ClinVar Miner

Variants studied for benign neoplasm

Included ClinVar conditions (124):
Minimum submission review status: Collection method:
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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
457 173 1636 947 332 37 2 3 21 3550

Gene and significance breakdown #

Total genes and gene combinations: 135
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Gene or gene combination pathogenic likely pathogenic uncertain significance likely benign benign association risk factor other not provided total
SDHB 161 46 508 315 19 0 0 0 1 1040
SDHD 67 20 263 147 12 0 0 0 0 502
PDGFRB 17 1 88 178 79 0 0 0 1 359
RET 12 3 203 78 53 0 0 0 0 346
TMEM127 7 19 93 15 26 0 0 0 0 152
LOC126861339, SDHD 17 3 43 34 2 0 0 0 0 98
KRT4 3 0 24 15 42 0 0 0 0 83
FGFR1 4 7 43 26 2 0 0 0 2 80
MAX 0 1 37 9 19 0 0 0 0 63
HNF1A 6 4 33 16 1 0 0 0 0 60
KRT13 2 0 17 6 35 0 0 0 0 60
LOC129929542, SDHB 6 0 27 26 0 0 0 0 0 59
NOTCH3 9 5 17 20 2 0 0 0 3 54
KIF1B 0 0 37 4 6 0 0 0 0 47
NSDHL 10 5 8 9 2 0 0 0 4 35
VHL 4 2 27 2 0 0 0 0 0 35
TP53 17 3 6 5 2 0 0 0 0 33
LOC107303340, VHL 5 4 15 4 0 0 0 0 0 28
LOC129934333, TMEM127 1 5 20 0 3 0 0 0 1 28
MED12 0 0 0 0 0 28 0 0 0 28
FGFR3 11 0 10 5 1 0 0 0 0 27
SDHC 0 0 21 2 2 0 0 0 0 25
HRAS, LRRC56 10 0 8 4 0 0 0 0 1 23
KRAS 6 2 4 6 0 0 0 0 5 22
PIK3CA 13 4 4 0 0 0 0 0 3 20
PTPN14 2 0 9 0 7 0 0 0 0 18
ELMO2 5 2 1 2 3 0 0 0 0 12
LOC129929541, SDHB 2 0 1 9 0 0 0 0 0 12
LOC106736614, RET 0 0 7 2 2 0 0 0 0 11
LOC130055850, MAX 0 0 5 1 5 0 0 0 0 11
​intergenic 2 3 2 0 0 0 0 0 0 7
KDR 1 1 3 1 1 0 1 0 0 7
NRAS 5 1 1 0 0 0 0 0 0 7
SDHAF2 0 0 6 0 0 0 0 0 0 6
SDHA 1 0 2 2 0 0 0 0 0 5
ALG9, BTG4, C11orf52, CFAP68, CRYAB, DIXDC1, DLAT, FDXACB1, HOATZ, HSPB2, LAYN, MIR34B, MIR34BHG, MIR34C, NKAPD1, PIH1D2, POU2AF1, POU2AF3, PPP2R1B, SDHD, SIK2, TIMM8B 3 0 1 0 0 0 0 0 0 4
CLDN14 0 0 2 0 0 2 0 0 0 4
CTNNB1, LOC126806658 0 4 0 0 0 0 0 0 0 4
GNA14 0 1 3 0 0 0 0 0 0 4
LOC129929541, LOC129929542, SDHB 2 0 2 0 0 0 0 0 0 4
TSC1 1 0 3 0 0 0 0 0 0 4
ANTXR1 0 0 0 1 1 0 1 0 0 3
ATP1A1 3 0 0 0 0 0 0 0 0 3
ATP2B3 3 0 0 0 0 0 0 0 0 3
EPHB4 0 1 0 0 0 2 0 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
PIK3R1 0 3 0 0 0 0 0 0 0 3
BRAF 2 0 0 0 0 0 0 0 0 2
C12orf43, HNF1A 0 0 2 0 0 0 0 0 0 2
FAT4 0 0 2 0 0 0 0 0 0 2
FLT4 1 0 1 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
KEL 0 0 0 0 0 2 0 0 0 2
KIF1B, LOC129388446 0 0 1 1 0 0 0 0 0 2
KRIT1 1 1 0 0 0 0 0 0 0 2
LEMD3 1 0 1 0 0 0 0 0 0 2
LOC100506321, MAX 1 0 1 0 0 0 0 0 0 2
MFN2 1 0 1 0 0 0 0 0 0 2
MPZ, SDHC 0 0 0 0 2 0 0 0 0 2
NF1 1 0 1 0 0 0 0 0 0 2
PCSK7 0 0 2 0 0 0 0 0 0 2
PTCH1 0 0 2 0 0 0 0 0 0 2
TSC2 1 1 0 0 0 0 0 0 0 2
ADGRV1 0 0 1 0 0 0 0 0 0 1
ADRA2B, ASTL, DUSP2, GPAT2, STARD7, TMEM127 0 0 1 0 0 0 0 0 0 1
