ClinVar Miner

Variants with conflicting interpretations studied for Squamous cell lung carcinoma

Coded as:
Minimum review status of the submission for Squamous cell lung carcinoma: Y axis collection method of the submission for Squamous cell lung carcinoma:
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
7 119 0 80 0 5 71 146

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
Squamous cell lung carcinoma pathogenic uncertain significance likely benign benign drug response other
likely pathogenic 80 67 2 2 4 1

Condition to condition summary #

Total conditions: 76
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 13 0 31 0 0 49 79
Hereditary cancer-predisposing syndrome 0 32 0 23 0 0 15 38
not provided 0 13 0 29 0 0 9 38
Li-Fraumeni syndrome 1 0 3 0 9 0 0 4 13
Neoplasm of the large intestine 0 181 0 13 0 0 0 13
Non-small cell lung cancer 0 8 0 13 0 0 0 13
not specified 0 2 0 4 0 0 8 12
Neoplasm of the breast 0 177 0 8 0 0 0 8
Ovarian Neoplasms 0 55 0 8 0 0 0 8
Breast adenocarcinoma 0 0 0 6 0 0 0 6
Neoplasm of ovary 0 0 0 6 0 0 0 6
Carcinoma of colon 0 1 0 4 0 0 0 4
Congenital lipomatous overgrowth, vascular malformations, and epidermal nevi 0 0 0 4 0 0 0 4
Keratosis, seborrheic 0 0 0 4 0 0 0 4
PIK3CA related overgrowth spectrum 0 0 0 4 0 0 0 4
Capillary malformation of the lower lip, lymphatic malformation of face and neck, asymmetry of face and limbs, and partial/generalized overgrowth 0 0 0 3 0 0 0 3
Epidermal nevus 0 0 0 3 0 0 0 3
Juvenile myelomonocytic leukemia 0 0 0 3 0 0 0 3
Li-Fraumeni-like syndrome 0 0 0 3 0 0 0 3
Megalencephaly cutis marmorata telangiectatica congenita 0 0 0 3 0 0 0 3
PTEN hamartoma tumor syndrome 0 0 0 2 0 0 1 3
Rasopathy 0 0 0 3 0 0 0 3
Achondroplasia; Camptodactyly, tall stature, and hearing loss syndrome; Carcinoma of cervix; Crouzon syndrome with acanthosis nigricans; Levy-Hollister syndrome; Muenke syndrome; Thanatophoric dysplasia type 1; Thanatophoric dysplasia, type 2; Bladder cancer, somatic; Hypochondroplasia; Epidermal nevus; Severe achondroplasia with developmental delay and acanthosis nigricans; Malignant tumor of testis; Carcinoma of colon 0 0 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 0 0 2 0 0 0 2
Cowden syndrome 0 0 0 1 0 0 1 2
Cowden syndrome 1 0 0 0 2 0 0 0 2
Hepatocellular carcinoma 0 149 0 2 0 0 0 2
Hereditary cutaneous melanoma 0 0 0 0 0 0 2 2
Lung cancer 0 1 0 2 0 0 0 2
Malignant tumor of prostate 0 0 0 0 0 0 2 2
Neoplasm of stomach 0 0 0 2 0 0 0 2
Neoplasm of the thyroid gland 0 8 0 2 0 0 0 2
Non-Hodgkin lymphoma 0 15 0 2 0 0 0 2
Noonan syndrome 0 0 0 2 0 0 0 2
Ovarian epithelial cancer 0 0 0 2 0 0 0 2
PARP Inhibitor response 0 0 0 0 0 2 0 2
Thanatophoric dysplasia type 1 0 0 0 2 0 0 0 2
Age-related cortical cataract 0 0 0 0 0 0 1 1
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
Atypical teratoid/rhabdoid tumor 0 0 0 1 0 0 0 1
Bladder cancer, somatic 0 1 0 1 0 0 0 1
Carcinoma of cervix 0 0 0 1 0 0 0 1
Cardio-facio-cutaneous syndrome 0 0 0 1 0 0 0 1
Cardiofaciocutaneous syndrome 1 0 0 0 1 0 0 0 1
Cataract 6, multiple types 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
Costello syndrome 0 1 0 1 0 0 0 1
Cowden syndrome 5 0 0 0 1 0 0 0 1
Cowden syndrome 6 0 0 0 0 0 0 1 1
Craniosynostosis 0 0 0 1 0 0 0 1
Embryonal rhabdomyosarcoma 0 0 0 0 0 1 0 1
Endometrial carcinoma 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
Histone Methylation Therapy response 0 0 0 0 0 1 0 1
IMMUNODEFICIENCY, DEVELOPMENTAL DELAY, AND HYPOHOMOCYSTEINEMIA 0 0 0 1 0 0 0 1
Inborn genetic diseases 0 1 0 1 0 0 0 1
Lung adenocarcinoma 0 201 0 1 0 0 0 1
MACRODACTYLY, SOMATIC 0 0 0 1 0 0 0 1
Macrodactyly of toe; Stroke 0 0 0 1 0 0 0 1
Malignant Colorectal Neoplasm 0 1 0 1 0 0 0 1
Multiple myeloma 0 74 0 1 0 0 0 1
NEVUS SPILUS, SOMATIC 0 0 0 1 0 0 0 1
Nasopharyngeal carcinoma 0 0 0 1 0 0 0 1
Nevus sebaceous 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
Pfeiffer syndrome 0 0 0 1 0 0 0 1
Proteus syndrome 0 0 0 1 0 0 0 1
Rosette-forming glioneuronal tumor 0 0 0 1 0 0 0 1
SPITZ NEVUS, SOMATIC 0 0 0 1 0 0 0 1
Sarcoma 0 1 0 1 0 0 0 1
Skeletal dysplasia with acanthosis nigricans 0 0 0 1 0 0 0 1
Skeletal dysplasia; Short stature; Growth delay; Short ribs; Narrow chest; Small for gestational age; Bell-shaped thorax; Femoral bowing; Bowed humerus; Disproportionate short-limb short stature; Lethal short-limbed short stature; Lower limb undergrowth; Upper limb undergrowth 0 0 0 1 0 0 0 1
Tyrosine kinase inhibitor response 0 0 0 0 0 1 0 1

