ClinVar Miner

Variants from International Society for Gastrointestinal Hereditary Tumours (InSiGHT) with conflicting interpretations

Location: United Kingdom  Primary collection method: research
Minimum review status of the submission from International Society for Gastrointestinal Hereditary Tumours (InSiGHT): Collection method of the submission from International Society for Gastrointestinal Hereditary Tumours (InSiGHT):
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
1334 237 43 82 20 0 8 143

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 submitters
International Society for Gastrointestinal Hereditary Tumours (InSiGHT) pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 28 2 0 0
likely pathogenic 24 0 3 0 0
uncertain significance 2 1 0 3 0
likely benign 0 0 10 0 17
benign 0 0 7 13 43

Submitter to submitter summary #

Total submitters: 23
Download table as spreadsheet
Submitter 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
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 0 68 36 17 0 0 0 53
All of Us Research Program, National Institutes of Health 0 74 10 12 6 0 1 29
Myriad Genetics, Inc. 0 19 0 13 2 0 1 16
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 65 0 13 0 0 0 13
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia 0 0 5 2 4 0 0 11
University of Washington Department of Laboratory Medicine, University of Washington 0 25 0 8 1 0 2 11
Counsyl 0 4 0 2 6 0 1 9
Illumina Laboratory Services, Illumina 0 4 0 7 2 0 0 9
Department of Pathology and Laboratory Medicine, Sinai Health System 0 30 1 6 0 0 1 8
Mendelics 0 16 0 5 0 0 1 6
CSER _CC_NCGL, University of Washington 0 4 1 1 1 0 0 3
Genome Diagnostics Laboratory, Amsterdam University Medical Center 0 1 0 3 0 0 0 3
Pathway Genomics 0 2 0 2 0 0 0 2
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 1 0 2 0 0 0 2
KCCC/NGS Laboratory, Kuwait Cancer Control Center 0 7 0 2 0 0 0 2
Baylor Genetics 0 6 0 0 0 0 1 1
Center for Human Genetics, Inc, Center for Human Genetics, Inc 0 0 0 0 1 0 0 1
MGZ Medical Genetics Center 0 0 0 1 0 0 0 1
Genome Diagnostics Laboratory, University Medical Center Utrecht 0 1 0 1 0 0 0 1
Invitae 0 25 0 1 0 0 0 1
Centre for Mendelian Genomics, University Medical Centre Ljubljana 0 1 0 1 0 0 0 1
Institute of Human Genetics, University of Leipzig Medical Center 0 2 0 1 0 0 0 1
St. Jude Molecular Pathology, St. Jude Children's Research Hospital 0 2 1 0 0 0 0 1