AKT3 0 1 0 0 0 0 0 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
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
CCNH, RASA1 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
CFTR 1 0 0 0 0 0 0 0 0 1
CHURC1-FNTB, FNTB, LOC126861966, MAX 0 0 0 1 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
CYFIP1, NIPA1, NIPA2, TUBGCP5 0 0 1 0 0 0 0 0 0 1
DDX46 0 0 1 0 0 0 0 0 0 1
DIPK1A, RPL5 1 0 0 0 0 0 0 0 0 1
DLX3 0 1 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
EPHB4, LOC126860124 1 0 0 0 0 0 0 0 0 1
ERCC2 0 1 0 0 0 0 0 0 0 1
FH 0 1 0 0 0 0 0 0 0 1
FOXO3 0 0 0 0 0 0 0 1 0 1
GJA4 1 0 0 0 0 0 0 0 0 1
GLMN 1 0 0 0 0 0 0 0 0 1
GNA11 1 0 0 0 0 0 0 0 0 1
HMGA2 0 0 1 0 0 0 0 0 0 1
KAT6A 0 0 0 0 0 1 0 0 0 1
KIF1B, LOC126805614 0 0 1 0 0 0 0 0 0 1
KIF1B, LOC129929363 0 0 0 1 0 0 0 0 0 1
KMT2D 0 0 0 0 0 1 0 0 0 1
KRT10 0 1 0 0 0 0 0 0 0 1
LOC129929541, LOC129929542, LOC129929543, PADI2, SDHB 1 0 0 0 0 0 0 0 0 1
LOC129929542, LOC129929543, SDHB 1 0 0 0 0 0 0 0 0 1
LOC130002133, PTCH1 0 0 1 0 0 0 0 0 0 1
LOC130063807, NOTCH3 0 0 1 0 0 0 0 0 0 1
LZTR1 1 0 0 0 0 0 0 0 0 1
MAP3K3 1 0 0 0 0 0 0 0 0 1
MAP4K4 0 1 0 0 0 0 0 0 0 1
MINPP1 1 0 0 0 0 0 0 0 0 1
MYH9 0 1 0 0 0 0 0 0 0 1
NF2 0 0 0 0 0 0 0 1 0 1
NLRP3 1 0 0 0 0 0 0 0 0 1
NOTCH1 0 0 1 0 0 0 0 0 0 1
NOTCH4 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
PDCD10 0 1 0 0 0 0 0 0 0 1
PIEZO1 0 1 0 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
RASA1 1 0 0 0 0 0 0 0 0 1
RNF213 0 1 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
SMARCA2 0 0 0 0 0 1 0 0 0 1
SOS1 1 0 0 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
TEK 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: 101
Download table as spreadsheet
Submitter pathogenic likely pathogenic uncertain significance likely benign benign association risk factor other not provided total
Invitae 261 58 922 698 106 0 0 0 0 2044
Fulgent Genetics, Fulgent Genetics 57 18 315 162 10 0 0 0 0 562
Illumina Laboratory Services, Illumina 0 0 273 75 188 0 0 0 0 536
Baylor Genetics 6 3 62 0 0 0 0 0 0 71
OMIM 68 0 0 0 0 0 2 0 0 70
St. Jude Molecular Pathology, St. Jude Children's Research Hospital 1 1 26 1 0 0 0 0 0 29
Genome-Nilou Lab 0 0 0 0 29 0 0 0 0 29
Rajkovic Lab, University of Pittsburgh 0 0 0 0 0 28 0 0 0 28
Centre for Mendelian Genomics, University Medical Centre Ljubljana 9 7 10 0 1 0 0 0 0 27
Familial Cancer Clinic, Veneto Institute of Oncology 0 19 0 0 0 0 0 0 0 19
Clinical Genomics Laboratory, Washington University in St. Louis 5 2 11 0 0 0 0 0 0 18
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne 13 0 3 0 0 0 0 0 0 16
GeneReviews 1 0 0 0 0 0 0 0 14 15
Demoulin lab, University of Louvain 13 0 0 0 0 0 0 0 0 13
Yale Center for Mendelian Genomics, Yale University 1 3 0 0 0 9 0 0 0 13
