ClinVar Miner

Variants with conflicting interpretations studied for Neoplasm of brain

Coded as:
Minimum review status of the submission for Neoplasm of brain: Y axis collection method of the submission for Neoplasm of brain:
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
2 103 0 80 0 8 58 132

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 of brain pathogenic uncertain significance likely benign drug response risk factor other
likely pathogenic 80 57 1 4 3 1

Condition to condition summary #

Total conditions: 70
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
Li-Fraumeni syndrome 0 16 0 22 0 0 43 64
Hereditary cancer-predisposing syndrome 0 35 0 23 0 0 17 39
not provided 0 14 0 28 0 0 5 32
Neoplasm of the large intestine 0 177 0 15 0 0 0 15
Li-Fraumeni syndrome 1 0 3 0 9 0 0 3 12
Neoplasm of the breast 0 182 0 12 0 0 0 12
Non-small cell lung cancer 0 4 0 11 0 0 0 11
Ovarian Neoplasms 0 60 0 10 0 0 0 10
Cutaneous melanoma 0 1 0 9 0 0 0 9
Acute myeloid leukemia 0 65 0 7 0 0 0 7
not specified 0 4 0 3 0 0 4 7
Breast adenocarcinoma 0 0 0 6 0 0 0 6
Carcinoma of colon 0 1 0 5 0 0 0 5
Neoplasm of ovary 0 0 0 4 0 0 0 4
PIK3CA related overgrowth spectrum 0 1 0 4 0 0 0 4
PTEN hamartoma tumor syndrome 0 0 0 4 0 0 0 4
Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi 0 0 0 3 0 0 0 3
Neuroblastoma 3 0 0 0 3 0 3 0 3
Ovarian epithelial cancer 0 0 0 3 0 0 0 3
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 2 0 0 0 2
Capillary malformation of the lower lip, lymphatic malformation of face and neck, asymmetry of face and limbs, and partial/generalized overgrowth 0 0 0 2 0 0 0 2
Congenital giant melanocytic nevus 0 0 0 2 0 0 0 2
Cowden syndrome 0 0 0 2 0 0 0 2
Cowden syndrome 1 0 0 0 2 0 0 0 2
Epidermal nevus 0 0 0 2 0 0 0 2
Hepatocellular carcinoma 0 149 0 2 0 0 0 2
Keratosis, seborrheic 0 0 0 2 0 0 0 2
Li-Fraumeni-like syndrome 0 0 0 2 0 0 0 2
Macrocephaly/autism syndrome 0 0 0 2 0 0 0 2
Macrocephaly/autism syndrome; Meningioma, familial; Malignant tumor of prostate; VACTERL association with hydrocephalus; Glioma susceptibility 2; PTEN hamartoma tumor syndrome; Cowden syndrome 1 0 0 0 2 0 0 0 2
Malignant tumor of prostate 0 1 0 0 0 0 2 2
Megalencephaly cutis marmorata telangiectatica congenita 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
PARP Inhibitor response 0 0 0 0 0 2 0 2
Anaplastic thyroid carcinoma 0 0 0 1 0 0 0 1
Astrocytoma, anaplastic 0 0 0 1 0 0 0 1
Astrocytoma, anaplastic; Pleomorphic xanthoastrocytoma 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
Cardio-facio-cutaneous syndrome 0 0 0 1 0 0 0 1
Cowden syndrome 5 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
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 0 0 0 1 0 0 0 1
Germ cell tumor, nonseminomatous 0 0 0 1 0 0 0 1
Glioblastoma multiforme, somatic 0 0 0 1 0 0 0 1
Hepatoblastoma 0 0 0 1 0 0 0 1
Histone Methylation Therapy response 0 0 0 0 0 1 0 1
Inborn genetic diseases 0 1 0 1 0 0 0 1
Lung cancer 0 1 0 1 0 0 0 1
MACRODACTYLY, SOMATIC 0 0 0 1 0 0 0 1
Macrocephaly/autism syndrome; Cowden syndrome 1 0 0 0 1 0 0 0 1
Macrodactyly of toe; Stroke 0 0 0 1 0 0 0 1
Malignant Colorectal Neoplasm 0 0 0 1 0 0 0 1
Medulloblastoma 0 26 0 0 0 1 0 1
Nasopharyngeal carcinoma 0 0 0 1 0 0 0 1
Neuroblastoma 0 9 0 1 0 0 0 1
Non-Hodgkin lymphoma 0 15 0 1 0 0 0 1
Osteosarcoma 0 0 0 1 0 0 0 1
PTEN-related disorder 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
Proteus-like syndrome 0 0 0 1 0 0 0 1
RAS Inhibitor response 0 0 0 0 0 1 0 1
Rasopathy 0 1 0 0 0 0 1 1
Rosette-forming glioneuronal tumor 0 0 0 1 0 0 0 1
Sarcoma 0 1 0 1 0 0 0 1

