ClinVar Miner

Variants with conflicting interpretations studied for Neoplasm

Coded as:
Minimum review status of the submission for Neoplasm: Y axis collection method of the submission for Neoplasm:
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
55 14 0 41 0 0 10 49

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
Neoplasm pathogenic uncertain significance likely benign benign
likely pathogenic 41 10 4 4

Condition to condition summary #

Total conditions: 72
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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
not provided 0 1 0 16 0 0 4 20
Hereditary cancer-predisposing syndrome 0 2 0 11 0 0 6 17
Non-small cell lung cancer 0 0 0 7 0 0 0 7
not specified 0 0 0 2 0 0 5 7
Li-Fraumeni syndrome 0 0 0 6 0 0 0 6
Li-Fraumeni syndrome 1 0 0 0 6 0 0 0 6
Carcinoma of colon 0 0 0 4 0 0 0 4
McCune-Albright syndrome 0 0 0 4 0 0 0 4
Neoplasm of the large intestine 0 14 0 4 0 0 0 4
Renal cell carcinoma, papillary, 1 0 2 0 2 0 0 2 4
Adrenocortical carcinoma, hereditary; Familial cancer of breast; Glioma susceptibility 1; Osteosarcoma; Li-Fraumeni syndrome 1; Nasopharyngeal carcinoma; Carcinoma of pancreas; Choroid plexus papilloma; Carcinoma of colon; Basal cell carcinoma, susceptibility to, 7; Hepatocellular carcinoma 0 0 0 3 0 0 0 3
Cutaneous melanoma 0 4 0 3 0 0 0 3
Lung cancer 0 0 0 3 0 0 0 3
Ovarian Neoplasms 0 6 0 3 0 0 0 3
Peutz-Jeghers syndrome 0 0 0 2 0 0 1 3
Rasopathy 0 2 0 3 0 0 0 3
Cushing's syndrome 0 0 0 2 0 0 0 2
Gastrointestinal stroma tumor 0 0 0 1 0 0 1 2
Hereditary cutaneous melanoma 0 0 0 1 0 0 1 2
Multiple endocrine neoplasia, type 2 0 0 0 2 0 0 0 2
Neoplasm of stomach 0 0 0 2 0 0 0 2
Neoplasm of the thyroid gland 0 3 0 2 0 0 0 2
PITUITARY ADENOMA 3, MULTIPLE TYPES 0 0 0 2 0 0 0 2
Retinoblastoma 0 0 0 2 0 0 0 2
Sex cord-stromal tumor 0 0 0 2 0 0 0 2
Anaplastic thyroid carcinoma 0 0 0 1 0 0 0 1
Astrocytoma, anaplastic 0 0 0 1 0 0 0 1
Astrocytoma, low-grade, somatic 0 0 0 1 0 0 0 1
Atypical teratoid/rhabdoid tumor 0 0 0 1 0 0 0 1
Breast adenocarcinoma 0 0 0 1 0 0 0 1
Burkitt lymphoma 0 0 0 1 0 0 0 1
Cardio-facio-cutaneous syndrome 0 1 0 1 0 0 0 1
Childhood hepatocellular carcinoma 0 0 0 1 0 0 0 1
Colon cancer, advanced 0 0 0 1 0 0 0 1
Congenital diaphragmatic hernia 0 0 0 0 0 0 1 1
Congenital giant melanocytic nevus; Epidermal nevus syndrome; Bladder cancer, somatic; Costello syndrome; Epidermal nevus; Follicular thyroid carcinoma 0 0 0 1 0 0 0 1
Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi 0 0 0 1 0 0 0 1
Costello syndrome 0 0 0 1 0 0 0 1
Cowden syndrome 1 0 0 0 1 0 0 0 1
Cutaneous malignant melanoma 1 0 0 0 1 0 0 0 1
Cystic epithelial invagination containing papillae lined by columnar epithelium 0 0 0 1 0 0 0 1
Epidermal nevus syndrome 0 0 0 1 0 0 0 1
Erythrocytosis, familial, 2; Von Hippel-Lindau syndrome 0 0 0 0 0 0 1 1
Familial medullary thyroid carcinoma 0 0 0 1 0 0 0 1
Follicular thyroid carcinoma 0 0 0 1 0 0 0 1
Germ cell tumor, nonseminomatous 0 0 0 1 0 0 0 1
Hepatocellular carcinoma 0 11 0 1 0 0 0 1
Keratosis, seborrheic 0 0 0 1 0 0 0 1
Li-Fraumeni-like syndrome 0 0 0 1 0 0 0 1
MACRODACTYLY, SOMATIC 0 0 0 1 0 0 0 1
Malignant Colorectal Neoplasm 0 0 0 1 0 0 0 1
Malignant tumor of esophagus 0 0 0 1 0 0 0 1
Malignant tumor of prostate 0 0 0 0 0 0 1 1
Multiple endocrine neoplasia, type 2a 0 1 0 1 0 0 0 1
Neoplasm of ovary 0 0 0 1 0 0 0 1
Neoplasm of the breast 0 16 0 1 0 0 0 1
Non-Hodgkin lymphoma 0 2 0 1 0 0 0 1
Noonan syndrome 0 0 0 1 0 0 0 1
Noonan syndrome 1 0 0 0 1 0 0 0 1
Noonan syndrome 7 0 0 0 1 0 0 0 1
Ovarian epithelial cancer 0 0 0 1 0 0 0 1
PIK3CA related overgrowth spectrum 0 0 0 1 0 0 0 1
PTEN hamartoma tumor syndrome 0 0 0 1 0 0 0 1
Papillary thyroid carcinoma 0 0 0 1 0 0 0 1
Pectus excavatum; Acute myeloid leukemia; Short stature; Cognitive impairment; Webbed neck; Pancytopenia; Abnormality of the tongue 0 0 0 1 0 0 0 1
Pheochromocytoma 0 0 0 1 0 0 0 1
Retinoblastoma, trilateral 0 0 0 1 0 0 0 1
Rosette-forming glioneuronal tumor 0 0 0 1 0 0 0 1
Sarcoma 0 0 0 1 0 0 0 1
Small cell lung cancer 0 4 0 1 0 0 0 1
Von Hippel-Lindau syndrome 0 0 0 1 0 0 1 1
Wilms Tumor 0 0 0 0 0 0 1 1