Beijing Key Laboratory for Genetic Research of Skeletal Deformity, Peking Union Medical College Hospital 4 8 0 0 0 0 0 0 0 12
KCCC/NGS Laboratory, Kuwait Cancer Control Center 1 0 2 2 6 0 0 0 0 11
Endocrinology Clinic, Seth G.S. Medical College 0 10 0 0 0 0 0 0 0 10
Seattle Children's Hospital Molecular Genetics Laboratory, Seattle Children's Hospital 6 2 2 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 Munich, Klinikum Rechts Der Isar, TU München 6 1 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
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories 0 0 1 3 2 0 0 0 0 6
MGZ Medical Genetics Center 2 3 1 0 0 0 0 0 0 6
Mendelics 1 0 2 2 1 0 0 0 0 6
Institute of Human Genetics, University of Leipzig Medical Center 3 2 0 0 0 0 0 0 0 5
Arin Greene Laboratory, Boston Children's Hospital, Harvard Medical School 5 0 0 0 0 0 0 0 0 5
3billion 3 0 2 0 0 0 0 0 0 5
Laboratorio de Genetica e Diagnostico Molecular, Hospital Israelita Albert Einstein 2 3 0 0 0 0 0 0 0 5
Revvity Omics, Revvity 0 0 4 0 0 0 0 0 0 4
Database of Curated Mutations (DoCM) 0 4 0 0 0 0 0 0 0 4
deCODE genetics, Amgen 0 4 0 0 0 0 0 0 0 4
New York Genome Center 1 1 2 0 0 0 0 0 0 4
Donald Williams Parsons Laboratory, Baylor College of Medicine 0 0 0 0 0 0 0 3 0 3
Genetics and Molecular Pathology, SA Pathology 0 1 1 1 0 0 0 0 0 3
Center for Genomics, Ann and Robert H. Lurie Children's Hospital of Chicago 2 0 1 0 0 0 0 0 0 3
Department of Pharmacy, The First Affiliated Hospital of Zhengzhou University 2 0 1 0 0 0 0 0 0 3
Department of Clinical Genetics, Copenhagen University Hospital, Rigshospitalet 1 1 0 0 0 0 0 0 0 2
Institute of Human Genetics, University of Goettingen 0 0 2 0 0 0 0 0 0 2
North West Genomic Laboratory Hub, Manchester University NHS Foundation Trust 2 0 0 0 0 0 0 0 0 2
Women's Health and Genetics/Laboratory Corporation of America, LabCorp 1 0 0 0 1 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
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology 0 1 1 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
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 1 0 0 0 0 2
GenomeConnect - CureCADASIL 0 0 0 0 0 0 0 0 2 2
Institute of Human Genetics, University Hospital Muenster 1 1 0 0 0 0 0 0 0 2
GenomeConnect - Invitae Patient Insights Network 0 0 0 0 0 0 0 0 2 2
Institute of Human Genetics, Clinical Exome/Genome Diagnostics Group, University Hospital Bonn 0 1 1 0 0 0 0 0 0 2
Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center 0 1 1 0 0 0 0 0 0 2
Clinical Genetics Laboratory, University Hospital Schleswig-Holstein 1 0 1 0 0 0 0 0 0 2
Division of Human Genetics, National Health Laboratory Service/University of the Witwatersrand 0 1 1 0 0 0 0 0 0 2
