ClinVar Miner

Variants studied for benign neoplasm

Included ClinVar conditions (93):
Minimum submission review status: Collection method:
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Gene type:
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If a variant has more than one submission, it may be counted in more than one significance column. If this is the case, the total number of variants will be less than the sum of the other cells.

pathogenic likely pathogenic uncertain significance likely benign benign association risk factor other not provided total
333 128 945 281 257 28 2 3 5 1942

Gene and significance breakdown #

Total genes and gene combinations: 97
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign association risk factor other not provided total
SDHB 99 34 336 99 10 0 0 0 1 577
SDHD 48 14 192 64 8 0 0 0 0 323
RET 10 1 91 24 47 0 0 0 0 172
TMEM127 4 20 74 13 28 0 0 0 0 133
FH 43 12 46 17 18 0 0 0 2 119
PDGFRB 15 1 22 25 33 0 0 0 1 94
KRT4 3 0 24 15 42 0 0 0 0 83
MAX 0 0 30 8 24 0 0 0 0 62
KRT13 2 0 17 6 33 0 0 0 0 58
KIF1B 1 0 21 4 2 0 0 0 0 28
MED12 0 0 0 0 0 28 0 0 0 28
SDHC 0 0 21 2 2 0 0 0 0 25
NSDHL 12 4 0 0 1 0 0 0 0 17
TP53 8 1 4 0 0 0 0 0 0 13
PIK3CA 6 2 3 0 0 0 0 0 0 11
FGFR1 3 3 6 0 0 0 0 0 0 10
FGFR3 7 0 3 0 0 0 0 0 0 10
NOTCH3 3 4 3 0 0 0 0 0 1 10
HRAS, LRRC56 8 0 0 1 0 0 0 0 0 9
LOC107303340, VHL 3 4 2 0 0 0 0 0 0 9
VHL 4 2 3 0 0 0 0 0 0 9
LOC106736614, RET 0 0 5 1 2 0 0 0 0 8
​intergenic 2 3 2 0 0 0 0 0 0 7
HNF1A 4 0 2 0 0 0 0 0 0 6
SDHAF2 0 0 6 0 0 0 0 0 0 6
ELMO2 3 1 1 0 1 0 0 0 0 5
KRAS 3 1 1 0 0 0 0 0 0 5
NRAS 5 0 0 0 0 0 0 0 0 5
SDHA 1 0 2 2 0 0 0 0 0 5
CTNNB1 0 4 0 0 0 0 0 0 0 4
TSC1 1 0 3 0 0 0 0 0 0 4
ATP1A1 3 0 0 0 0 0 0 0 0 3
ATP2B3 3 0 0 0 0 0 0 0 0 3
KDR 1 0 0 0 1 0 1 0 0 3
MEN1 3 0 0 0 0 0 0 0 0 3
NEK9 3 0 0 0 0 0 0 0 0 3
PTCH1 0 0 3 0 0 0 0 0 0 3
TSC2 0 0 3 0 0 0 0 0 0 3
