ClinVar Miner

Variants with conflicting interpretations studied for Renal cell carcinoma, papillary, 1

Coded as:
Minimum review status of the submission for Renal cell carcinoma, papillary, 1: Y axis collection method of the submission for Renal cell carcinoma, papillary, 1:
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
398 161 11 68 37 3 26 121

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
Renal cell carcinoma, papillary, 1 pathogenic likely pathogenic uncertain significance likely benign benign drug response
pathogenic 0 4 0 0 0 0
likely pathogenic 34 0 21 1 0 3
uncertain significance 2 0 8 21 4 0
likely benign 0 2 23 0 13 0
benign 0 2 9 28 3 0

Condition to condition summary #

Total conditions: 59
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 0 108 0 35 25 0 8 65
not provided 0 19 11 17 12 0 2 37
not specified 0 29 0 23 6 0 0 25
Renal cell carcinoma, papillary, 1 622 36 0 11 11 0 0 22
Li-Fraumeni syndrome 0 7 0 5 0 0 13 17
Neoplasm of the large intestine 0 68 0 8 0 0 0 8
Non-small cell lung cancer 0 1 0 8 0 0 0 8
Li-Fraumeni syndrome 1 0 2 0 4 0 0 2 6
Neoplasm of the breast 0 74 0 6 0 0 0 6
Ovarian Neoplasms 0 18 0 6 0 0 0 6
Cutaneous melanoma 0 1 0 5 0 0 0 5
Carcinoma 0 0 0 3 0 0 1 4
Neoplasm 0 2 0 2 0 0 2 4
Breast adenocarcinoma 0 0 0 3 0 0 0 3
Carcinoma of colon 0 0 0 3 0 0 0 3
PIK3CA related overgrowth spectrum 0 0 0 3 0 0 0 3
Congenital giant melanocytic nevus 0 0 0 2 0 0 0 2
Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi 0 0 0 2 0 0 0 2
Epidermal nevus 0 0 0 2 0 0 0 2
Focal cortical dysplasia type II 0 0 0 2 0 0 0 2
Hepatocellular carcinoma 0 57 0 2 0 0 0 2
Keratosis, seborrheic 0 0 0 2 0 0 0 2
Kidney Carcinoma 0 1 0 2 0 0 0 2
Megalencephaly cutis marmorata telangiectatica congenita 0 0 0 2 0 0 0 2
Neoplasm of ovary 0 0 0 2 0 0 0 2
Neoplasm of stomach 0 0 0 2 0 0 0 2
Neurocutaneous melanosis 0 0 0 2 0 0 0 2
Ovarian epithelial cancer 0 0 0 2 0 0 0 2
PTEN hamartoma tumor syndrome 0 0 0 1 0 0 1 2
Von Hippel-Lindau syndrome 0 1 0 2 0 0 0 2
Astrocytoma, anaplastic; Pleomorphic xanthoastrocytoma 0 0 0 1 0 0 0 1
Capillary malformation of the lower lip, lymphatic malformation of face and neck, asymmetry of face and limbs, and partial/generalized overgrowth 0 0 0 1 0 0 0 1
Congenital diaphragmatic hernia 0 0 0 0 1 0 0 1
Cowden syndrome 0 1 0 1 0 0 0 1
Cowden syndrome 1 0 0 0 1 0 0 0 1
Endometrial carcinoma 0 0 0 1 0 0 0 1
Epidermal nevus syndrome 0 0 0 1 0 0 0 1
Erythrocytosis, familial, 2; Pheochromocytoma; Von Hippel-Lindau syndrome; Renal cell carcinoma, nonpapillary 0 0 0 1 0 0 0 1
Erythrocytosis, familial, 2; Von Hippel-Lindau syndrome 0 1 0 1 0 0 0 1