All variants with conflicting interpretations #

Total variants: 49
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HGVS dbSNP
NM_000077.4(CDKN2A):c.172C>T (p.Arg58Ter) rs121913387
NM_000077.4(CDKN2A):c.247C>T (p.His83Tyr) rs121913385
NM_000077.4(CDKN2A):c.250G>T (p.Asp84Tyr) rs11552822
NM_000077.4(CDKN2A):c.329G>A (p.Trp110Ter) rs1057519852
NM_000222.2(KIT):c.154G>A (p.Asp52Asn) rs121913505
NM_000245.3(MET):c.2908C>T (p.Arg970Cys) rs34589476
NM_000245.3(MET):c.2975C>T (p.Thr992Ile) rs56391007
NM_000314.4(PTEN):c.700C>T (p.Arg234Trp) rs786201730
NM_000314.7(PTEN):c.389G>A (p.Arg130Gln) rs121909229
NM_000321.2(RB1):c.1666C>T (p.Arg556Ter) rs121913304
NM_000321.2(RB1):c.2242G>T (p.Glu748Ter) rs121913297
NM_000321.2(RB1):c.409G>T (p.Glu137Ter) rs121913296
NM_000455.4(STK11):c.109C>T (p.Gln37Ter) rs121913324
NM_000455.4(STK11):c.508C>T (p.Gln170Ter) rs121913323
NM_000455.4(STK11):c.580G>A (p.Asp194Asn) rs121913315
NM_000455.4(STK11):c.842C>T (p.Pro281Leu) rs121913322
NM_000516.5(GNAS):c.601C>T (p.Arg201Cys) rs11554273
NM_000516.5(GNAS):c.602G>A (p.Arg201His) rs121913495
NM_000516.5(GNAS):c.602G>T (p.Arg201Leu) rs121913495
NM_000516.5(GNAS):c.680A>T (p.Gln227Leu) rs121913494
NM_000546.5(TP53):c.524G>A (p.Arg175His) rs28934578
NM_000546.5(TP53):c.733G>A (p.Gly245Ser) rs28934575
NM_000546.5(TP53):c.742C>T (p.Arg248Trp) rs121912651
NM_000546.5(TP53):c.743G>A (p.Arg248Gln) rs11540652
NM_000546.5(TP53):c.817C>T (p.Arg273Cys) rs121913343
NM_000546.5(TP53):c.818G>A (p.Arg273His) rs28934576
NM_000551.3(VHL):c.241C>T (p.Pro81Ser) rs104893829
NM_001005862.2(ERBB2):c.2236G>A (p.Gly746Ser) rs28933369
NM_001127500.2(MET):c.3328G>A (p.Val1110Ile) rs786202724
NM_001127500.2(MET):c.3743A>G (p.Tyr1248Cys) rs121913246
NM_001127500.2(MET):c.3804G>A (p.Met1268Ile) rs121913676
NM_002467.5(MYC):c.302A>C (p.Asn101Thr) rs121918683
NM_002524.4(NRAS):c.38G>T (p.Gly13Val) rs121434596
NM_004333.4(BRAF):c.1391G>A (p.Gly464Glu) rs121913348
NM_004333.4(BRAF):c.1406G>C (p.Gly469Ala) rs121913355
NM_004333.4(BRAF):c.1406G>T (p.Gly469Val) rs121913355
NM_004333.4(BRAF):c.1796C>T (p.Thr599Ile) rs121913375
NM_004333.5(BRAF):c.1391G>T (p.Gly464Val) rs121913348
NM_004333.5(BRAF):c.1756G>A (p.Glu586Lys) rs121913340
NM_004333.5(BRAF):c.1785T>G (p.Phe595Leu) rs121913341
NM_004333.5(BRAF):c.1789C>G (p.Leu597Val) rs121913369
NM_004333.5(BRAF):c.1799T>A (p.Val600Glu) rs113488022
NM_004333.5(BRAF):c.1801A>G (p.Lys601Glu) rs121913364
NM_005343.4(HRAS):c.37G>T (p.Gly13Cys) rs104894228
NM_006218.4(PIK3CA):c.3140A>G (p.His1047Arg) rs121913279
NM_020975.4(RET):c.1901G>A (p.Cys634Tyr) rs75996173
NM_020975.4(RET):c.2304G>C (p.Glu768Asp) rs78014899
NM_176795.4(HRAS):c.182A>G (p.Gln61Arg) rs121913233
NM_198291.2(SRC):c.1591C>T (p.Gln531Ter) rs121913314

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