ClinVar Miner

Submissions for variant NM_004329.2(BMPR1A):c.1560G>A (p.Thr520=) (rs142775086)

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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000174534 SCV000167204 benign not specified 2014-02-26 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 RCV000123861 SCV000213642 likely benign Hereditary cancer-predisposing syndrome 2014-10-30 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.
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000174534 SCV000225849 benign not specified 2015-04-25 criteria provided, single submitter clinical testing
Invitae RCV001079281 SCV000261826 benign Juvenile polyposis syndrome 2020-12-08 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000174534 SCV000600221 benign not specified 2017-07-13 criteria provided, single submitter clinical testing
Color Health, Inc RCV000123861 SCV000682877 benign Hereditary cancer-predisposing syndrome 2016-03-09 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000759480 SCV000888822 benign not provided 2017-07-13 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000174534 SCV000691805 likely benign not specified no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV001356619 SCV001551837 likely benign Carcinoma of colon no assertion criteria provided clinical testing The BMPR1A p.Thr520= variant was not identified in the literature nor was it identified in the Cosmic or LOVD 3.0 databases. The variant was identified in dbSNP (ID: rs142775086) as "With other allele" and ClinVar (classified as benign by GeneDx, Invitae, Color Genomics and two other clinical laboratories; as likely benign by Ambry Genetics and Mayo Clinic). The variant was identified in control databases in 108 of 277220 chromosomes at a frequency of 0.0004 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 99 of 24020 chromosomes (freq: 0.004), Latino in 7 of 34420 chromosomes (freq: 0.0002), and South Asian in 2 of 30780 chromosomes (freq: 0.00007); it was not observed in the Other, European, Ashkenazi Jewish, East Asian, or Finnish populations. The p.Thr520= 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, the clinical significance of this variant cannot be determined with certainty at this time although we would lean towards a more benign role for this variant. This variant is classified as likely benign.

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