All variants with conflicting interpretations #

Total variants: 132
Download table as spreadsheet
HGVS dbSNP
NM_000314.6(PTEN):c.1003C>T (p.Arg335Ter) rs121909231
NM_000314.6(PTEN):c.388C>T (p.Arg130Ter) rs121909224
NM_000314.6(PTEN):c.517C>T (p.Arg173Cys) rs121913293
NM_000314.6(PTEN):c.518G>A (p.Arg173His) rs121913294
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.394A>G (p.Lys132Glu) rs747342068
NM_000546.5(TP53):c.395A>G (p.Lys132Arg) rs1057519996
NM_000546.5(TP53):c.395A>T (p.Lys132Met) rs1057519996
NM_000546.5(TP53):c.403T>G (p.Cys135Gly) rs1057519975
NM_000546.5(TP53):c.405C>G (p.Cys135Trp) rs1057519976
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.451C>A (p.Pro151Thr) rs28934874
NM_000546.5(TP53):c.451C>G (p.Pro151Ala) rs28934874
NM_000546.5(TP53):c.451C>T (p.Pro151Ser) rs28934874
NM_000546.5(TP53):c.452C>A (p.Pro151His) rs1057520000
NM_000546.5(TP53):c.452C>G (p.Pro151Arg) rs1057520000
NM_000546.5(TP53):c.487T>A (p.Tyr163Asn) rs786203436
NM_000546.5(TP53):c.488A>G (p.Tyr163Cys) rs148924904
NM_000546.5(TP53):c.517G>A (p.Val173Met) rs876660754
NM_000546.5(TP53):c.517G>T (p.Val173Leu) rs876660754
NM_000546.5(TP53):c.518T>A (p.Val173Glu) rs1057519747
NM_000546.5(TP53):c.523C>G (p.Arg175Gly) rs138729528
NM_000546.5(TP53):c.523C>T (p.Arg175Cys) rs138729528
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.535C>A (p.His179Asn) rs587780070
NM_000546.5(TP53):c.535C>T (p.His179Tyr) rs587780070
NM_000546.5(TP53):c.536A>G (p.His179Arg) rs1057519991
NM_000546.5(TP53):c.536A>T (p.His179Leu) rs1057519991
NM_000546.5(TP53):c.578A>T (p.His193Leu) rs786201838
NM_000546.5(TP53):c.581T>A (p.Leu194His) rs1057519998
NM_000546.5(TP53):c.581T>C (p.Leu194Pro) rs1057519998
NM_000546.5(TP53):c.581T>G (p.Leu194Arg) rs1057519998
NM_000546.5(TP53):c.584T>A (p.Ile195Asn) rs760043106
NM_000546.5(TP53):c.584T>C (p.Ile195Thr) rs760043106
NM_000546.5(TP53):c.585C>G (p.Ile195Met) rs1057519994
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.646G>A (p.Val216Met) rs730882025
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.706T>A (p.Tyr236Asn) rs587782289
NM_000546.5(TP53):c.706T>G (p.Tyr236Asp) rs587782289
NM_000546.5(TP53):c.709A>G (p.Met237Val) rs730882004
NM_000546.5(TP53):c.711G>A (p.Met237Ile) rs587782664
NM_000546.5(TP53):c.712T>C (p.Cys238Arg) rs1057519981
NM_000546.5(TP53):c.713G>A (p.Cys238Tyr) rs730882005
NM_000546.5(TP53):c.713G>T (p.Cys238Phe) rs730882005
NM_000546.5(TP53):c.722C>T (p.Ser241Phe) rs28934573
NM_000546.5(TP53):c.730G>A (p.Gly244Ser) rs1057519989
NM_000546.5(TP53):c.730G>T (p.Gly244Cys) rs1057519989
NM_000546.5(TP53):c.731G>A (p.Gly244Asp) rs985033810
NM_000546.5(TP53):c.733G>A (p.Gly245Ser) rs28934575
NM_000546.5(TP53):c.733G>C (p.Gly245Arg) rs28934575
NM_000546.5(TP53):c.733G>T (p.Gly245Cys) rs28934575
NM_000546.5(TP53):c.734G>A (p.Gly245Asp) rs121912656
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.764T>A (p.Ile255Asn) rs876659675
NM_000546.5(TP53):c.764T>C (p.Ile255Thr) rs876659675
