ClinVar Miner

Variants with conflicting interpretations studied for Li-Fraumeni syndrome 1

Coded as:
Minimum review status of the submission for Li-Fraumeni syndrome 1: Y axis collection method of the submission for Li-Fraumeni syndrome 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
15 47 1 35 25 3 18 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
Li-Fraumeni syndrome 1 pathogenic likely pathogenic uncertain significance likely benign benign drug response risk factor
pathogenic 0 17 2 1 0 1 0
likely pathogenic 7 0 4 1 1 0 0
uncertain significance 3 10 0 19 9 1 1
likely benign 0 0 4 0 11 0 0
benign 0 0 2 3 1 1 0

Condition to condition summary #

Total conditions: 56
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 66 0 16 19 0 6 40
Li-Fraumeni syndrome 0 46 0 16 12 0 5 32
not provided 0 53 1 8 10 0 5 22
not specified 0 26 0 8 10 0 4 21
Squamous cell carcinoma of the head and neck 0 11 0 11 2 0 5 17
Neoplasm of the breast 0 6 0 10 0 0 6 16
Lung adenocarcinoma 0 3 0 10 0 0 5 15
Hepatocellular carcinoma 0 3 0 10 0 0 4 14
Ovarian Serous Cystadenocarcinoma 0 3 0 10 0 0 4 14
Pancreatic adenocarcinoma 0 3 0 10 0 0 4 14
Carcinoma of esophagus 0 3 0 8 0 0 5 13
Glioblastoma 0 3 0 9 0 0 4 13
Squamous cell lung carcinoma 0 3 0 9 0 0 4 13
Adenocarcinoma of stomach 0 3 0 10 0 0 2 12
Neoplasm of brain 0 3 0 9 0 0 3 12
Neoplasm of the large intestine 0 3 0 10 0 0 2 12
Ovarian Neoplasms 0 4 0 10 0 0 2 12
Uterine Carcinosarcoma 0 1 0 8 0 0 4 12
Transitional cell carcinoma of the bladder 0 2 0 10 0 0 1 11
Adenocarcinoma of prostate 0 1 0 9 0 0 0 9
Malignant neoplasm of body of uterus 0 2 0 7 0 0 2 9
Brainstem glioma 0 1 0 6 0 0 0 6
Malignant melanoma of skin 0 3 0 6 0 0 0 6
Multiple myeloma 0 0 0 4 0 0 2 6
Neoplasm 0 0 0 6 0 0 0 6
Renal cell carcinoma, papillary, 1 0 2 0 4 0 0 2 6
Squamous cell carcinoma of the skin 0 3 0 5 0 0 1 6
Acute myeloid leukemia 0 2 0 4 0 0 1 5
Li-Fraumeni syndrome 1 119 9 0 3 1 0 1 5
Small cell lung cancer 0 2 0 4 0 0 1 5
Chronic lymphocytic leukemia 0 0 0 3 0 0 1 4
Medulloblastoma 0 0 0 4 0 0 0 4
Non-Hodgkin lymphoma 0 1 0 1 0 0 2 3
Adrenocortical carcinoma 0 1 0 2 0 0 0 2
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 4 0 2 0 0 0 2
Myelodysplastic syndrome 0 0 0 2 0 0 0 2
Adenocarcinoma 0 0 0 1 0 0 0 1
Adenoid cystic carcinoma 0 0 0 1 0 0 0 1
Anaplastic thyroid carcinoma 0 0 0 1 0 0 0 1
Basal cell carcinoma, susceptibility to, 7 0 0 0 0 0 1 0 1
CODON 72 POLYMORPHISM 0 0 0 0 1 0 0 1
Familial colorectal cancer 0 0 0 0 0 0 1 1
Lymphoma 0 0 0 1 0 0 0 1
Malignant Colorectal Neoplasm 0 0 0 1 0 0 0 1
Malignant tumor of prostate 0 0 0 0 0 0 1 1
Nasopharyngeal Neoplasms 0 0 0 1 0 0 0 1
Neoplasm of stomach 0 0 0 0 0 0 1 1
PARP Inhibitor response 0 0 0 0 0 1 0 1
Papillary renal cell carcinoma, sporadic 0 0 0 1 0 0 0 1
Rhabdomyosarcoma 0 0 0 0 1 0 0 1
Sarcoma 0 0 0 1 0 0 0 1
antineoplastic agents response - Efficacy, Toxicity/ADR 0 0 0 0 0 1 0 1
cisplatin response - Efficacy, Toxicity/ADR 0 0 0 0 0 1 0 1
cyclophosphamide response - Efficacy, Toxicity/ADR 0 0 0 0 0 1 0 1
fluorouracil response - Efficacy, Toxicity/ADR 0 0 0 0 0 1 0 1
paclitaxel response - Efficacy, Toxicity/ADR 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 71
Download table as spreadsheet
HGVS dbSNP
NM_000546.5(TP53):c.319T>C (p.Tyr107His) rs368771578
NM_000546.5(TP53):c.672+18G>C rs199578278
NM_000546.5(TP53):c.673-37C>T rs374907737
NM_000546.5(TP53):c.74+14T>C rs184743157
NM_000546.5(TP53):c.782+12C>T rs17881780
NM_000546.5(TP53):c.993+13G>C rs369599972
NM_000546.5(TP53):c.993+326_993+341del rs730882013