ALG9, BTG4, C11orf1, C11orf52, COLCA2, CRYAB, DIXDC1, DLAT, FDXACB1, HOATZ, HSPB2, LAYN, LOC728196, MIR34B, MIR34C, NKAPD1, PIH1D2, POU2AF1, PPP2R1B, SDHD, SIK2, TIMM8B 1 0 1 0 0 0 0 0 0 2
BRAF 2 0 0 0 0 0 0 0 0 2
GLI2 0 0 2 0 0 0 0 0 0 2
IL17RD 0 1 1 0 0 0 0 0 0 2
KRIT1 1 1 0 0 0 0 0 0 0 2
MPZ, SDHC 0 0 0 0 2 0 0 0 0 2
PCSK7 0 0 2 0 0 0 0 0 0 2
PTPN14 2 0 0 0 0 0 0 0 0 2
ADGRV1 0 0 1 0 0 0 0 0 0 1
AKT3 0 1 0 0 0 0 0 0 0 1
ANTXR1 0 0 0 0 0 0 1 0 0 1
APC 1 0 0 0 0 0 0 0 0 1
ARG2, RDH11, RDH12, VTI1B, ZFYVE26 0 0 1 0 0 0 0 0 0 1
ARID1B 1 0 0 0 0 0 0 0 0 1
BMPR1A 0 0 1 0 0 0 0 0 0 1
BRCA1 0 0 1 0 0 0 0 0 0 1
CACNA1H 0 0 1 0 0 0 0 0 0 1
CASR 0 1 0 0 0 0 0 0 0 1
CCM2 1 0 0 0 0 0 0 0 0 1
CDC73 1 0 0 0 0 0 0 0 0 1
CDH2 0 1 0 0 0 0 0 0 0 1
CFAP126, SDHC 0 0 0 0 1 0 0 0 0 1
CHML, CHRM3, EXO1, FH, FMN2, GREM2, KMO, MAP1LC3C, OPN3, PLD5, RGS7, RYR2, WDR64, ZP4 1 0 0 0 0 0 0 0 0 1
COL7A1 0 1 0 0 0 0 0 0 0 1
CSMD3 0 0 0 0 1 0 0 0 0 1
DIPK1A, RPL5 1 0 0 0 0 0 0 0 0 1
EGFR 0 1 0 0 0 0 0 0 0 1
ENG 1 0 0 0 0 0 0 0 0 1
ENG, LOC102723566 1 0 0 0 0 0 0 0 0 1
EPHB4 0 1 0 0 0 0 0 0 0 1
ERCC2 0 1 0 0 0 0 0 0 0 1
FLT4 1 0 0 0 0 0 0 0 0 1
FOXO3 0 0 0 0 0 0 0 1 0 1
GLMN 1 0 0 0 0 0 0 0 0 1
HMGA2 0 0 1 0 0 0 0 0 0 1
LEMD3 1 0 0 0 0 0 0 0 0 1
MAP4K4 0 1 0 0 0 0 0 0 0 1
MYH9 0 1 0 0 0 0 0 0 0 1
NF1 0 0 1 0 0 0 0 0 0 1
NF2 0 0 0 0 0 0 0 1 0 1
NOTCH1 0 0 1 0 0 0 0 0 0 1
NPC1 0 0 1 0 0 0 0 0 0 1
NRIP3-DT, SCUBE2 0 1 0 0 0 0 0 0 0 1
NSD1 0 0 0 0 0 0 0 1 0 1
PADI2, SDHB 1 0 0 0 0 0 0 0 0 1
PDCD10 0 1 0 0 0 0 0 0 0 1
PHOX2B 0 0 1 0 0 0 0 0 0 1
PITPNM3 1 0 0 0 0 0 0 0 0 1
PKD1 0 1 0 0 0 0 0 0 0 1
PREX2 0 1 0 0 0 0 0 0 0 1
PRLR 1 0 0 0 1 0 0 0 0 1
PTEN 1 0 0 0 0 0 0 0 0 1
SARS1 1 0 0 0 0 0 0 0 0 1
SDHD, TIMM8B 1 0 0 0 0 0 0 0 0 1
SMARCA4 0 0 1 0 0 0 0 0 0 1
SRD5A3 0 0 1 0 0 0 0 0 0 1
SUFU 0 0 1 0 0 0 0 0 0 1
SYN3, TIMP3 0 1 0 0 0 0 0 0 0 1
ZFYVE16 0 1 0 0 0 0 0 0 0 1

