ClinVar Miner

Variants with conflicting interpretations studied for Hereditary nonpolyposis colorectal cancer type 4

Coded as:
Minimum review status of the submission for Hereditary nonpolyposis colorectal cancer type 4: Y axis collection method of the submission for Hereditary nonpolyposis colorectal cancer type 4:
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
13 73 26 46 40 0 5 83

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
Hereditary nonpolyposis colorectal cancer type 4 pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 4 2 0 0
likely pathogenic 10 0 2 0 0
uncertain significance 0 2 4 28 8
likely benign 0 0 9 0 18
benign 0 0 8 26 22

Condition to condition summary #

Total conditions: 10
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 92 0 25 24 0 2 49
Lynch syndrome 0 41 18 26 7 0 4 35
not provided 0 71 14 17 10 0 2 34
Hereditary nonpolyposis colon cancer 0 88 0 19 11 0 1 30
not specified 0 43 0 22 10 0 0 29
Hereditary nonpolyposis colorectal cancer type 4 136 20 0 12 2 0 1 13
Lynch syndrome I 0 7 0 4 1 0 1 6
Turcot syndrome 0 2 0 3 0 0 0 3
Turcot syndrome; Hereditary nonpolyposis colorectal cancer type 4 0 14 0 3 0 0 0 3
Pituitary carcinoma 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 83
Download table as spreadsheet
HGVS dbSNP
NM_000535.5(PMS2):c.*17G>C rs556089649
NM_000535.5(PMS2):c.1080A>G (p.Ile360Met) rs567102013
NM_000535.5(PMS2):c.2007-6C>G rs376018314
NM_000535.5(PMS2):c.2182A>G (p.Thr728Ala) rs141893001
NM_000535.5(PMS2):c.2186_2187delTC (p.Leu729Glnfs) rs587779335
NM_000535.5(PMS2):c.2192_2196delTAACT (p.Leu731Cysfs) rs63750695
NM_000535.5(PMS2):c.2T>C (p.Met1Thr) rs587780059
NM_000535.5(PMS2):c.384G>A (p.Ser128=) rs371342884
NM_000535.5(PMS2):c.695G>A (p.Gly232Glu) rs201811667
NM_000535.6(PMS2):c.1004A>G (p.Asn335Ser) rs200513014
NM_000535.6(PMS2):c.1144+2T>A rs267608158
NM_000535.6(PMS2):c.1237_1239del (p.Lys413del) rs267608159
NM_000535.6(PMS2):c.123_131delGTTAGTAGA (p.Leu42_Glu44del) rs863224676
NM_000535.6(PMS2):c.1266G>A (p.Glu422=) rs138049175
NM_000535.6(PMS2):c.137G>T (p.Ser46Ile) rs121434629
NM_000535.6(PMS2):c.1408C>T (p.Pro470Ser) rs1805321
NM_000535.6(PMS2):c.1437C>G (p.His479Gln) rs63750685
NM_000535.6(PMS2):c.1454C>A (p.Thr485Lys) rs1805323
NM_000535.6(PMS2):c.1488C>T (p.His496=) rs1805320
NM_000535.6(PMS2):c.1490G>A (p.Gly497Asp) rs199739859
NM_000535.6(PMS2):c.1531A>G (p.Thr511Ala) rs2228007
NM_000535.6(PMS2):c.1532C>T (p.Thr511Met) rs74902811
NM_000535.6(PMS2):c.1567T>A (p.Ser523Thr) rs63751132
NM_000535.6(PMS2):c.1569C>G (p.Ser523=) rs141458772
NM_000535.6(PMS2):c.1688G>T (p.Arg563Leu) rs63750668
NM_000535.6(PMS2):c.1711C>A (p.Leu571Ile) rs63750055
NM_000535.6(PMS2):c.1717A>T (p.Thr573Ser) rs63751211
NM_000535.6(PMS2):c.1731_1732delGCinsAGT (p.Arg578Valfs) rs1057515572
