ClinVar Miner

Submissions for variant NM_004329.3(BMPR1A):c.777G>A (p.Ala259=)

gnomAD frequency: 0.00192  dbSNP: rs56108371
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Total submissions: 13
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000212148 SCV000167201 benign not specified 2014-04-21 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 RCV000123858 SCV000213015 likely benign Hereditary cancer-predisposing syndrome 2014-10-06 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 RCV001507244 SCV000260104 benign Juvenile polyposis syndrome 2021-12-18 criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV001082852 SCV000365649 likely benign Generalized juvenile polyposis/juvenile polyposis coli 2018-10-29 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases allowed determination this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Color Diagnostics, LLC DBA Color Health RCV000123858 SCV000682918 benign Hereditary cancer-predisposing syndrome 2016-03-21 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000588975 SCV000698327 benign not provided 2016-07-01 criteria provided, single submitter clinical testing Variant summary: The BMPR1A c.777G>A (p.Ala259Ala) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant while 4/5 splice tools predict the variant not to have an impact on normal splicing. This variant was found in 113/120202 control chromosomes at a frequency of 0.0009401, which is approximately 470 times the estimated maximal expected allele frequency of a pathogenic BMPR1A variant (0.000002), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as Benign/Likely Benign. Taken together, this variant is classified as Benign.
PreventionGenetics,PreventionGenetics RCV000212148 SCV000806609 benign not specified 2017-01-06 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000588975 SCV000887612 benign not provided 2021-03-19 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000212148 SCV001157610 benign not specified 2018-09-09 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000212148 SCV002070234 likely benign not specified 2021-11-30 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000588975 SCV002497056 benign not provided 2022-03-01 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000123858 SCV002531119 likely benign Hereditary cancer-predisposing syndrome 2021-02-17 criteria provided, single submitter curation
True Health Diagnostics RCV000123858 SCV000805225 likely benign Hereditary cancer-predisposing syndrome 2018-04-27 no assertion criteria provided clinical testing

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