ClinVar Miner

Submissions for variant NM_004281.3(BAG3):c.772C>T (p.Arg258Trp) (rs117671123)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Biesecker Lab/Clinical Genomics Section,National Institutes of Health RCV000037897 SCV000054734 benign not specified 2013-06-24 criteria provided, single submitter research
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000037897 SCV000061559 benign not specified 2015-03-18 criteria provided, single submitter clinical testing p.Arg258Trp in exon 3 of BAG3: This variant is not expected to have clinical sig nificance because it has been identified in 1.6% (135/8628) of East Asian chromo somes by the Exome Aggregation Consortium (ExAC, http://exac.broadinstitute.org; dbSNP rs117671123).
GeneDx RCV000037897 SCV000235738 benign not specified 2017-02-02 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.
Soonchunhyang University Bucheon Hospital,Soonchunhyang University Medical Center RCV000490529 SCV000267220 benign Myofibrillar myopathy, BAG3-related 2016-03-18 criteria provided, single submitter reference population
Invitae RCV001081302 SCV000288309 benign Myofibrillar myopathy, BAG3-related; Dilated cardiomyopathy 1HH 2019-12-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000490529 SCV000360582 benign Myofibrillar myopathy, BAG3-related 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.
Integrated Genetics/Laboratory Corporation of America RCV000590218 SCV000698282 benign not provided 2017-08-02 criteria provided, single submitter clinical testing Variant summary: The BAG3 c.772C>T (p.Arg258Trp) variant involves the alteration of a non-conserved nucleotide. 4/4 in silico tools predict a damaging outcome for this variant (SNPsandGO not captured due to low reliability index). This variant was found in 141/120824 control chromosomes (1 homozygote) from ExAC, predominantly observed in the East Asian subpopulation at a frequency of 0.015647 (135/8628). This frequency is about 401 times the estimated maximal expected allele frequency of a pathogenic BAG3 variant (0.0000391), suggesting this is likely a benign polymorphism found primarily in the populations of East Asian origin. This variant has been found in one patient with patient with restrictive lung disease, a rapidly progressive proximal myopathy, rigid spine, bilateral Achilles tendon tightening, hypertrophic cardiomyopathy with restrictive physiology and a prolonged QT interval (Lee_2012). The patient also carried a de novo variant c.626C>T (p.Pro209Leu) which is regarded to explain the cardiac disease in the patient. In addition, father who was incidentally found to have prolonged QT interval also carried the variant of interest p.Arg258Trp. Thus the variant of interest may be a functional polymorphism. Multiple clinical diagnostic laboratories in ClinVar classified this variant as benign/likely benign. Taken together, this variant is classified as benign.
Ambry Genetics RCV000618102 SCV000736150 benign Cardiovascular phenotype 2017-12-07 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
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000590218 SCV000885058 benign not provided 2018-02-22 criteria provided, single submitter clinical testing
Mendelics RCV000490529 SCV001138176 benign Myofibrillar myopathy, BAG3-related 2019-05-28 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001107316 SCV001264457 likely benign Dilated cardiomyopathy 1HH 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 likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease.
OMIM RCV000032662 SCV000056425 uncertain significance Myofibrillar myopathy 2012-04-01 no assertion criteria provided literature only

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