ClinVar Miner

Submissions for variant NM_004329.3(BMPR1A):c.961C>T (p.Leu321=)

gnomAD frequency: 0.00011  dbSNP: rs377412651
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Total submissions: 11
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV000163921 SCV000214516 likely benign Hereditary cancer-predisposing syndrome 2014-10-31 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 RCV001507227 SCV000288404 benign Juvenile polyposis syndrome 2021-12-17 criteria provided, single submitter clinical testing
GeneDx RCV000436587 SCV000512266 benign not specified 2015-04-28 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 RCV000163921 SCV000537479 likely benign Hereditary cancer-predisposing syndrome 2016-03-21 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000586080 SCV000698328 benign not provided 2017-07-21 criteria provided, single submitter clinical testing Variant summary: The BMPR1A c.961C>T (p.Leu321Leu) variant involves the alteration of a conserved nucleotide causing a synonymous change and 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may create an ESE binding site. However, these predictions have yet to be confirmed by functional studies. This variant was found in 55/276926 control chromosomes at a frequency of 0.0001986, which is approximately 99 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 likely benign/benign. Taken together, this variant is classified as benign.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000586080 SCV000885063 likely benign not provided 2018-01-24 criteria provided, single submitter clinical testing The BMPR1A c.961C>T; p.Leu321Leu variant (rs377412651), to our knowledge, is not reported in the medical literature but is reported as benign or likely benign in ClinVar (Variation ID: 184634). This variant is observed in the general population with an overall allele frequency of 0.02% (55/276926 alleles) in the Genome Aggregation Database. This is a synonymous change and computational algorithms do not predict this variant to impact splicing (Alamut v.2.10). Based on available information, this variant is considered likely benign.
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000586080 SCV000887616 benign not provided 2018-06-18 criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV001084234 SCV001263369 benign Generalized juvenile polyposis/juvenile polyposis coli 2017-06-20 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 was too high to be consistent with this variant causing disease. Therefore, this variant is classified as benign.
Genetic Services Laboratory,University of Chicago RCV000436587 SCV002070272 likely benign not specified 2021-06-15 criteria provided, single submitter clinical testing
Sema4,Sema4 RCV000163921 SCV002531125 benign Hereditary cancer-predisposing syndrome 2020-12-23 criteria provided, single submitter curation
Wendy Chung Laboratory, Columbia University Medical Center RCV001823873 SCV002073616 not provided Pulmonary arterial hypertension no assertion provided literature only

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