ClinVar Miner

Variants with conflicting interpretations studied for Gastrointestinal stromal tumor

Coded as:
Minimum review status of the submission for Gastrointestinal stromal tumor: Collection method of the submission for Gastrointestinal stromal 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 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
5238 149 0 21 42 0 9 71

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 stromal tumor pathogenic likely pathogenic uncertain significance likely benign benign
pathogenic 0 5 0 0 0
likely pathogenic 5 0 9 0 0
uncertain significance 0 9 0 39 4
likely benign 0 0 39 0 16
benign 0 0 4 16 0

Condition to condition summary #

Total conditions: 1
Download table as spreadsheet
Condition 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
Gastrointestinal stromal tumor 5238 149 0 21 42 0 9 71

All variants with conflicting interpretations #

Total variants: 71
Download table as spreadsheet
HGVS dbSNP gnomAD frequency
NM_000222.3(KIT):c.2586G>C (p.Leu862=) rs3733542 0.16755
NM_000222.3(KIT):c.*217G>A rs17084733 0.10193
NM_000222.3(KIT):c.1621A>C (p.Met541Leu) rs3822214 0.07727
NM_006206.6(PDGFRA):c.368-3C>T rs55947416 0.04647
NM_006206.6(PDGFRA):c.201C>T (p.Ser67=) rs35805947 0.00429
NM_006206.6(PDGFRA):c.2778C>T (p.Tyr926=) rs138519829 0.00372
NM_000222.3(KIT):c.1383A>G (p.Thr461=) rs151016327 0.00324
NM_006206.6(PDGFRA):c.661C>T (p.Leu221Phe) rs139913632 0.00307
NM_006206.6(PDGFRA):c.996C>T (p.Val332=) rs142498442 0.00204
NM_006206.6(PDGFRA):c.1122G>C (p.Arg374Ser) rs61735622 0.00183
NM_000222.3(KIT):c.2805T>A (p.Ile935=) rs72549296 0.00176
NM_006206.6(PDGFRA):c.3228C>T (p.Ile1076=) rs148629782 0.00076
NM_006206.6(PDGFRA):c.3156G>A (p.Thr1052=) rs55996208 0.00064
NM_000222.3(KIT):c.1195G>A (p.Val399Ile) rs143707288 0.00059
NM_000222.3(KIT):c.200C>G (p.Thr67Ser) rs144933028 0.00045
NM_000222.3(KIT):c.821C>T (p.Thr274Met) rs138585275 0.00035
NM_000222.3(KIT):c.878A>G (p.Asn293Ser) rs137909416 0.00034
NM_000222.3(KIT):c.67+12C>T rs374618962 0.00031
NM_006206.6(PDGFRA):c.276G>A (p.Ala92=) rs140725151 0.00030
NM_000222.3(KIT):c.1594G>A (p.Val532Ile) rs55792975 0.00028
NM_006206.6(PDGFRA):c.801A>G (p.Pro267=) rs55966236 0.00024
NM_000222.3(KIT):c.2349C>T (p.Leu783=) rs151046591 0.00022
NM_000222.3(KIT):c.952A>G (p.Met318Val) rs143388949 0.00019
NM_000222.3(KIT):c.1674G>A (p.Lys558=) rs200375589 0.00016
NM_000222.3(KIT):c.2484C>T (p.Asn828=) rs141347955 0.00015
NM_000222.3(KIT):c.2234-3C>T rs370131461 0.00014
NM_006206.6(PDGFRA):c.1135T>G (p.Leu379Val) rs199827643 0.00014
NM_000222.3(KIT):c.978C>T (p.Asn326=) rs148594615 0.00011
NM_000222.3(KIT):c.1694G>T (p.Gly565Val) rs200945282 0.00009
NM_006206.6(PDGFRA):c.17C>T (p.Pro6Leu) rs754092062 0.00009
NM_000222.3(KIT):c.910A>G (p.Thr304Ala) rs202052259 0.00006
NM_006206.6(PDGFRA):c.2742G>C (p.Arg914=) rs56384252 0.00006
NM_006206.6(PDGFRA):c.827C>T (p.Thr276Met) rs142492533 0.00006
NM_000222.3(KIT):c.2802+9A>G rs369450271 0.00004
NM_006206.6(PDGFRA):c.3039C>T (p.Ser1013=) rs138150216 0.00004
NM_006206.6(PDGFRA):c.2811G>A (p.Pro937=) rs190260215 0.00002
NM_000222.3(KIT):c.2118T>G (p.Leu706=) rs766840704 0.00001
NM_000222.3(KIT):c.2562C>G (p.Ser854=) rs750039813 0.00001
NM_000222.3(KIT):c.2670C>T (p.Leu890=) rs745967881 0.00001
NM_003001.5(SDHC):c.380A>G (p.His127Arg) rs786203457 0.00001
NM_006206.6(PDGFRA):c.1122-6T>A rs754623338 0.00001
NM_006206.6(PDGFRA):c.1794C>T (p.Val598=) rs1218651787 0.00001
NM_006206.6(PDGFRA):c.2003-7C>T rs886059447 0.00001
NM_006206.6(PDGFRA):c.2232C>T (p.Pro744=) rs1060504254 0.00001
NM_006206.6(PDGFRA):c.2266G>A (p.Asp756Asn) rs555347387 0.00001
NM_006206.6(PDGFRA):c.2881-8G>A rs778161572 0.00001
NM_006206.6(PDGFRA):c.345G>A (p.Arg115=) rs778510648 0.00001
NM_000222.3(KIT):c.1185C>A (p.Ser395=) rs755864184
NM_000222.3(KIT):c.1232-6C>G rs1553890995
NM_000222.3(KIT):c.1669T>G (p.Trp557Gly) rs121913235
NM_000222.3(KIT):c.1670G>C (p.Trp557Ser) rs1057520032
NM_000222.3(KIT):c.1675G>A (p.Val559Ile) rs121913520
NM_000222.3(KIT):c.1676T>A (p.Val559Asp) rs121913517
NM_000222.3(KIT):c.1924A>G (p.Lys642Glu) rs121913512
NM_000222.3(KIT):c.1961T>C (p.Val654Ala) rs121913523
NM_000222.3(KIT):c.2009C>T (p.Thr670Ile) rs121913516
NM_000222.3(KIT):c.2447A>T (p.Asp816Val) rs121913507
NM_000222.3(KIT):c.2466T>A (p.Asn822Lys) rs121913514
NM_000222.3(KIT):c.2466T>G (p.Asn822Lys) rs121913514
NM_000222.3(KIT):c.252G>A (p.Thr84=) rs56411694
NM_000222.3(KIT):c.252G>T (p.Thr84=) rs56411694
NM_006206.6(PDGFRA):c.1596G>C (p.Leu532=) rs1723603076
NM_006206.6(PDGFRA):c.1821G>C (p.Val607=) rs886059446
NM_006206.6(PDGFRA):c.2040A>C (p.Gly680=) rs773679384
NM_006206.6(PDGFRA):c.219T>C (p.Asn73=) rs886059443
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.2574C>A (p.Pro858=) rs771421611
NM_006206.6(PDGFRA):c.3195G>A (p.Glu1065=) rs1724822643
NM_006206.6(PDGFRA):c.451C>T (p.Arg151Cys) rs1449637193
NM_006206.6(PDGFRA):c.480C>T (p.Thr160=) rs1461385164

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