All variants with conflicting interpretations #

Total variants: 146
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HGVS dbSNP
NM_000077.4(CDKN2A):c.149A>G (p.Gln50Arg) rs587778189
NM_000077.4(CDKN2A):c.341C>T (p.Pro114Leu) rs121913386
NM_000142.4(FGFR3):c.742C>T (p.Arg248Cys) rs121913482
NM_000142.4(FGFR3):c.746C>G (p.Ser249Cys) rs121913483
NM_000314.7(PTEN):c.389G>A (p.Arg130Gln) rs121909229
NM_000314.7(PTEN):c.389G>C (p.Arg130Pro) rs121909229
NM_000314.7(PTEN):c.389G>T (p.Arg130Leu) rs121909229
NM_000455.4(STK11):c.1060T>C (p.Phe354Leu) rs1057520018
NM_001079846.1(CREBBP):c.4222C>T (p.Arg1408Cys) rs398124146
NM_001126112.2(TP53):c.332T>C (p.Leu111Pro) rs1057519997
NM_001126112.2(TP53):c.374C>A (p.Thr125Lys) rs786201057
NM_001126112.2(TP53):c.374C>G (p.Thr125Arg) rs786201057
NM_001126112.2(TP53):c.374C>T (p.Thr125Met) rs786201057
NM_001126112.2(TP53):c.394A>G (p.Lys132Glu) rs747342068
NM_001126112.2(TP53):c.395A>G (p.Lys132Arg) rs1057519996
NM_001126112.2(TP53):c.395A>T (p.Lys132Met) rs1057519996
NM_001126112.2(TP53):c.396G>C (p.Lys132Asn) rs866775781
NM_001126112.2(TP53):c.403T>A (p.Cys135Ser) rs1057519975
NM_001126112.2(TP53):c.403T>G (p.Cys135Gly) rs1057519975
NM_001126112.2(TP53):c.405C>G (p.Cys135Trp) rs1057519976
NM_001126112.2(TP53):c.422G>A (p.Cys141Tyr) rs587781288
NM_001126112.2(TP53):c.423C>G (p.Cys141Trp) rs1057519977
NM_001126112.2(TP53):c.451C>A (p.Pro151Thr) rs28934874
NM_001126112.2(TP53):c.451C>G (p.Pro151Ala) rs28934874
NM_001126112.2(TP53):c.451C>T (p.Pro151Ser) rs28934874
NM_001126112.2(TP53):c.452C>A (p.Pro151His) rs1057520000
NM_001126112.2(TP53):c.452C>G (p.Pro151Arg) rs1057520000
NM_001126112.2(TP53):c.487T>A (p.Tyr163Asn) rs786203436
NM_001126112.2(TP53):c.488A>G (p.Tyr163Cys) rs148924904
NM_001126112.2(TP53):c.523C>G (p.Arg175Gly) rs138729528
NM_001126112.2(TP53):c.523C>T (p.Arg175Cys) rs138729528
NM_001126112.2(TP53):c.526T>A (p.Cys176Ser) rs967461896
NM_001126112.2(TP53):c.527G>A (p.Cys176Tyr) rs786202962
NM_001126112.2(TP53):c.528C>G (p.Cys176Trp) rs1057519980
NM_001126112.2(TP53):c.535C>A (p.His179Asn) rs587780070
NM_001126112.2(TP53):c.535C>T (p.His179Tyr) rs587780070
NM_001126112.2(TP53):c.536A>G (p.His179Arg) rs1057519991
NM_001126112.2(TP53):c.536A>T (p.His179Leu) rs1057519991
NM_001126112.2(TP53):c.537T>G (p.His179Gln) rs876660821
NM_001126112.2(TP53):c.578A>C (p.His193Pro) rs786201838
NM_001126112.2(TP53):c.578A>T (p.His193Leu) rs786201838
NM_001126112.2(TP53):c.584T>A (p.Ile195Asn) rs760043106
NM_001126112.2(TP53):c.584T>C (p.Ile195Thr) rs760043106
NM_001126112.2(TP53):c.585C>G (p.Ile195Met) rs1057519994