NM_000546.5(TP53):c.797G>T (p.Gly266Val) rs193920774
NM_000546.5(TP53):c.817C>A (p.Arg273Ser) rs121913343
NM_000546.5(TP53):c.818G>A (p.Arg273His) rs28934576
NM_000546.5(TP53):c.818G>C (p.Arg273Pro) rs28934576
NM_000546.5(TP53):c.818G>T (p.Arg273Leu) rs28934576
NM_000546.5(TP53):c.820G>C (p.Val274Leu) rs1057520005
NM_000546.5(TP53):c.821T>G (p.Val274Gly) rs1057520006
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.832C>A (p.Pro278Thr) rs17849781
NM_000546.5(TP53):c.832C>G (p.Pro278Ala) rs17849781
NM_000546.5(TP53):c.832C>T (p.Pro278Ser) rs17849781
NM_000546.5(TP53):c.833C>A (p.Pro278His) rs876659802
NM_000546.5(TP53):c.833C>G (p.Pro278Arg) rs876659802
NM_000546.5(TP53):c.833C>T (p.Pro278Leu) rs876659802
NM_000546.5(TP53):c.838A>G (p.Arg280Gly) rs753660142
NM_000546.5(TP53):c.839G>A (p.Arg280Lys) rs121912660
NM_000546.5(TP53):c.839G>C (p.Arg280Thr) rs121912660
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_000546.5(TP53):c.856G>A (p.Glu286Lys) rs786201059
NM_000546.5(TP53):c.857A>G (p.Glu286Gly) rs1057519985
NM_001126115.1(TP53):c.401G>A (p.Gly134Glu) rs193920774
NM_001126115.1(TP53):c.443G>T (p.Arg148Ile) rs121912660
NM_001282386.1(IDH1):c.395G>A (p.Arg132His) rs121913500
NM_001282387.1(IDH1):c.394C>A (p.Arg132Ser) rs121913499
NM_001282387.1(IDH1):c.394C>G (p.Arg132Gly) rs121913499
NM_001282387.1(IDH1):c.394C>T (p.Arg132Cys) rs121913499
NM_001289910.1(IDH2):c.359G>A (p.Arg120Lys) rs121913503
NM_001289910.1(IDH2):c.359G>T (p.Arg120Met) rs121913503
NM_001904.3(CTNNB1):c.98C>G (p.Ser33Cys) rs121913400
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_002834.4(PTPN11):c.214G>A (p.Ala72Thr) rs121918453
NM_002834.4(PTPN11):c.215C>T (p.Ala72Val) rs121918454
NM_004304.4(ALK):c.3383G>C (p.Gly1128Ala) rs113994088
NM_004304.4(ALK):c.3575G>C (p.Arg1192Pro) rs113994089
NM_004304.4(ALK):c.3824G>A (p.Arg1275Gln) rs113994087
NM_004333.4(BRAF):c.1780G>A (p.Asp594Asn) rs397516896
NM_004333.4(BRAF):c.1780G>C (p.Asp594His) rs397516896
NM_004333.4(BRAF):c.1781A>G (p.Asp594Gly) rs121913338
NM_004333.5(BRAF):c.1799T>A (p.Val600Glu) rs113488022
NM_005896.3(IDH1):c.395G>T (p.Arg132Leu) rs121913500
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.1636C>G (p.Gln546Glu) rs121913286
NM_006218.3(PIK3CA):c.1637A>T (p.Gln546Leu) rs397517201
NM_006218.3(PIK3CA):c.3129G>A (p.Met1043Ile) rs121913283
NM_006218.3(PIK3CA):c.3139C>T (p.His1047Tyr) rs121913281
NM_006218.3(PIK3CA):c.353G>A (p.Gly118Asp) rs587777790
NM_006218.4(PIK3CA):c.1624G>A (p.Glu542Lys) rs121913273
NM_006218.4(PIK3CA):c.1624G>C (p.Glu542Gln) rs121913273
NM_006218.4(PIK3CA):c.1633G>A (p.Glu545Lys) rs104886003
NM_006218.4(PIK3CA):c.1636C>A (p.Gln546Lys) rs121913286
NM_006218.4(PIK3CA):c.1637A>C (p.Gln546Pro) rs397517201
NM_006218.4(PIK3CA):c.1637A>G (p.Gln546Arg) rs397517201
NM_006218.4(PIK3CA):c.3140A>G (p.His1047Arg) rs121913279
NM_006218.4(PIK3CA):c.3140A>T (p.His1047Leu) rs121913279

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