ClinVar Miner

Submissions for variant NM_004329.2(BMPR1A):c.618A>G (p.Leu206=) (rs55992440)

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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001507159 SCV000153928 benign Juvenile polyposis syndrome 2020-12-03 criteria provided, single submitter clinical testing
GeneDx RCV000212146 SCV000167200 benign not specified 2014-02-17 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 RCV000123857 SCV000213123 likely benign Hereditary cancer-predisposing syndrome 2014-12-21 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.
Counsyl RCV000119191 SCV000487813 likely benign Generalized juvenile polyposis/juvenile polyposis coli 2015-11-17 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000212146 SCV000600226 benign not specified 2017-04-28 criteria provided, single submitter clinical testing
Color Health, Inc RCV000123857 SCV000682904 benign Hereditary cancer-predisposing syndrome 2016-03-09 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000212146 SCV000806606 benign not specified 2017-03-27 criteria provided, single submitter clinical testing
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000212146 SCV000861274 benign not specified 2018-05-29 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000758775 SCV000887606 benign not provided 2017-04-28 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine,Sinai Health System RCV000758775 SCV001551252 likely benign not provided no assertion criteria provided clinical testing The BMPR1A p.Leu206= variant was not identified in the literature nor was it identified in the LOVD 3.0 database. The variant was identified in dbSNP (ID: rs55992440) as "With other allele", and ClinVar (classified as benign by Invitae, GeneDx and five other submitters; as likely benign by two submitters). The variant was identified in control databases in 226 of 277110 chromosomes (1 homozygous) at a frequency of 0.0008 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 199 of 24032 chromosomes (freq: 0.008), Other in 1 of 6458 chromosomes (freq: 0.0002), Latino in 25 of 34400 chromosomes (freq: 0.0008), European in 1 of 126628 chromosomes (freq: 0.000008), while the variant was not observed in the Ashkenazi Jewish, East Asian, Finnish, and South Asian populations. The p.Leu206= 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) 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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