ClinVar Miner

Submissions for variant NM_004329.2(BMPR1A):c.1419T>G (p.Val473=) (rs145756629)

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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000212150 SCV000167203 benign not specified 2014-01-07 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.
Ambry Genetics RCV000123860 SCV000213157 likely benign Hereditary cancer-predisposing syndrome 2014-06-24 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: 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.
Invitae RCV001507243 SCV000252783 benign Juvenile polyposis syndrome 2020-12-08 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000212150 SCV000310100 likely benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001082611 SCV000365656 benign Generalized juvenile polyposis/juvenile polyposis coli 2018-01-13 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.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000212150 SCV000600219 likely benign not specified 2017-01-15 criteria provided, single submitter clinical testing
Color Health, Inc RCV000123860 SCV000682867 benign Hereditary cancer-predisposing syndrome 2016-03-30 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000679547 SCV000806600 likely benign not provided 2016-02-11 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000679547 SCV000885065 likely benign not provided 2017-07-20 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000679547 SCV000888819 benign not provided 2018-05-19 criteria provided, single submitter clinical testing
CeGaT Praxis fuer Humangenetik Tuebingen RCV000679547 SCV001148030 likely benign not provided 2018-05-01 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000212150 SCV001550104 benign not specified no assertion criteria provided clinical testing The BMPR1A p.Val473= variant was not identified in the literature nor was it identified in the Cosmic, MutDB, LOVD 3.0 databases. The variant was identified in dbSNP (ID: rs145756629) as “With other allele”, ClinVar (as benign by GeneDx, Invitae, and Color Genomics, and as likely benign by Ambry Genetics, Illumina, Quest Diagnostics, and Prevention Genetics), and Clinvitae (4x). The variant was identified in control databases in 275 of 277250 chromosomes (1 homozygous) at a frequency of 0.000992 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). It was observed in the following populations: “Other” in 5 of 6468 chromosomes (freq: 0.000773), Latino in 16 of 34420 chromosomes (freq: 0.000465), European (Non-Finnish) in 62 of 126732 chromosomes (freq: 0.000489), Ashkenazi Jewish in 176 of 10152 chromosomes (freq: 0.01734), and South Asian in 16 of 30782 chromosomes (freq: 0.00052); was not observed in the African, East Asian, or European (Finnish) populations. The p.Val473= variant is not expected to have clinical significance because it does not result in a change of amino acid and is not located in a known consensus splice site. In addition, in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer, HumanSpliceFinder) do not predict a difference in splicing. In summary, based on the above information this variant meets our laboratory's criteria to be classified as benign.

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