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
1102 139 11 47 32 7 7 90

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 0 0 0
likely pathogenic 22 0 2 0 0 0 0 2
uncertain significance 6 3 9 13 7 3 3 3
likely benign 0 0 20 0 21 0 0 0
benign 0 0 5 20 2 0 0 0

Condition to condition summary #

Total conditions: 49
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
Gastrointestinal stroma tumor 1285 15 0 20 9 0 2 31
not provided 0 3 11 4 11 2 0 25
Idiopathic hypereosinophilic syndrome 0 75 0 12 5 0 0 17
not specified 0 39 0 8 9 0 0 17
Cutaneous melanoma 0 4 0 14 0 0 3 16
Mastocytosis 0 25 0 7 2 0 0 9
Partial albinism 0 24 0 6 2 0 0 8
Disorders of Intracellular Cobalamin Metabolism 0 0 0 0 5 0 0 5
Gastrointestinal stromal tumor, familial 0 2 0 3 1 0 0 4
Thymoma 0 0 0 3 0 0 1 4
Acute myeloid leukemia 0 1 0 2 0 0 2 3
Cleft palate, isolated 0 1 0 0 2 0 0 2
Cutaneous mastocytosis 0 0 0 2 0 0 1 2
Dysgerminoma 0 0 0 0 0 2 0 2
Hereditary cancer-predisposing syndrome 0 1 0 1 1 0 0 2
MTHFR deficiency, thermolabile type 0 0 0 0 2 0 1 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
Piebaldism 0 0 0 0 2 0 0 2
Brainstem glioma 0 0 0 1 0 0 0 1
Carney triad 0 0 0 1 0 0 0 1
Down syndrome, susceptibility to 0 0 0 0 0 1 0 1
Gastrointestinal stroma tumor; Idiopathic hypereosinophilic syndrome 0 5 0 0 1 0 0 1
Glioblastoma 0 0 0 1 0 0 0 1
Hematologic neoplasm 0 3 0 0 0 0 1 1
Hereditary Paraganglioma-Pheochromocytoma Syndromes 0 1 0 1 0 0 0 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
Multiple myeloma 0 0 0 1 0 0 0 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
Regorafenib response 0 0 0 0 0 1 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
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: 90
Download table as spreadsheet
HGVS dbSNP
NM_000222.2(KIT):c.-14T>A rs140909964
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.1199A>G (p.Asn400Ser) rs72549294
NM_000222.2(KIT):c.1232-6C>G rs1553890995
NM_000222.2(KIT):c.1403C>T (p.Pro468Leu) rs200518498
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.1694G>T (p.Gly565Val) rs200945282
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>G (p.Asn655Lys) rs1057519708
NM_000222.2(KIT):c.2089C>T (p.His697Tyr) rs763308199
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.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.2805T>A (p.Ile935=) rs72549296
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.532G>A (p.Ala178Thr) rs115585711
NM_000222.2(KIT):c.776A>G (p.Tyr259Cys) rs200422460
NM_000222.2(KIT):c.821C>T (p.Thr274Met) rs138585275
NM_000222.2(KIT):c.839C>T (p.Ala280Val) rs386833402
NM_000222.2(KIT):c.910A>G (p.Thr304Ala) rs202052259
NM_000222.2(KIT):c.952A>G (p.Met318Val) rs143388949
NM_000254.2(MTR):c.2756A>G (p.Asp919Gly) rs1805087
NM_002454.2(MTRR):c.1049A>G (p.Lys350Arg) rs162036
NM_002454.2(MTRR):c.1783C>T (p.His595Tyr) rs10380
NM_002454.2(MTRR):c.524C>T (p.Ser175Leu) rs1532268
NM_002454.2(MTRR):c.66A>G (p.Ile22Met) rs1801394
NM_003000.2(SDHB):c.178A>G (p.Thr60Ala) rs34599281
NM_003001.3(SDHC):c.405+1G>A rs587776653
NM_004333.5(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_006206.5(PDGFRA):c.1019G>A (p.Arg340Gln) rs77524207
NM_006206.5(PDGFRA):c.1099G>A (p.Val367Met) rs147982027
NM_006206.5(PDGFRA):c.1122G>C (p.Arg374Ser) rs61735622
NM_006206.5(PDGFRA):c.1135T>G (p.Leu379Val) rs199827643
NM_006206.5(PDGFRA):c.1202C>A (p.Ala401Asp) rs397514549
NM_006206.5(PDGFRA):c.1285G>A (p.Gly429Arg) rs150577828
NM_006206.5(PDGFRA):c.1320G>A (p.Thr440=) rs56026726
NM_006206.5(PDGFRA):c.1325T>C (p.Leu442Pro) rs139236922
NM_006206.5(PDGFRA):c.1432T>C (p.Ser478Pro) rs35597368
NM_006206.5(PDGFRA):c.1471G>A (p.Ala491Thr) rs563016888
NM_006206.5(PDGFRA):c.1631T>C (p.Val544Ala) rs181854060
NM_006206.5(PDGFRA):c.1731G>A (p.Pro577=) rs55830582
NM_006206.5(PDGFRA):c.201C>T (p.Ser67=) rs35805947
NM_006206.5(PDGFRA):c.2266G>A (p.Asp756Asn) rs555347387
NM_006206.5(PDGFRA):c.2291G>A (p.Arg764His) rs141047712
NM_006206.5(PDGFRA):c.236G>A (p.Gly79Asp) rs36035373
NM_006206.5(PDGFRA):c.2526_2537del (p.Ile843_Asp846del) rs1553906053
NM_006206.5(PDGFRA):c.2536G>T (p.Asp846Tyr) rs121908588
NM_006206.5(PDGFRA):c.2742G>C (p.Arg914=) rs56384252
NM_006206.5(PDGFRA):c.2778C>T (p.Tyr926=) rs138519829
NM_006206.5(PDGFRA):c.2897A>G (p.His966Arg) rs200042995
NM_006206.5(PDGFRA):c.3004G>T (p.Asp1002Tyr) rs200676118
NM_006206.5(PDGFRA):c.3156G>A (p.Thr1052=) rs55996208
NM_006206.5(PDGFRA):c.3228C>T (p.Ile1076=) rs148629782
NM_006206.5(PDGFRA):c.368-3C>T rs55947416
NM_006206.5(PDGFRA):c.599C>G (p.Thr200Ser) rs149951350
NM_006206.5(PDGFRA):c.661C>T (p.Leu221Phe) rs139913632
NM_006206.5(PDGFRA):c.672G>A (p.Val224=) rs151259376
NM_006206.5(PDGFRA):c.801A>G (p.Pro267=) rs55966236
NM_006206.5(PDGFRA):c.896T>C (p.Val299Ala) rs200033396
NM_006206.5(PDGFRA):c.996C>T (p.Val332=) rs142498442
NM_033360.3(KRAS):c.35G>C (p.Gly12Ala) rs121913529

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.