Familial cancer of breast; Megalencephaly cutis marmorata telangiectatica congenita; Lung cancer; Congenital macrodactylia; Keratosis, seborrheic; Epidermal nevus; Neoplasm of ovary; Capillary malformation of the lower lip, lymphatic malformation of face and neck, asymmetry of face and limbs, and partial/generalized overgrowth; Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi; Carcinoma of colon; Neoplasm of stomach; Cowden syndrome 5; Hepatocellular carcinoma 0 0 0 1 0 0 0 1
Follicular thyroid carcinoma 0 0 0 1 0 0 0 1
Gastrointestinal stroma tumor; Paragangliomas 4; Pheochromocytoma 0 0 0 0 1 0 0 1
Hemimegalencephaly 0 0 0 1 0 0 0 1
Hepatoblastoma 0 0 0 1 0 0 0 1
Hereditary Paraganglioma-Pheochromocytoma Syndromes 0 0 0 0 0 0 1 1
Hereditary nonpolyposis colon cancer 0 0 0 0 1 0 0 1
Histone Methylation Therapy response 0 0 0 0 0 1 0 1
Li-Fraumeni-like syndrome 0 0 0 1 0 0 0 1
Lynch syndrome 0 0 0 0 0 0 1 1
MACRODACTYLY, SOMATIC 0 0 0 1 0 0 0 1
Macrodactyly of toe; Stroke 0 0 0 1 0 0 0 1
Osteosarcoma 0 0 0 1 0 0 0 1
PARP Inhibitor response 0 0 0 0 0 1 0 1
Paragangliomas 4 0 0 0 0 1 0 0 1
Pheochromocytoma 0 0 0 1 0 0 0 1
RAS Inhibitor response 0 0 0 0 0 1 0 1
Rasopathy 0 0 0 0 0 0 1 1
Rosette-forming glioneuronal tumor 0 0 0 1 0 0 0 1
Smith-Kingsmore syndrome 0 0 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 121
Download table as spreadsheet
HGVS dbSNP
NM_000245.3(MET):c.1019A>G (p.Asp340Gly) rs200690492
NM_000245.3(MET):c.110T>C (p.Val37Ala) rs201315884
NM_000245.3(MET):c.1124A>G (p.Asn375Ser) rs33917957
NM_000245.3(MET):c.1180C>A (p.His394Asn) rs201628326
NM_000245.3(MET):c.1810C>G (p.Leu604Val) rs201861645
NM_000245.3(MET):c.2383A>G (p.Asn795Asp) rs200633053
NM_000245.3(MET):c.2908C>T (p.Arg970Cys) rs34589476
NM_000245.3(MET):c.2975C>T (p.Thr992Ile) rs56391007
NM_000245.3(MET):c.3356G>C (p.Gly1119Ala) rs201037977
NM_000245.3(MET):c.4151C>G (p.Ala1384Gly) rs202166889
NM_000245.3(MET):c.504G>T (p.Glu168Asp) rs55985569
NM_000245.3(MET):c.607T>A (p.Ser203Thr) rs200861145
NM_000245.3(MET):c.71G>A (p.Gly24Glu) rs180985111
NM_000245.3(MET):c.948A>G (p.Ile316Met) rs35225896
NM_000245.3(MET):c.967A>G (p.Ser323Gly) rs201467281
NM_000251.2(MSH2):c.1045C>G (p.Pro349Ala) rs267607939
NM_000314.4(PTEN):c.389G>T (p.Arg130Leu) rs121909229
NM_000314.6(PTEN):c.388C>G (p.Arg130Gly) rs121909224
NM_000314.6(PTEN):c.389G>C (p.Arg130Pro) rs121909229
NM_000314.7(PTEN):c.389G>A (p.Arg130Gln) rs121909229
NM_000546.5(TP53):c.374C>A (p.Thr125Lys) rs786201057
NM_000546.5(TP53):c.374C>G (p.Thr125Arg) rs786201057
NM_000546.5(TP53):c.374C>T (p.Thr125Met) rs786201057
NM_000546.5(TP53):c.422G>A (p.Cys141Tyr) rs587781288
