Submissions for variant NM_004329.3(BMPR1A):c.676-6A>C

gnomAD frequency: 0.00014  dbSNP: rs186999445

Total submissions: 11

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Invitae	RCV001420982	SCV000166533	likely benign	Juvenile polyposis syndrome	2024-01-29	criteria provided, single submitter	clinical testing
Illumina Laboratory Services, Illumina	RCV000123227	SCV000365647	likely benign	Generalized juvenile polyposis/juvenile polyposis coli	2018-12-10	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.
Counsyl	RCV000123227	SCV000488319	uncertain significance	Generalized juvenile polyposis/juvenile polyposis coli	2016-02-25	criteria provided, single submitter	clinical testing
GeneDx	RCV000441358	SCV000518111	likely benign	not specified	2017-08-24	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.
Color Diagnostics, LLC DBA Color Health	RCV000580484	SCV000682907	likely benign	Hereditary cancer-predisposing syndrome	2016-06-13	criteria provided, single submitter	clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp	RCV000587362	SCV000698320	benign	not provided	2016-12-15	criteria provided, single submitter	clinical testing	Variant summary: The BMPR1A c.676-6A>C variant involves the alteration of a non-conserved intronic nucleotide. Mutation taster predicts a benign outcome for this substitution along with 5/5 splice prediction tools predicting the variant not to have an impact on normal splicing. This variant was found in 14/118044 control chromosomes, predominantly observed in the Latino subpopulation at a frequency of 0.0002616 (3/11468). This frequency greatly exceeds the estimated maximal expected allele frequency of a pathogenic BMPR1A variant (0.000002), suggesting this is likely a benign polymorphism found primarily in the populations of Latino origin. The variant of interest has not, to our knowledge, been reported in affected individuals via publications; nor evaluated for functional impact by in vivo/vitro studies. Multiple clinical diagnostic laboratories/reputable databases classified this variant as likely benign. Taken together, this variant is classified as benign.
Quest Diagnostics Nichols Institute San Juan Capistrano	RCV000441358	SCV001469978	benign	not specified	2019-10-18	criteria provided, single submitter	clinical testing
Sema4, Sema4	RCV000580484	SCV002531109	benign	Hereditary cancer-predisposing syndrome	2022-02-09	criteria provided, single submitter	curation
Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital	RCV000441358	SCV002550411	likely benign	not specified	2023-08-15	criteria provided, single submitter	clinical testing
Myriad Genetics, Inc.	RCV001420982	SCV004019455	likely benign	Juvenile polyposis syndrome	2023-03-02	criteria provided, single submitter	clinical testing	This variant is considered likely benign. This variant is intronic and is not expected to impact mRNA splicing.
PreventionGenetics, part of Exact Sciences	RCV003905179	SCV004723863	likely benign	BMPR1A-related disorder	2019-04-10	criteria provided, single submitter	clinical testing	This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).