ClinVar Miner

Variants with conflicting interpretations studied for Gastrointestinal stroma tumor

Coded as:
Minimum review status of the submission for Gastrointestinal stroma tumor: Y axis collection method of the submission for Gastrointestinal stroma tumor:
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
917 223 8 51 52 8 10 109

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
Gastrointestinal stroma tumor pathogenic likely pathogenic uncertain significance likely benign benign drug response risk factor other
pathogenic 0 4 0 0 0 1 0 1
likely pathogenic 24 0 5 0 0 0 0 2
uncertain significance 6 4 7 36 7 3 3 3
likely benign 1 0 14 0 25 0 0 0
benign 0 0 0 2 1 0 0 0

Condition to condition summary #

Total conditions: 54
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 0 133 0 16 30 0 1 47
not provided 0 11 8 21 12 2 0 40
not specified 0 30 0 10 8 0 0 18
Cutaneous melanoma 0 4 0 16 0 0 2 17
Gastrointestinal stroma tumor 1228 11 0 4 3 0 3 10
Disorders of Intracellular Cobalamin Metabolism 0 0 0 0 5 0 0 5
Cowden syndrome 0 5 0 0 4 0 0 4
Thymoma 0 0 0 3 0 0 1 4
Acute myeloid leukemia 0 1 0 2 0 0 2 3
Gastrointestinal stroma tumor; Paragangliomas 4; Pheochromocytoma 0 5 0 2 0 0 1 3
Mastocytosis 0 31 0 3 0 0 0 3
Paragangliomas 4 0 3 0 2 2 0 0 3
Cutaneous mastocytosis 0 0 0 2 0 0 1 2
Dysgerminoma 0 0 0 0 0 2 0 2
Gastrointestinal stromal tumor, familial 0 1 0 2 0 0 0 2
Hereditary Paraganglioma-Pheochromocytoma Syndromes 0 1 0 1 0 0 1 2
Idiopathic hypereosinophilic syndrome 0 90 0 0 2 0 0 2
MTHFR deficiency, thermolabile type 0 0 0 0 2 0 1 2
Multiple myeloma 0 0 0 2 0 0 0 2
Neoplasm 0 0 0 1 0 0 1 2
Neural tube defects, folate-sensitive 0 0 0 0 2 0 0 2
Neural tube defects, folate-sensitive, susceptibility to 0 0 0 0 0 2 0 2
Partial albinism 0 30 0 2 0 0 0 2
Brainstem glioma 0 0 0 1 0 0 0 1
Carney triad 0 0 0 1 0 0 0 1
Colorectal cancer 0 0 0 0 0 1 0 1
Down syndrome, susceptibility to 0 0 0 0 0 1 0 1
Glioblastoma 0 0 0 1 0 0 0 1
Hematologic neoplasm 0 3 0 0 0 0 1 1
Lung adenocarcinoma 0 1 0 1 0 0 0 1
MAST CELL LEUKEMIA, SOMATIC 0 0 0 1 0 0 1 1
MASTOCYTOSIS WITH ASSOCIATED HEMATOLOGIC DISORDER, SOMATIC 0 0 0 1 0 0 1 1
MASTOCYTOSIS, CUTANEOUS AND SYSTEMIC, SOMATIC 0 0 0 1 0 0 0 1
MASTOCYTOSIS, SYSTEMIC, SOMATIC 0 0 0 1 0 0 1 1
Malignant melanoma of skin 0 1 0 1 0 0 0 1
Malignant tumor of testis 0 0 0 1 0 0 0 1
Mast cell leukemia 0 0 0 0 0 0 1 1
Neoplasm of brain 0 0 0 1 0 0 0 1
Neoplasm of the colon 0 0 0 1 0 0 0 1
Neoplasm of the large intestine 0 1 0 1 0 0 0 1
Non-small cell lung cancer 0 2 0 1 0 0 0 1
Ovarian Neoplasms 0 1 0 1 0 0 0 1
Papillary renal cell carcinoma, sporadic 0 0 0 1 0 0 0 1
Polyps, multiple and recurrent inflammatory fibroid, gastrointestinal 0 1 0 1 0 0 1 1
Regorafenib response 0 0 0 0 0 1 0 1
Renal cell carcinoma, papillary, 1 0 0 0 0 1 0 0 1
Schizophrenia, susceptibility to 0 0 0 0 0 1 0 1
Squamous cell carcinoma of the head and neck 0 0 0 1 0 0 0 1
Trametinib-Dabrafenib Response 0 0 0 0 0 1 0 1
Vemurafenib-Cobimetinib Response 0 0 0 0 0 1 0 1