All variants with conflicting interpretations #

Total variants: 143
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000535.7(PMS2):c.780C>G (p.Ser260=) rs1805319 0.82058
NM_000179.3(MSH6):c.3802-40C>G rs3136367 0.73398
NM_000251.3(MSH2):c.211+9C>G rs2303426 0.55454
NM_000251.3(MSH2):c.1077-80G>A rs2347794 0.53152
NM_000249.4(MLH1):c.1668-19A>G rs9876116 0.41821
NM_000251.3(MSH2):c.1661+12G>A rs3732183 0.40290
NM_000535.7(PMS2):c.1408C>T (p.Pro470Ser) rs1805321 0.37107
NM_000535.7(PMS2):c.705+17A>G rs62456182 0.33782
NM_000535.7(PMS2):c.2570G>C (p.Gly857Ala) rs1802683 0.30966
NM_000179.3(MSH6):c.540T>C (p.Asp180=) rs1800935 0.23857
NM_000249.4(MLH1):c.655A>G (p.Ile219Val) rs1799977 0.23048
NM_000179.3(MSH6):c.116G>A (p.Gly39Glu) rs1042821 0.18742
NM_000179.3(MSH6):c.276A>G (p.Pro92=) rs1800932 0.14697
NM_000535.7(PMS2):c.1621= (p.Lys541=) rs2228006 0.13518
NM_000179.3(MSH6):c.186C>A (p.Arg62=) rs1042820 0.12806
NM_000535.7(PMS2):c.2007-7C>T rs55954143 0.12135
NM_000535.7(PMS2):c.2466T>C (p.Leu822=) rs10000 0.11447
NM_000251.3(MSH2):c.1511-9A>T rs12998837 0.09123
NM_000251.3(MSH2):c.2006-6T>C rs2303428 0.08349
NM_000179.2(MSH6):c.-159C>T rs41540312 0.07535
NM_000179.3(MSH6):c.642C>T (p.Tyr214=) rs1800937 0.07457
NM_000535.7(PMS2):c.59G>A (p.Arg20Gln) rs10254120 0.07445
NM_000535.7(PMS2):c.1454C>A (p.Thr485Lys) rs1805323 0.05742
NM_000249.4(MLH1):c.1558+14G>A rs41562513 0.05554
NM_000535.7(PMS2):c.1532C>T (p.Thr511Met) rs74902811 0.02492
NM_000249.4(MLH1):c.2152C>T (p.His718Tyr) rs2020873 0.02345
NM_000251.3(MSH2):c.380A>G (p.Asn127Ser) rs17217772 0.02317
NM_000535.7(PMS2):c.1531A>G (p.Thr511Ala) rs2228007 0.02174
NM_000179.3(MSH6):c.2253T>C (p.Asn751=) rs2020913 0.02003
NM_000249.4(MLH1):c.381-41A>G rs4647245 0.01794
NM_000251.3(MSH2):c.965G>A (p.Gly322Asp) rs4987188 0.01714
NM_000535.7(PMS2):c.1866G>A (p.Met622Ile) rs1805324 0.01651
NM_000251.3(MSH2):c.1077-10T>C rs17224360 0.01428
NM_000249.4(MLH1):c.474C>T (p.Asn158=) rs4647256 0.01161
NM_000249.4(MLH1):c.1039-8T>A rs193922367 0.01153
NM_000251.3(MSH2):c.2766T>C (p.Phe922=) rs55859129 0.01118
NM_000535.7(PMS2):c.1789A>T (p.Thr597Ser) rs1805318 0.01006
NM_000249.4(MLH1):c.1959G>T (p.Leu653=) rs1800146 0.00913
NM_000179.3(MSH6):c.3306T>A (p.Thr1102=) rs2020910 0.00869
NM_000535.7(PMS2):c.52A>G (p.Ile18Val) rs63750123 0.00861
NM_000249.4(MLH1):c.637G>A (p.Val213Met) rs2308317 0.00818
NM_000249.4(MLH1):c.1038+51C>T rs55986674 0.00582
NM_000249.4(MLH1):c.589-15C>T rs55658850 0.00582
NM_000179.3(MSH6):c.1186C>G (p.Leu396Val) rs2020908 0.00565
NM_000251.3(MSH2):c.1666T>C (p.Leu556=) rs61756466 0.00471