NM_001126112.2(TP53):c.613T>A (p.Tyr205Asn) rs1057520008
NM_001126112.2(TP53):c.613T>C (p.Tyr205His) 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.638G>C (p.Arg213Pro) rs587778720
NM_001126112.2(TP53):c.641A>G (p.His214Arg) rs1057519992
NM_001126112.2(TP53):c.646G>A (p.Val216Met) rs730882025
NM_001126112.2(TP53):c.658T>C (p.Tyr220His) rs530941076
NM_001126112.2(TP53):c.659A>C (p.Tyr220Ser) rs121912666
NM_001126112.2(TP53):c.659A>G (p.Tyr220Cys) rs121912666
NM_001126112.2(TP53):c.700T>A (p.Tyr234Asn) rs864622237
NM_001126112.2(TP53):c.700T>C (p.Tyr234His) rs864622237
NM_001126112.2(TP53):c.700T>G (p.Tyr234Asp) rs864622237
NM_001126112.2(TP53):c.701A>G (p.Tyr234Cys) rs587780073
NM_001126112.2(TP53):c.706T>A (p.Tyr236Asn) rs587782289
NM_001126112.2(TP53):c.706T>G (p.Tyr236Asp) rs587782289
NM_001126112.2(TP53):c.709A>G (p.Met237Val) rs730882004
NM_001126112.2(TP53):c.711G>A (p.Met237Ile) rs587782664
NM_001126112.2(TP53):c.724T>A (p.Cys242Ser) rs1057519982
NM_001126112.2(TP53):c.724T>G (p.Cys242Gly) rs1057519982
NM_001126112.2(TP53):c.725G>A (p.Cys242Tyr) rs121912655
NM_001126112.2(TP53):c.725G>T (p.Cys242Phe) rs121912655
NM_001126112.2(TP53):c.730G>A (p.Gly244Ser) rs1057519989
NM_001126112.2(TP53):c.730G>T (p.Gly244Cys) rs1057519989
NM_001126112.2(TP53):c.731G>A (p.Gly244Asp) rs985033810
NM_001126112.2(TP53):c.733G>A (p.Gly245Ser) rs28934575
NM_001126112.2(TP53):c.733G>C (p.Gly245Arg) 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.743G>T (p.Arg248Leu) rs11540652
NM_001126112.2(TP53):c.745A>G (p.Arg249Gly) rs587782082
NM_001126112.2(TP53):c.745A>T (p.Arg249Trp) rs587782082
NM_001126112.2(TP53):c.746G>A (p.Arg249Lys) rs587782329
NM_001126112.2(TP53):c.746G>T (p.Arg249Met) rs587782329
NM_001126112.2(TP53):c.796G>C (p.Gly266Arg) rs1057519990
NM_001126112.2(TP53):c.797G>A (p.Gly266Glu) rs193920774
NM_001126112.2(TP53):c.797G>T (p.Gly266Val) rs193920774
NM_001126112.2(TP53):c.809T>C (p.Phe270Ser) rs1057519986
NM_001126112.2(TP53):c.817C>A (p.Arg273Ser) rs121913343
NM_001126112.2(TP53):c.818G>A (p.Arg273His) rs28934576
NM_001126112.2(TP53):c.818G>C (p.Arg273Pro) rs28934576
NM_001126112.2(TP53):c.818G>T (p.Arg273Leu) rs28934576
NM_001126112.2(TP53):c.832C>A (p.Pro278Thr) rs17849781
NM_001126112.2(TP53):c.832C>G (p.Pro278Ala) rs17849781
NM_001126112.2(TP53):c.832C>T (p.Pro278Ser) rs17849781
NM_001126112.2(TP53):c.833C>A (p.Pro278His) rs876659802
NM_001126112.2(TP53):c.833C>G (p.Pro278Arg) rs876659802
NM_001126112.2(TP53):c.833C>T (p.Pro278Leu) rs876659802
NM_001126112.2(TP53):c.838A>G (p.Arg280Gly) rs753660142
NM_001126112.2(TP53):c.839G>A (p.Arg280Lys) rs121912660