carboplatin response - Efficacy 0 0 0 0 0 1 0 1
cyclophosphamide response - Toxicity/ADR 0 0 0 0 0 1 0 1
methotrexate response - Dosage, Efficacy, Toxicity/ADR 0 0 0 0 0 1 0 1
methotrexate response - Toxicity/ADR 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 109
Download table as spreadsheet
HGVS dbSNP
NM_000222.2(KIT):c.-14T>A rs140909964
NM_000222.2(KIT):c.101C>T (p.Pro34Leu) rs55755457
NM_000222.2(KIT):c.1116-5T>C rs376229086
NM_000222.2(KIT):c.1119C>T (p.Tyr373=) rs72549293
NM_000222.2(KIT):c.1195G>A (p.Val399Ile) rs143707288
NM_000222.2(KIT):c.1207A>G (p.Ile403Val) rs878853759
NM_000222.2(KIT):c.1230T>C (p.Asn410=) rs140536677
NM_000222.2(KIT):c.1232-6C>G rs1553890995
NM_000222.2(KIT):c.1264G>A (p.Val422Met) rs1560414398
NM_000222.2(KIT):c.1403C>T (p.Pro468Leu) rs200518498
NM_000222.2(KIT):c.153C>T (p.Gly51=) rs147363921
NM_000222.2(KIT):c.154G>A (p.Asp52Asn) rs121913505
NM_000222.2(KIT):c.1621A>C (p.Met541Leu) rs3822214
NM_000222.2(KIT):c.1638A>G (p.Lys546=) rs55986963
NM_000222.2(KIT):c.1669T>A (p.Trp557Arg) rs121913235
NM_000222.2(KIT):c.1669T>C (p.Trp557Arg) rs121913235
NM_000222.2(KIT):c.1674G>T (p.Lys558Asn) rs200375589
NM_000222.2(KIT):c.1676T>A (p.Val559Asp) rs121913517
NM_000222.2(KIT):c.1676T>C (p.Val559Ala) rs121913517
NM_000222.2(KIT):c.1676T>G (p.Val559Gly) rs121913517
NM_000222.2(KIT):c.1679T>A (p.Val560Asp) rs121913521
NM_000222.2(KIT):c.1679T>G (p.Val560Gly) rs121913521
NM_000222.2(KIT):c.1727T>C (p.Leu576Pro) rs121913513
NM_000222.2(KIT):c.1794A>T (p.Gly598=) rs72549292
NM_000222.2(KIT):c.1924A>G (p.Lys642Glu) rs121913512
NM_000222.2(KIT):c.1961T>C (p.Val654Ala) rs121913523
NM_000222.2(KIT):c.1964A>G (p.Asn655Ser) rs1057519707
NM_000222.2(KIT):c.1965T>A (p.Asn655Lys) rs1057519708
NM_000222.2(KIT):c.1965T>G (p.Asn655Lys) rs1057519708
NM_000222.2(KIT):c.200C>G (p.Thr67Ser) rs144933028
NM_000222.2(KIT):c.2089C>T (p.His697Tyr) rs763308199
NM_000222.2(KIT):c.2231T>C (p.Ile744Thr) rs549887751
NM_000222.2(KIT):c.2263G>A (p.Ala755Thr) rs201165084
NM_000222.2(KIT):c.2394C>T (p.Ile798=) rs55789615
NM_000222.2(KIT):c.2446G>C (p.Asp816His) rs121913506
NM_000222.2(KIT):c.2446G>T (p.Asp816Tyr) rs121913506
NM_000222.2(KIT):c.2447A>T (p.Asp816Val) rs121913507
NM_000222.2(KIT):c.2465A>T (p.Asn822Ile) rs993022333
NM_000222.2(KIT):c.2466T>A (p.Asn822Lys) rs121913514
NM_000222.2(KIT):c.2466T>G (p.Asn822Lys) rs121913514
NM_000222.2(KIT):c.2484C>T (p.Asn828=) rs141347955
NM_000222.2(KIT):c.2485G>C (p.Ala829Pro) rs1057519713
NM_000222.2(KIT):c.2515G>A (p.Glu839Lys) rs121913509
NM_000222.2(KIT):c.252G>T (p.Thr84=) rs56411694
NM_000222.2(KIT):c.2586G>C (p.Leu862=) rs3733542
NM_000222.2(KIT):c.2670C>T (p.Leu890=) rs745967881
NM_000222.2(KIT):c.2802+9A>G rs369450271
NM_000222.2(KIT):c.2847C>T (p.Pro949=) rs56288823
NM_000222.2(KIT):c.2881G>A (p.Gly961Ser) rs773828910
NM_000222.2(KIT):c.2928C>G (p.Val976=) rs182068450
NM_000222.2(KIT):c.734C>T (p.Thr245Met) rs755508624
NM_000222.2(KIT):c.776A>G (p.Tyr259Cys) rs200422460