NM_000249.4(MLH1):c.453+25A>G rs4647246 0.00414
NM_000251.3(MSH2):c.339G>A (p.Lys113=) rs35898375 0.00313
NM_000249.4(MLH1):c.1963A>G (p.Ile655Val) rs55907433 0.00297
NM_000251.3(MSH2):c.1387-8G>T rs187525243 0.00143
NM_000251.3(MSH2):c.1737A>G (p.Lys579=) rs61756467 0.00138
NM_000249.4(MLH1):c.1217G>A (p.Ser406Asn) rs41294980 0.00087
NM_000251.3(MSH2):c.1680T>C (p.Asn560=) rs200056411 0.00043
NM_000249.4(MLH1):c.198C>T (p.Thr66=) rs61751642 0.00040
NM_000249.4(MLH1):c.977T>C (p.Val326Ala) rs63751049 0.00037
NM_000179.3(MSH6):c.3217C>T (p.Pro1073Ser) rs142254875 0.00028
NM_000535.7(PMS2):c.2324A>G (p.Asn775Ser) rs17420802 0.00025
NM_000535.7(PMS2):c.137G>T (p.Ser46Ile) rs121434629 0.00018
NM_000535.7(PMS2):c.2253T>C (p.Phe751=) rs1805325 0.00018
NM_000249.4(MLH1):c.2101C>A (p.Gln701Lys) rs63750114 0.00016
NM_000179.3(MSH6):c.2398G>C (p.Val800Leu) rs61748083 0.00014
NM_000179.3(MSH6):c.59C>T (p.Ala20Val) rs63750664 0.00013
NM_000179.3(MSH6):c.1875C>T (p.Ser625=) rs63749886 0.00010
NM_000251.3(MSH2):c.4G>A (p.Ala2Thr) rs63750466 0.00008
NM_000535.7(PMS2):c.384G>A (p.Ser128=) rs371342884 0.00007
NM_000249.4(MLH1):c.1733A>G (p.Glu578Gly) rs63751612 0.00006
NM_000251.3(MSH2):c.499G>C (p.Asp167His) rs63750255 0.00006
NM_000249.4(MLH1):c.1128T>C (p.Asp376=) rs267607824 0.00005
NM_000535.7(PMS2):c.1A>G (p.Met1Val) rs587779333 0.00004
NM_000251.3(MSH2):c.1963G>A (p.Val655Ile) rs549467183 0.00003
NM_000251.3(MSH2):c.991A>G (p.Asn331Asp) rs267607938 0.00003
NM_000249.4(MLH1):c.303T>G (p.Gly101=) rs4647220 0.00002
NM_000251.3(MSH2):c.304G>A (p.Val102Ile) rs193922373 0.00002
NM_000179.3(MSH6):c.1403G>A (p.Arg468His) rs41295268 0.00001
NM_000179.3(MSH6):c.241G>A (p.Ala81Thr) rs587779239 0.00001
NM_000179.3(MSH6):c.892C>T (p.Arg298Ter) rs146816935 0.00001
NM_000249.4(MLH1):c.1652A>G (p.Asn551Ser) rs63750271 0.00001
NM_000249.4(MLH1):c.244A>G (p.Thr82Ala) rs587778998 0.00001
NM_000251.3(MSH2):c.164G>A (p.Arg55Gln) rs748196422 0.00001
NM_000251.3(MSH2):c.2437A>G (p.Met813Val) rs63749841 0.00001
NM_000535.7(PMS2):c.2404C>T (p.Arg802Ter) rs63751466 0.00001
MSH6:c.3647-51_3647-35del17 rs267607687
NM_000179.3(MSH6):c.1100A>G (p.His367Arg) rs1553412495
NM_000179.3(MSH6):c.1615CTT[1] (p.Leu540del) rs1064793600
NM_000179.3(MSH6):c.2300C>T (p.Thr767Ile) rs587781462
NM_000179.3(MSH6):c.2314C>T (p.Arg772Trp) rs63750138
NM_000179.3(MSH6):c.2535dup (p.Glu846Ter) rs587779241
NM_000179.3(MSH6):c.2983G>T (p.Glu995Ter) rs63750258
NM_000179.3(MSH6):c.3188T>G (p.Leu1063Arg) rs1060502901
NM_000179.3(MSH6):c.3246G>T (p.Pro1082=) rs3136351
NM_000179.3(MSH6):c.3261dup (p.Phe1088fs) rs267608078