NM_001126112.2(TP53):c.839G>C (p.Arg280Thr) rs121912660
NM_001126112.2(TP53):c.839G>T (p.Arg280Ile) rs121912660
NM_001126112.2(TP53):c.841G>A (p.Asp281Asn) rs764146326
NM_001126112.2(TP53):c.841G>T (p.Asp281Tyr) rs764146326
NM_001126112.2(TP53):c.842A>G (p.Asp281Gly) rs587781525
NM_001126112.2(TP53):c.842A>T (p.Asp281Val) rs587781525
NM_001126112.2(TP53):c.843C>G (p.Asp281Glu) rs1057519984
NM_001126112.2(TP53):c.844C>G (p.Arg282Gly) rs28934574
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.845G>C (p.Arg282Pro) rs730882008
NM_001304718.2(PTEN):c.-363C>G rs121909224
NM_001349798.2(FBXW7):c.1514G>A (p.Arg505His) rs1057519896
NM_002834.4(PTPN11):c.1508G>T (p.Gly503Val) rs397507546
NM_002834.4(PTPN11):c.226G>A (p.Glu76Lys) rs121918464
NM_002834.4(PTPN11):c.227A>C (p.Glu76Ala) rs121918465
NM_002834.4(PTPN11):c.227A>G (p.Glu76Gly) rs121918465
NM_004333.6(BRAF):c.1397G>T (p.Gly466Val) rs121913351
NM_004333.6(BRAF):c.1405G>C (p.Gly469Arg) rs121913357
NM_004333.6(BRAF):c.1406G>A (p.Gly469Glu) rs121913355
NM_004333.6(BRAF):c.1406G>C (p.Gly469Ala) rs121913355
NM_004333.6(BRAF):c.1406G>T (p.Gly469Val) rs121913355
NM_004431.5(EPHA2):c.1171G>A (p.Gly391Arg) rs34192549
NM_005163.2(AKT1):c.49G>A (p.Glu17Lys) rs121434592
NM_005228.5(EGFR):c.2240T>C (p.Leu747Ser) rs397517097
NM_005228.5(EGFR):c.2303G>T (p.Ser768Ile) rs121913465
NM_005228.5(EGFR):c.2582T>A (p.Leu861Gln) rs121913444
NM_005228.5(EGFR):c.2582T>G (p.Leu861Arg) rs121913444
NM_005343.4(HRAS):c.37G>C (p.Gly13Arg) rs104894228
NM_005343.4(HRAS):c.37G>T (p.Gly13Cys) rs104894228
NM_005343.4(HRAS):c.38G>T (p.Gly13Val) rs104894226
NM_006164.5(NFE2L2):c.235G>A (p.Glu79Lys) rs1057519922
NM_006182.4(DDR2):c.1513G>A (p.Gly505Ser) rs115169993
NM_006218.4(PIK3CA):c.1258T>C (p.Cys420Arg) rs121913272
NM_006218.4(PIK3CA):c.1357G>A (p.Glu453Lys) rs1057519925
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.1633G>C (p.Glu545Gln) rs104886003
NM_006218.4(PIK3CA):c.1634A>C (p.Glu545Ala) rs121913274
NM_006218.4(PIK3CA):c.1634A>G (p.Glu545Gly) rs121913274
NM_006218.4(PIK3CA):c.1635G>T (p.Glu545Asp) rs121913275
NM_006218.4(PIK3CA):c.2176G>A (p.Glu726Lys) rs867262025
NM_006218.4(PIK3CA):c.3139C>T (p.His1047Tyr) rs121913281
NM_006218.4(PIK3CA):c.3140A>G (p.His1047Arg) rs121913279
NM_006218.4(PIK3CA):c.3140A>T (p.His1047Leu) rs121913279
NM_006218.4(PIK3CA):c.317G>T (p.Gly106Val) rs1057519930
NM_006218.4(PIK3CA):c.353G>A (p.Gly118Asp) rs587777790
NM_022970.3(FGFR2):c.870G>C (p.Trp290Cys) rs121918499
NM_033360.4(KRAS):c.183A>T (p.Gln61His) rs17851045

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