NM_000222.2(KIT):c.839C>T (p.Ala280Val) rs386833402
NM_000254.2(MTR):c.2756A>G (p.Asp919Gly) rs1805087
NM_002454.3(MTRR):c.1049A>G (p.Lys350Arg) rs162036
NM_002454.3(MTRR):c.1783C>T (p.His595Tyr) rs10380
NM_002454.3(MTRR):c.524C>T (p.Ser175Leu) rs1532268
NM_002454.3(MTRR):c.66A>G (p.Ile22Met) rs1801394
NM_003000.2(SDHB):c.178A>G (p.Thr60Ala) rs34599281
NM_003000.2(SDHB):c.200+7A>G rs371329778
NM_003000.2(SDHB):c.32G>A (p.Arg11His) rs111430410
NM_003000.2(SDHB):c.423+20T>A rs190139590
NM_003000.2(SDHB):c.487T>C (p.Ser163Pro) rs33927012
NM_003000.2(SDHB):c.650G>A (p.Arg217His) rs747518441
NM_003000.2(SDHB):c.8C>G (p.Ala3Gly) rs11203289
NM_003001.3(SDHC):c.405+1G>A rs587776653
NM_004333.6(BRAF):c.1799T>A (p.Val600Glu) rs113488022
NM_005957.4(MTHFR):c.1286A>C (p.Glu429Ala) rs1801131
NM_005957.4(MTHFR):c.665C>T (p.Ala222Val) rs1801133
NM_006206.6(PDGFRA):c.1019G>A (p.Arg340Gln) rs77524207
NM_006206.6(PDGFRA):c.1099G>A (p.Val367Met) rs147982027
NM_006206.6(PDGFRA):c.1122G>C (p.Arg374Ser) rs61735622
NM_006206.6(PDGFRA):c.1285G>A (p.Gly429Arg) rs150577828
NM_006206.6(PDGFRA):c.1320G>A (p.Thr440=) rs56026726
NM_006206.6(PDGFRA):c.1422G>A (p.Thr474=) rs149899465
NM_006206.6(PDGFRA):c.1432T>C (p.Ser478Pro) rs35597368
NM_006206.6(PDGFRA):c.1471G>A (p.Ala491Thr) rs563016888
NM_006206.6(PDGFRA):c.1731G>A (p.Pro577=) rs55830582
NM_006206.6(PDGFRA):c.1821G>C (p.Val607=) rs886059446
NM_006206.6(PDGFRA):c.2003-7C>T rs886059447
NM_006206.6(PDGFRA):c.201C>T (p.Ser67=) rs35805947
NM_006206.6(PDGFRA):c.2266G>A (p.Asp756Asn) rs555347387
NM_006206.6(PDGFRA):c.236G>A (p.Gly79Asp) rs36035373
NM_006206.6(PDGFRA):c.249G>A (p.Thr83=) rs569343676
NM_006206.6(PDGFRA):c.2526_2537del (p.Ile843_Asp846del) rs1553906053
NM_006206.6(PDGFRA):c.2536G>T (p.Asp846Tyr) rs121908588
NM_006206.6(PDGFRA):c.2742G>C (p.Arg914=) rs56384252
NM_006206.6(PDGFRA):c.2778C>T (p.Tyr926=) rs138519829
NM_006206.6(PDGFRA):c.2897A>G (p.His966Arg) rs200042995
NM_006206.6(PDGFRA):c.2936G>A (p.Arg979His) rs587778598
NM_006206.6(PDGFRA):c.3004G>T (p.Asp1002Tyr) rs200676118
NM_006206.6(PDGFRA):c.3156G>A (p.Thr1052=) rs55996208
NM_006206.6(PDGFRA):c.3211G>A (p.Asp1071Asn) rs376544204
NM_006206.6(PDGFRA):c.3228C>T (p.Ile1076=) rs148629782
NM_006206.6(PDGFRA):c.342C>T (p.Gly114=) rs1553902455
NM_006206.6(PDGFRA):c.368-3C>T rs55947416
NM_006206.6(PDGFRA):c.368-4A>G rs944515268
NM_006206.6(PDGFRA):c.451C>T (p.Arg151Cys)
NM_006206.6(PDGFRA):c.517G>A (p.Asp173Asn) rs763718380
NM_006206.6(PDGFRA):c.590A>C (p.Lys197Thr) rs200484286
NM_006206.6(PDGFRA):c.599C>G (p.Thr200Ser) rs149951350
NM_006206.6(PDGFRA):c.661C>T (p.Leu221Phe) rs139913632
NM_006206.6(PDGFRA):c.672G>A (p.Val224=) rs151259376
NM_006206.6(PDGFRA):c.738A>G (p.Gln246=) rs377699966
NM_006206.6(PDGFRA):c.784G>C (p.Glu262Gln) rs376265745
NM_006206.6(PDGFRA):c.801A>G (p.Pro267=) rs55966236
NM_006206.6(PDGFRA):c.827C>T (p.Thr276Met) rs142492533
NM_006206.6(PDGFRA):c.996C>T (p.Val332=) rs142498442
NM_033360.4(KRAS):c.35G>C (p.Gly12Ala) rs121913529

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