ClinVar Miner

Submissions for variant NM_003000.3(SDHB):c.487T>C (p.Ser163Pro) (rs33927012)

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Total submissions: 19
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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 General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
GeneDx RCV000122002 SCV000235633 likely benign not specified 2017-10-04 criteria provided, single submitter clinical testing This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease.
Division of Genomic Diagnostics,The 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 2019-12-31 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000122002 SCV000309334 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000282667 SCV000351418 benign Hereditary Paraganglioma-Pheochromocytoma Syndromes 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
Integrated Genetics/Laboratory Corporation of America 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.
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics 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 Praxis fuer Humangenetik Tuebingen RCV000034688 SCV001147171 likely benign not provided 2017-05-01 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,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.
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

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