63751225
NM_000249.3(MLH1):c.1990-6G>A rs117221851
NM_000249.3(MLH1):c.199G>A (p.Gly67Arg) rs63750206
NM_000249.3(MLH1):c.2040C>T (p.Cys680=) rs63749867
NM_000249.3(MLH1):c.2041G>A (p.Ala681Thr) rs63750217
NM_000249.3(MLH1):c.2059C>T (p.Arg687Trp) rs63751275
NM_000249.3(MLH1):c.2066A>G (p.Gln689Arg) rs63750702
NM_000249.3(MLH1):c.2070_2071insTT (p.Ile691Leufs) rs876659681
NM_000249.3(MLH1):c.2101C>A (p.Gln701Lys) rs63750114
NM_000249.3(MLH1):c.2146G>A (p.Val716Met) rs35831931
NM_000249.3(MLH1):c.2152C>T (p.His718Tyr) rs2020873
NM_000249.3(MLH1):c.2252A>G (p.Lys751Arg) rs140195825
NM_000249.3(MLH1):c.2252_2253delAA (p.Lys751Serfs) rs267607901
NM_000249.3(MLH1):c.245C>T (p.Thr82Ile) rs63750005
NM_000249.3(MLH1):c.277A>G (p.Ser93Gly) rs41295282
NM_000249.3(MLH1):c.283delT (p.Ser95Leufs) rs1064795441
NM_000249.3(MLH1):c.290A>G (p.Tyr97Cys) rs773647920
NM_000249.3(MLH1):c.375A>G (p.Ala125=) rs1800144
NM_000249.3(MLH1):c.381-43C>G rs368847278
NM_000249.3(MLH1):c.438A>G (p.Gln146=) rs377279035
NM_000249.3(MLH1):c.453+1G>T rs267607750
NM_000249.3(MLH1):c.454-1G>C rs193922370
NM_000249.3(MLH1):c.52C>T (p.Arg18Cys) rs367654552
NM_000249.3(MLH1):c.545+19G>T rs41285099
NM_000249.3(MLH1):c.579A>G (p.Ser193=) rs587781038
NM_000249.3(MLH1):c.595G>C (p.Glu199Gln) rs63749887
NM_000249.3(MLH1):c.626A>G (p.Asn209Ser) rs150478207
NM_000249.3(MLH1):c.655A>G (p.Ile219Val) rs1799977
NM_000249.3(MLH1):c.65G>C (p.Gly22Ala) rs41295280
NM_000249.3(MLH1):c.677+1G>A rs267607778
NM_000249.3(MLH1):c.677G>T (p.Arg226Leu) rs63751711
NM_000249.3(MLH1):c.69A>G (p.Glu23=) rs63750555
NM_000249.3(MLH1):c.790+10A>G rs182733777
NM_000249.3(MLH1):c.793C>T (p.Arg265Cys) rs63751194
NM_000249.3(MLH1):c.794G>A (p.Arg265His) rs63751448
NM_000249.3(MLH1):c.803A>G (p.Glu268Gly) rs63750650
NM_000249.3(MLH1):c.808A>G (p.Thr270Ala) rs371302926
NM_000249.3(MLH1):c.84delA (p.Ala29Leufs) rs587779045
NM_000249.3(MLH1):c.85G>T (p.Ala29Ser) rs63750656
NM_000249.3(MLH1):c.884+15A>G rs372817491
NM_000249.3(MLH1):c.884+16A>G rs377598055
NM_000249.3(MLH1):c.884+3A>G rs267607803
NM_000249.3(MLH1):c.885-16_885-15delCT rs267607804
NM_000249.3(MLH1):c.91_92delGCinsTG (p.Ala31Cys) rs63749994
NM_000249.3(MLH1):c.927C>T (p.Pro309=) rs63749896
NM_000249.3(MLH1):c.954C>T (p.His318=) rs146777069
NM_000249.3(MLH1):c.955G>A (p.Glu319Lys) rs63750796
NM_000249.3(MLH1):c.974G>A (p.Arg325Gln) rs63750268

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