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

gnomAD frequency: 0.00192  dbSNP: rs56108371

Total submissions: 15

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	2024-01-31	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, part of Exact Sciences	RCV000212148	SCV000806609	benign	not specified	2017-01-06	criteria provided, single submitter	clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000212148	SCV000887612	benign	not specified	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	2024-02-01	criteria provided, single submitter	clinical testing	BMPR1A: BP4, BP7, BS1, BS2
Sema4, Sema4	RCV000123858	SCV002531119	likely benign	Hereditary cancer-predisposing syndrome	2021-02-17	criteria provided, single submitter	curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000212148	SCV002760470	likely benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
KCCC/NGS Laboratory, Kuwait Cancer Control Center	RCV001507244	SCV004016735	benign	Juvenile polyposis syndrome	2023-07-07	criteria provided, single submitter	clinical testing
True Health Diagnostics	RCV000123858	SCV000805225	likely benign	Hereditary cancer-predisposing syndrome	2018-04-27	no assertion criteria provided	clinical testing