NM_000546.5(TP53):c.423C>G (p.Cys141Trp) rs1057519977
NM_000546.5(TP53):c.526T>A (p.Cys176Ser) rs967461896
NM_000546.5(TP53):c.527G>A (p.Cys176Tyr) rs786202962
NM_000546.5(TP53):c.528C>G (p.Cys176Trp) rs1057519980
NM_000546.5(TP53):c.613T>A (p.Tyr205Asn) rs1057520008
NM_000546.5(TP53):c.613T>C (p.Tyr205His) rs1057520008
NM_000546.5(TP53):c.613T>G (p.Tyr205Asp) rs1057520008
NM_000546.5(TP53):c.638G>A (p.Arg213Gln) rs587778720
NM_000546.5(TP53):c.638G>C (p.Arg213Pro) rs587778720
NM_000546.5(TP53):c.641A>G (p.His214Arg) rs1057519992
NM_000546.5(TP53):c.658T>C (p.Tyr220His) rs530941076
NM_000546.5(TP53):c.659A>C (p.Tyr220Ser) rs121912666
NM_000546.5(TP53):c.659A>G (p.Tyr220Cys) rs121912666
NM_000546.5(TP53):c.715A>G (p.Asn239Asp) rs876660807
NM_000546.5(TP53):c.716A>C (p.Asn239Thr) rs1057519999
NM_000546.5(TP53):c.722C>T (p.Ser241Phe) rs28934573
NM_000546.5(TP53):c.814G>A (p.Val272Met) rs121912657
NM_000546.5(TP53):c.814G>T (p.Val272Leu) rs121912657
NM_000546.5(TP53):c.815T>G (p.Val272Gly) rs876660333
NM_000546.5(TP53):c.824G>A (p.Cys275Tyr) rs863224451
NM_000546.5(TP53):c.824G>C (p.Cys275Ser) rs863224451
NM_000546.5(TP53):c.842A>G (p.Asp281Gly) rs587781525
NM_000546.5(TP53):c.842A>T (p.Asp281Val) rs587781525
NM_000546.5(TP53):c.843C>G (p.Asp281Glu) rs1057519984
NM_000546.5(TP53):c.844C>G (p.Arg282Gly) rs28934574
NM_000546.5(TP53):c.844C>T (p.Arg282Trp) rs28934574
NM_000546.5(TP53):c.845G>A (p.Arg282Gln) rs730882008
NM_000551.3(VHL):c.481C>T (p.Arg161Ter) rs5030818
NM_000551.3(VHL):c.499C>T (p.Arg167Trp) rs5030820
NM_001127500.1(MET):c.1039G>A (p.Ala347Thr) rs200074800
NM_001127500.1(MET):c.144G>A (p.Ala48=) rs11762213
NM_001127500.1(MET):c.3335A>G (p.His1112Arg) rs121913243
NM_001127500.1(MET):c.654G>A (p.Arg218=) rs35284565
NM_001127500.2(MET):c.-14-4G>A rs144126521
NM_001127500.2(MET):c.103A>T (p.Met35Leu) rs375353223
NM_001127500.2(MET):c.1076G>A (p.Arg359Gln) rs201274041
NM_001127500.2(MET):c.1085T>C (p.Met362Thr) rs77523018
NM_001127500.2(MET):c.1099A>G (p.Ile367Val) rs774146015
NM_001127500.2(MET):c.1191C>T (p.Cys397=) rs35763409
NM_001127500.2(MET):c.1263C>T (p.Thr421=) rs45499391
NM_001127500.2(MET):c.12C>T (p.Pro4=) rs772251895
NM_001127500.2(MET):c.1715G>A (p.Ser572Asn) rs199771406
NM_001127500.2(MET):c.1723C>A (p.Leu575Ile) rs587778445
NM_001127500.2(MET):c.1863-5dupT rs766900241
NM_001127500.2(MET):c.1932C>T (p.His644=) rs45520237
NM_001127500.2(MET):c.2110A>G (p.Asn704Asp) rs373030463
NM_001127500.2(MET):c.2198C>T (p.Thr733Ile) rs201271860
NM_001127500.2(MET):c.2332A>G (p.Ile778Val) rs786202191
NM_001127500.2(MET):c.2372C>T (p.Pro791Leu) rs771333219