NM_000535.6(PMS2):c.1760G>A (p.Ser587Asn) rs762100304
NM_000535.6(PMS2):c.1789A>T (p.Thr597Ser) rs1805318
NM_000535.6(PMS2):c.1866G>A (p.Met622Ile) rs1805324
NM_000535.6(PMS2):c.1A>G (p.Met1Val) rs587779333
NM_000535.6(PMS2):c.2006+6G>A rs111905775
NM_000535.6(PMS2):c.2007-4G>A rs1805326
NM_000535.6(PMS2):c.2007-7C>T rs55954143
NM_000535.6(PMS2):c.2149G>A (p.Val717Met) rs201671325
NM_000535.6(PMS2):c.2187C>G (p.Leu729=) rs373630535
NM_000535.6(PMS2):c.2253T>C (p.Phe751=) rs1805325
NM_000535.6(PMS2):c.2276-10A>G rs573900018
NM_000535.6(PMS2):c.23+10G>C rs192027828
NM_000535.6(PMS2):c.2324A>G (p.Asn775Ser) rs17420802
NM_000535.6(PMS2):c.2340C>T (p.Pro780=) rs142230276
NM_000535.6(PMS2):c.2347G>A (p.Val783Ile) rs553286217
NM_000535.6(PMS2):c.2356C>A (p.Leu786Met) rs576055272
NM_000535.6(PMS2):c.241G>T (p.Glu81Ter) rs730881919
NM_000535.6(PMS2):c.251-2A>T rs587779340
NM_000535.6(PMS2):c.255G>A (p.Leu85=) rs200491279
NM_000535.6(PMS2):c.2570G>C (p.Gly857Ala) rs1802683
NM_000535.6(PMS2):c.288C>T (p.Ala96=) rs12532895
NM_000535.6(PMS2):c.353+6A>G rs376449640
NM_000535.6(PMS2):c.353+9A>C rs139990791
NM_000535.6(PMS2):c.354-7C>T rs758471869
NM_000535.6(PMS2):c.383C>T (p.Ser128Leu) rs116373169
NM_000535.6(PMS2):c.477G>A (p.Val159=) rs147701251
NM_000535.6(PMS2):c.52A>G (p.Ile18Val) rs63750123
NM_000535.6(PMS2):c.572A>G (p.Tyr191Cys) rs375289386
NM_000535.6(PMS2):c.595C>T (p.Arg199Cys) rs372297364
NM_000535.6(PMS2):c.59G>A (p.Arg20Gln) rs10254120
NM_000535.6(PMS2):c.614A>C (p.Gln205Pro) rs587779342
NM_000535.6(PMS2):c.682G>A (p.Gly228Ser) rs376258383
NM_000535.6(PMS2):c.705+17A>G rs62456182
NM_000535.6(PMS2):c.706-4delT rs60794673
NM_000535.6(PMS2):c.706-4dup rs60794673
NM_000535.6(PMS2):c.706-5_706-4delTT rs60794673
NM_000535.6(PMS2):c.709C>T (p.Gln237Ter) rs1458321358
NM_000535.6(PMS2):c.738C>G (p.Pro246=) rs202094399
NM_000535.6(PMS2):c.780C>G (p.Ser260=) rs1805319
NM_000535.7(PMS2):c.1379G>A (p.Gly460Asp) rs150201462
NM_000535.7(PMS2):c.1394A>G (p.Lys465Arg) rs141084758
NM_000535.7(PMS2):c.139C>G (p.Leu47Val) rs766203500
NM_000535.7(PMS2):c.1556A>G (p.Tyr519Cys) rs63750649
NM_000535.7(PMS2):c.1559C>T (p.Ala520Val) rs63751300
NM_000535.7(PMS2):c.1688G>A (p.Arg563Gln) rs63750668
NM_000535.7(PMS2):c.1714G>A (p.Ala572Thr) rs63751023
NM_000535.7(PMS2):c.1952A>G (p.Lys651Arg) rs267608167
NM_000535.7(PMS2):c.2350G>A (p.Asp784Asn) rs143340522
NM_000535.7(PMS2):c.538-2A>G rs758304323
NM_000535.7(PMS2):c.708G>T (p.Leu236Phe) rs201395630
NM_000535.7(PMS2):c.823C>G (p.Gln275Glu) rs587780062
NM_000535.7(PMS2):c.89A>G (p.Gln30Arg) rs56203955
NM_000535.7(PMS2):c.903G>T (p.Lys301Asn) rs267608153
NM_000535.7(PMS2):c.904-2A>G rs587781339
NM_000535.7(PMS2):c.936G>A (p.Met312Ile) rs139194813

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