Vascular Anomalies Center, Boston Children's Hospital, Harvard Medical School 0 2 0 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
Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine 0 1 0 0 0 0 0 0 0 1
Institute of Human Genetics, Cologne University 0 0 1 0 0 0 0 0 0 1
Centogene AG - the Rare Disease Company 0 0 1 0 0 0 0 0 0 1
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute 1 0 0 0 0 0 0 0 0 1
Institute of Human Genetics, FAU Erlangen, Friedrich-Alexander-Universität Erlangen-Nürnberg 1 0 0 0 0 0 0 0 0 1
Institute for Human Genetics and Genomic Medicine, Uniklinik RWTH Aachen 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
Oxford Medical Genetics Laboratories, Oxford University Hospitals NHS Foundation Trust 0 0 1 0 0 0 0 0 0 1
Baylor-Hopkins Center for Mendelian Genomics, Johns Hopkins University School of Medicine 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
KK Women’s and Children’s Hospital 0 0 1 0 0 0 0 0 0 1
Medical Genetics Laboratory, Aldo Moro University of Bari 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
Department of Pediatrics, Memorial Sloan Kettering Cancer Center 1 0 0 0 0 0 0 0 0 1
GenomeConnect, ClinGen 0 0 0 0 0 0 0 0 1 1
Center for Personalized Medicine, Children's Hospital Los Angeles 1 0 0 0 0 0 0 0 0 1
Laboratory of Medical Genetics Unit, Bambino Gesù Children's Hospital 0 0 1 0 0 0 0 0 0 1
Clinical Bioinformatic Lab, Royan Institute 0 1 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
Genomics For Life 1 0 0 0 0 0 0 0 0 1
Department Of Genetics, Sultan Qaboos University Hospital, Sultan Qaboos University 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
Department of Medicine, University of Texas Health Science Center at San Antonio 1 0 0 0 0 0 0 0 0 1
Cancer medicine, Gaomi People's Hospital 1 0 0 0 0 0 0 0 0 1
Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology 0 1 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
Molecular Genetics Lab, CHRU Brest 0 0 1 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
Beijing Key Laboratry for Genetics of Birth Defects, Beijing Children's Hospital 1 0 0 0 0 0 0 0 0 1
Keith Choate Laboratory, Yale University 1 0 0 0 0 0 0 0 0 1
Suma Genomics 1 0 0 0 0 0 0 0 0 1
Neuberg Centre For Genomic Medicine, NCGM 1 0 0 0 0 0 0 0 0 1
Molecular Genetics, Royal Melbourne Hospital 0 0 1 0 0 0 0 0 0 1
James Bennett Lab, Seattle Childrens Research Institute 1 0 0 0 0 0 0 0 0 1
Laboratory of Cyto-molecular Genetics, Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi 0 0 1 0 0 0 0 0 0 1
Cytogenetics, Genetics Associates, Inc. 0 0 1 0 0 0 0 0 0 1
Coban-Akdemir Lab, University of Texas Health Science Center 0 0 1 0 0 0 0 0 0 1

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