NM_001127500.2(MET):c.2488C>G (p.Gln830Glu) rs398123568
NM_001127500.2(MET):c.2638-7del rs587780736
NM_001127500.2(MET):c.2638-9T>C rs74994656
NM_001127500.2(MET):c.2712C>T (p.His904=) rs748950533
NM_001127500.2(MET):c.2716C>T (p.His906Tyr) rs115574135
NM_001127500.2(MET):c.2769C>T (p.Ser923=) rs45572835
NM_001127500.2(MET):c.3119G>A (p.Arg1040Gln) rs45612435
NM_001127500.2(MET):c.3271C>T (p.Pro1091Ser) rs398123569
NM_001127500.2(MET):c.3272C>T (p.Pro1091Leu) rs370529693
NM_001127500.2(MET):c.3328G>A (p.Val1110Ile) rs786202724
NM_001127500.2(MET):c.3575A>G (p.His1192Arg) rs372830789
NM_001127500.2(MET):c.3576T>C (p.His1192=) rs146651797
NM_001127500.2(MET):c.3603C>T (p.Gly1201=) rs371165052
NM_001127500.2(MET):c.3736G>A (p.Asp1246Asn) rs121913671
NM_001127500.2(MET):c.3743A>G (p.Tyr1248Cys) rs121913246
NM_001127500.2(MET):c.3864C>T (p.Gly1288=) rs200865810
NM_001127500.2(MET):c.390C>T (p.Leu130=) rs150588908
NM_001127500.2(MET):c.4128C>T (p.Asn1376=) rs772860611
NM_001127500.2(MET):c.4141G>A (p.Ala1381Thr) rs45578433
NM_001127500.2(MET):c.4159T>C (p.Leu1387=) rs45575438
NM_001127500.2(MET):c.4171G>C (p.Asp1391His) rs398123570
NM_001127500.2(MET):c.467C>T (p.Ser156Leu) rs56311081
NM_001127500.2(MET):c.468G>A (p.Ser156=) rs576502224
NM_001127500.2(MET):c.632T>G (p.Leu211Trp) rs45483396
NM_001127500.2(MET):c.639G>A (p.Ser213=) rs587780738
NM_001127500.2(MET):c.690G>A (p.Thr230=) rs200138253
NM_001127500.2(MET):c.789G>A (p.Thr263=) rs554190225
NM_001127500.2(MET):c.798G>A (p.Arg266=) rs185301166
NM_001127500.2(MET):c.901A>G (p.Thr301Ala) rs201687037
NM_001127500.2(MET):c.959C>T (p.Ala320Val) rs35776110
NM_002524.3(NRAS):c.182A>C (p.Gln61Pro) rs11554290
NM_002524.3(NRAS):c.182A>G (p.Gln61Arg) rs11554290
NM_002524.3(NRAS):c.183A>T (p.Gln61His) rs121913255
NM_002524.4(NRAS):c.181C>A (p.Gln61Lys) rs121913254
NM_002524.4(NRAS):c.182A>T (p.Gln61Leu) rs11554290
NM_003000.2(SDHB):c.32G>A (p.Arg11His) rs111430410
NM_004958.3(MTOR):c.4447T>C (p.Cys1483Arg) rs1057519914
NM_004958.3(MTOR):c.4448G>T (p.Cys1483Phe) rs786205165
NM_004958.3(MTOR):c.6644C>A (p.Ser2215Tyr) rs587777894
NM_004958.3(MTOR):c.6644C>T (p.Ser2215Phe) rs587777894
NM_006218.3(PIK3CA):c.1633G>C (p.Glu545Gln) rs104886003
NM_006218.3(PIK3CA):c.1634A>C (p.Glu545Ala) rs121913274
NM_006218.3(PIK3CA):c.1634A>G (p.Glu545Gly) rs121913274
NM_006218.3(PIK3CA):c.1635G>T (p.Glu545Asp) rs121913275
NM_006218.3(PIK3CA):c.3139C>T (p.His1047Tyr) rs121913281
NM_006218.4(PIK3CA):c.1633G>A (p.Glu545Lys) rs104886003
NM_006218.4(PIK3CA):c.3140A>G (p.His1047Arg) rs121913279
NM_006218.4(PIK3CA):c.3140A>T (p.His1047Leu) rs121913279

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