ClinVar Miner

Submissions for variant NM_003000.3(SDHB):c.487T>C (p.Ser163Pro)

gnomAD frequency: 0.00921  dbSNP: rs33927012
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 29
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000132153 SCV000187226 benign Hereditary cancer-predisposing syndrome 2014-12-23 criteria provided, single submitter clinical testing This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
GeneDx RCV000034688 SCV000235633 benign not provided 2018-04-10 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 19215943, 16322339, 17298551, 16912137, 22995991, 19768395, 22584711, 19802898, 19399650, 22293219, 24735130, 20981092, 27153395, 18678321, 21979946, 25376524, 22938532, 22703879, 25694510, 23666964, 25333069, 24728327, 26071763, 17102082, 17102083, 22270996, 25695889, 17639058, 14985401, 26182300, 18419787, 19153209, 19522823, 19454582, 27279923, 27884173, 26092435, 28374168, 29386252, 30050099, 31019283)
Genomic Diagnostic Laboratory, Division of Genomic Diagnostics, Children's Hospital of Philadelphia RCV000202946 SCV000257933 benign Paragangliomas 4 2015-02-13 criteria provided, single submitter clinical testing
Invitae RCV000206861 SCV000262194 benign Gastrointestinal stromal tumor; Paragangliomas 4; Pheochromocytoma 2024-02-01 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV000122002 SCV000309334 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000282667 SCV000351418 benign Hereditary pheochromocytoma-paraganglioma 2018-03-06 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Counsyl RCV000202946 SCV000488422 benign Paragangliomas 4 2016-03-23 criteria provided, single submitter clinical testing
Genetic Services Laboratory, University of Chicago RCV000122002 SCV000596998 benign not specified 2018-04-03 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000122002 SCV000605078 likely benign not specified 2018-08-03 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000122002 SCV000698135 benign not specified 2017-05-08 criteria provided, single submitter clinical testing Variant summary: The SDHB c.487T>C (p.Ser163Pro) variant involves the alteration of a conserved nucleotide. 2/4 in silico tools predict a benign outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 1523/121404 control chromosomes (21 homozygotes) at a frequency of 0.0125449, which largely exceeds the estimated maximal expected allele frequency of a pathogenic SDHB variant (0.0000009), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. Taken together, this variant is classified as benign.
Eurofins Ntd Llc (ga) RCV000122002 SCV000702933 benign not specified 2016-11-16 criteria provided, single submitter clinical testing
Center for Human Genetics, Inc, Center for Human Genetics, Inc RCV000202946 SCV000782276 uncertain significance Paragangliomas 4 2016-11-01 criteria provided, single submitter clinical testing
Equipe Genetique des Anomalies du Developpement, Université de Bourgogne RCV000202946 SCV000883134 uncertain significance Paragangliomas 4 2018-11-21 criteria provided, single submitter clinical testing
Mendelics RCV000986263 SCV001135202 likely benign Gastrointestinal stromal tumor 2019-05-28 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000034688 SCV001147171 benign not provided 2024-04-01 criteria provided, single submitter clinical testing SDHB: BS1, BS2
Illumina Laboratory Services, Illumina RCV001099292 SCV001255735 benign Carney-Stratakis syndrome 2018-03-06 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden RCV000034688 SCV002010044 uncertain significance not provided 2021-11-03 criteria provided, single submitter clinical testing
Sema4, Sema4 RCV000132153 SCV002527080 benign Hereditary cancer-predisposing syndrome 2020-09-11 criteria provided, single submitter curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital RCV000122002 SCV002552130 benign not specified 2023-08-15 criteria provided, single submitter clinical testing
Myriad Genetics, Inc. RCV000202946 SCV004045350 benign Paragangliomas 4 2023-04-24 criteria provided, single submitter clinical testing This variant is considered benign. This variant has been observed at a population frequency that is significantly greater than expected given the associated disease prevalence and penetrance.
Color Diagnostics, LLC DBA Color Health RCV000202946 SCV004362272 benign Paragangliomas 4 2022-06-09 criteria provided, single submitter clinical testing
OMIM RCV000013633 SCV000033880 uncertain significance Cowden syndrome 2008-08-01 no assertion criteria provided literature only
Biesecker Lab/Clinical Genomics Section, National Institutes of Health RCV000034688 SCV000043485 no known pathogenicity not provided 2012-07-13 no assertion criteria provided research Converted during submission to Benign.
ITMI RCV000122002 SCV000086213 not provided not specified 2013-09-19 no assertion provided reference population
Center of Medical Genetics and Primary Health Care RCV001269360 SCV001448699 benign Malignant tumor of breast no assertion criteria provided clinical testing
Diagnostic Laboratory, Department of Genetics, University Medical Center Groningen RCV000122002 SCV001743804 benign not specified no assertion criteria provided clinical testing
Genome Diagnostics Laboratory, Amsterdam University Medical Center RCV000122002 SCV001807023 benign not specified no assertion criteria provided clinical testing
Clinical Genetics, Academic Medical Center RCV000122002 SCV001922351 benign not specified no assertion criteria provided clinical testing
Joint Genome Diagnostic Labs from Nijmegen and Maastricht, Radboudumc and MUMC+ RCV000122002 SCV001959772 benign not specified no assertion criteria provided clinical testing

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.