NM_001126112.2(TP53):c.*1175A>C rs78378222
NM_001126112.2(TP53):c.1000G>C (p.Gly334Arg) rs730882028
NM_001126112.2(TP53):c.1031T>C (p.Leu344Pro) rs121912662
NM_001126112.2(TP53):c.1079G>C (p.Gly360Ala) rs35993958
NM_001126112.2(TP53):c.107C>A (p.Pro36Gln) rs587781866
NM_001126112.2(TP53):c.108G>A (p.Pro36=) rs1800370
NM_001126112.2(TP53):c.139C>T (p.Pro47Ser) rs1800371
NM_001126112.2(TP53):c.173C>G (p.Pro58Arg) rs144386518
NM_001126112.2(TP53):c.215C>G (p.Pro72Arg) rs1042522
NM_001126112.2(TP53):c.234A>G (p.Ala78=) rs375099397
NM_001126112.2(TP53):c.248C>T (p.Ala83Val) rs201717599
NM_001126112.2(TP53):c.28G>A (p.Val10Ile) rs535274413
NM_001126112.2(TP53):c.31G>A (p.Glu11Lys) rs201382018
NM_001126112.2(TP53):c.374C>T (p.Thr125Met) rs786201057
NM_001126112.2(TP53):c.412G>C (p.Ala138Pro) rs28934875
NM_001126112.2(TP53):c.427G>A (p.Val143Met) rs587782620
NM_001126112.2(TP53):c.466C>T (p.Arg156Cys) rs563378859
NM_001126112.2(TP53):c.473G>A (p.Arg158His) rs587782144
NM_001126112.2(TP53):c.499C>T (p.Gln167Ter) rs1555526097
NM_001126112.2(TP53):c.524G>A (p.Arg175His) rs28934578
NM_001126112.2(TP53):c.535C>T (p.His179Tyr) rs587780070
NM_001126112.2(TP53):c.542G>A (p.Arg181His) rs397514495
NM_001126112.2(TP53):c.566C>T (p.Ala189Val) rs121912665
NM_001126112.2(TP53):c.613T>A (p.Tyr205Asn) rs1057520008
NM_001126112.2(TP53):c.613T>G (p.Tyr205Asp) rs1057520008
NM_001126112.2(TP53):c.638G>A (p.Arg213Gln) rs587778720
NM_001126112.2(TP53):c.639A>G (p.Arg213=) rs1800372
NM_001126112.2(TP53):c.642T>G (p.His214Gln) rs587781386
NM_001126112.2(TP53):c.645T>G (p.Ser215Arg) rs1057520001
NM_001126112.2(TP53):c.646G>A (p.Val216Met) rs730882025
NM_001126112.2(TP53):c.655C>T (p.Pro219Ser) rs879253894
NM_001126112.2(TP53):c.659A>C (p.Tyr220Ser) rs121912666
NM_001126112.2(TP53):c.665C>T (p.Pro222Leu) rs146340390
NM_001126112.2(TP53):c.666G>T (p.Pro222=) rs72661118
NM_001126112.2(TP53):c.6G>A (p.Glu2=) rs143458271
NM_001126112.2(TP53):c.704A>G (p.Asn235Ser) rs144340710
NM_001126112.2(TP53):c.724T>A (p.Cys242Ser) rs1057519982
NM_001126112.2(TP53):c.733G>A (p.Gly245Ser) rs28934575
NM_001126112.2(TP53):c.733G>T (p.Gly245Cys) rs28934575
NM_001126112.2(TP53):c.734G>A (p.Gly245Asp) rs121912656
NM_001126112.2(TP53):c.742C>T (p.Arg248Trp) rs121912651
NM_001126112.2(TP53):c.743G>A (p.Arg248Gln) rs11540652
NM_001126112.2(TP53):c.766A>G (p.Thr256Ala) rs587781433
NM_001126112.2(TP53):c.772G>A (p.Glu258Lys) rs121912652
NM_001126112.2(TP53):c.787A>G (p.Asn263Asp) rs72661119
NM_001126112.2(TP53):c.794T>C (p.Leu265Pro) rs879253942
NM_001126112.2(TP53):c.814G>T (p.Val272Leu) rs121912657
NM_001126112.2(TP53):c.817C>T (p.Arg273Cys) rs121913343
NM_001126112.2(TP53):c.818G>A (p.Arg273His) rs28934576
NM_001126112.2(TP53):c.844C>T (p.Arg282Trp) rs28934574
NM_001126112.2(TP53):c.845G>A (p.Arg282Gln) rs730882008
NM_001126112.2(TP53):c.847C>T (p.Arg283Cys) rs149633775
NM_001126112.2(TP53):c.848G>A (p.Arg283His) rs371409680
NM_001126112.2(TP53):c.869G>A (p.Arg290His) rs55819519
NM_001126112.2(TP53):c.885T>C (p.Pro295=) rs200073907
NM_001126112.2(TP53):c.892G>A (p.Glu298Lys) rs201744589
NM_001126112.2(TP53):c.919+1G>A rs1131691039
NM_001126112.2(TP53):c.91G>A (p.Val31Ile) rs201753350
NM_001126112.2(TP53):c.935C>G (p.Thr312Ser) rs145151284
NM_001126112.2(TP53):c.97-9C>T rs202217267
NM_001126112.2(TP53):c.993+12T>C rs1800899
NM_001126112.2(TP53):c.994-17C>T rs368691910
NM_001126113.2(TP53):c.1009C>T (p.Arg337Ter) rs554738122
NM_001126114.2(TP53):c.1021T>G (p.Cys341Gly) rs3021068

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