NM_000179.3(MSH6):c.3439-1G>T rs587779263
NM_000179.3(MSH6):c.3439-2A>G rs267608098
NM_000179.3(MSH6):c.3632T>C (p.Leu1211Pro) rs864622041
NM_000179.3(MSH6):c.3724_3726del (p.Arg1242del) rs63749942
NM_000179.3(MSH6):c.4002-10del rs59056100
NM_000249.3(MLH1):c.2104_2105delAG rs63751651
NM_000249.4(MLH1):c.*32CTT[1] rs193922366
NM_000249.4(MLH1):c.1011dup (p.Asn338fs) rs63750677
NM_000249.4(MLH1):c.1038G>A (p.Gln346=) rs63751715
NM_000249.4(MLH1):c.1039-2A>G rs267607815
NM_000249.4(MLH1):c.1136A>G (p.Tyr379Cys) rs143009528
NM_000249.4(MLH1):c.116G>A (p.Cys39Tyr) rs63751701
NM_000249.4(MLH1):c.1409+1G>A rs267607825
NM_000249.4(MLH1):c.156del (p.Glu53fs) rs63750028
NM_000249.4(MLH1):c.1649T>C (p.Leu550Pro) rs63750193
NM_000249.4(MLH1):c.1668-1G>A rs267607845
NM_000249.4(MLH1):c.1731+1G>C rs267607853
NM_000249.4(MLH1):c.1852_1853delinsGC (p.Lys618Ala) rs35502531
NM_000249.4(MLH1):c.1897-2A>G rs267607871
NM_000249.4(MLH1):c.1989+1G>T rs267607879
NM_000249.4(MLH1):c.2084C>A (p.Ser695Ter) rs63749995
NM_000249.4(MLH1):c.2250C>G (p.Tyr750Ter) rs267607893
NM_000249.4(MLH1):c.2262del (p.Arg755fs) rs267607904
NM_000249.4(MLH1):c.299G>C (p.Arg100Pro) rs63750266
NM_000249.4(MLH1):c.2T>C (p.Met1Thr) rs111052004
NM_000249.4(MLH1):c.304G>A (p.Glu102Lys) rs63750453
NM_000249.4(MLH1):c.453+1G>T rs267607750
NM_000249.4(MLH1):c.62C>T (p.Ala21Val) rs63750706
NM_000249.4(MLH1):c.791-2A>G rs267607794
NM_000249.4(MLH1):c.793C>A (p.Arg265Ser) rs63751194
NM_000249.4(MLH1):c.860del (p.Asn287fs) rs63750034
NM_000249.4(MLH1):c.885-2A>G rs267607805
NM_000249.4(MLH1):c.931A>G (p.Lys311Glu) rs876658657
NM_000251.2(MSH2):c.646-?_792+?del
NM_000251.3(MSH2):c.1046C>G (p.Pro349Arg) rs587779067
NM_000251.3(MSH2):c.1077-1G>T rs267607944
NM_000251.3(MSH2):c.1276+1G>A rs267607950
NM_000251.3(MSH2):c.1277-1G>A rs267607948
NM_000251.3(MSH2):c.1386+1G>A rs267607957
NM_000251.3(MSH2):c.1587del (p.Glu530fs) rs63750845
NM_000251.3(MSH2):c.1661+1G>T rs267607969
NM_000251.3(MSH2):c.2021G>A (p.Gly674Asp) rs267607996
NM_000251.3(MSH2):c.2210+1G>A rs267608002
NM_000251.3(MSH2):c.2211-2A>T rs267608001
NM_000251.3(MSH2):c.2335dup (p.Met779fs) rs63750149
NM_000251.3(MSH2):c.2634+1G>A rs267608019
NM_000251.3(MSH2):c.2634+1G>T rs267608019
NM_000251.3(MSH2):c.2714C>G (p.Thr905Arg) rs267608022
NM_000251.3(MSH2):c.301_306del (p.Glu101_Val102del) rs587779157
NM_000251.3(MSH2):c.482T>A (p.Val161Asp) rs63750126
NM_000251.3(MSH2):c.593A>G (p.Glu198Gly) rs63750327
NM_000251.3(MSH2):c.793-2A>C rs267607933
NM_000535.7(PMS2):c.1688G>T (p.Arg563Leu) rs63750668

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