Submitter and significance breakdown #

Total submitters: 59
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Submitter pathogenic likely pathogenic uncertain significance likely benign benign association risk factor other not provided total
Invitae 148 43 544 180 46 0 0 0 0 961
Illumina Clinical Services Laboratory,Illumina 0 0 306 92 206 0 0 0 0 589
OMIM 85 0 0 0 0 0 2 0 0 87
Fulgent Genetics,Fulgent Genetics 30 9 45 1 0 0 0 0 0 85
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics,Children's Hospital of Philadelphia 36 8 10 0 0 0 0 0 0 54
Rajkovic Lab, University of Pittsburgh 0 0 0 0 0 28 0 0 0 28
Centre for Mendelian Genomics,University Medical Centre Ljubljana 10 7 10 0 1 0 0 0 0 28
Familial Cancer Clinic,Veneto Institute of Oncology 0 19 0 0 0 0 0 0 0 19
St. Jude Clinical Genomics Lab, St. Jude Children's Research Hospital 1 1 13 0 0 0 0 0 0 15
Baylor Genetics 1 2 11 0 0 0 0 0 0 14
Demoulin lab,University of Louvain 13 0 0 0 0 0 0 0 0 13
GeneReviews 12 0 0 0 0 0 0 0 0 12
Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital 4 8 0 0 0 0 0 0 0 12
Endocrinology Clinic, Seth G.S. Medical College 0 10 0 0 0 0 0 0 0 10
Genetic Services Laboratory, University of Chicago 5 3 0 0 0 0 0 0 0 8
Institute of Human Genetics, Klinikum rechts der Isar 7 0 0 0 0 0 0 0 0 7
CSER _CC_NCGL, University of Washington 0 0 4 3 0 0 0 0 0 7
Talkowski Laboratory, Center for Human Genetic Research,Massachusetts General Hospital 2 3 2 0 0 0 0 0 0 7
Mendelics 1 0 2 2 1 0 0 0 0 6
Arin Greene Laboratory,Boston Children's Hospital, Harvard Medical School 5 0 0 0 0 0 0 0 0 5
Database of Curated Mutations (DoCM) 0 4 0 0 0 0 0 0 0 4
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 1 0 3 0 0 0 0 0 0 4
Integrated Genetics/Laboratory Corporation of America 1 1 0 0 1 0 0 0 0 3
Donald Williams Parsons Laboratory,Baylor College of Medicine 0 0 0 0 0 0 0 3 0 3
GenomeConnect, ClinGen 0 0 0 0 0 0 0 0 3 3
Institute of Human Genetics,Cologne University 1 0 1 0 0 0 0 0 0 2
Center for Applied Genomics,Children's Hospital of Philadelphia 0 0 0 0 0 0 0 0 2 2
University of Washington Center for Mendelian Genomics, University of Washington 0 2 0 0 0 0 0 0 0 2
Lupski Lab, Baylor-Hopkins CMG, Baylor College of Medicine 1 1 0 0 0 0 0 0 0 2
Institute of Human Genetics, University of Leipzig Medical Center 1 1 0 0 0 0 0 0 0 2
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen 0 0 0 1 1 0 0 0 0 2
Biochemical Molecular Genetic Laboratory,King Abdulaziz Medical City 0 1 1 0 0 0 0 0 0 2
Cancer Variant Interpretation Group UK, Institute of Cancer Research, London 1 0 0 1 0 0 0 0 0 2
New York Genome Center 0 1 1 0 0 0 0 0 0 2
Clinical Molecular Genetics Laboratory,Johns Hopkins All Children's Hospital 1 0 0 0 0 0 0 0 0 1
Clinical Genetics laboratory, University of Goettingen 0 0 1 0 0 0 0 0 0 1
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories 0 0 0 0 1 0 0 0 0 1
Academic Department of Medical Genetics, University of Cambridge 1 0 0 0 0 0 0 0 0 1
Institute of Human Genetics, Uniklinik RWTH Aachen 0 1 0 0 0 0 0 0 0 1
Center for Individualized Medicine,Mayo Clinic 0 1 0 0 0 0 0 0 0 1
Dobyns Lab,Seattle Children's Research Institute 1 0 0 0 0 0 0 0 0 1
Knight Diagnostic Laboratories, Oregon Health and Sciences University 0 0 1 0 0 0 0 0 0 1
Center of Genomic medicine, Geneva,University Hospital of Geneva 1 0 0 0 0 0 0 0 0 1
Baylor-Hopkins Center for Mendelian Genomics,Johns Hopkins University 0 1 0 0 0 0 0 0 0 1
Hunter Genetics General Clinical Genetics Service,Hunter Genetics 1 0 0 0 0 0 0 0 0 1
SIB Swiss Institute of Bioinformatics 1 0 0 0 0 0 0 0 0 1
Department of Pathology and Laboratory Medicine,Sinai Health System 0 0 0 1 0 0 0 0 0 1
CHLA Center for Personalized Medicine,Children's Hospital, Los Angeles 1 0 0 0 0 0 0 0 0 1
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 0 0 1 0 0 0 0 0 0 1
Institutes of Biomedical Sciences,Shanxi University 1 0 0 0 0 0 0 0 0 1
Kahle Lab,Yale University 0 1 0 0 0 0 0 0 0 1
Molecular Diagnostics Laboratory, M Health Fairview: University of Minnesota 1 0 0 0 0 0 0 0 0 1
Department of Genetics,Sultan Qaboos University Hospital, Oman 0 0 1 0 0 0 0 0 0 1
Genomic Medicine Lab, University of California San Francisco 0 0 1 0 0 0 0 0 0 1
Michigan Center for Translational Pathology,University of Michigan 1 0 0 0 0 0 0 0 0 1
Reproductive Health Research and Development,BGI Genomics 0 0 0 0 1 0 0 0 0 1
Cancer medicine,Gaomi People's Hospital 1 0 0 0 0 0 0 0 0 1
Division of Medical Genetics, University of Washington 1 0 0 0 0 0 0 0 0 1
Practice for Gait Abnormalities, David Pomarino,Competency Network Toe Walking c/o Practice Pomarino 0 1 0 0 0 0 0 0 0 1

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