ClinVar Miner

Submissions for variant NM_005359.5(SMAD4):c.1218G>A (p.Ala406=) (rs145097078)

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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000589974 SCV000884550 likely benign not provided 2017-08-25 criteria provided, single submitter clinical testing The SMAD4 c.1218G>A;p.Ala406Ala variant has not been published in the medical literature or in gene-specific databases. The variant is listed in the ClinVar database (Variation ID: 231979) and the dbSNP variant database (rs145097078) with an allele frequency of 0.0077 percent (1/13005 alleles) in the Exome Variant Server and 0.003608 percent (10/277190 alleles). The nucleotide at this position is not well conserved across species and computational algorithms predict this variant will not significant alter splicing. Considering available information, this variant is classified as likely benign.
Ambry Genetics RCV000220772 SCV000275987 likely benign Hereditary cancer-predisposing syndrome 2015-06-02 criteria provided, single submitter clinical testing
Color RCV000220772 SCV000686517 likely benign Hereditary cancer-predisposing syndrome 2016-10-09 criteria provided, single submitter clinical testing
GeneDx RCV000436523 SCV000515483 benign not specified 2015-07-31 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.
Integrated Genetics/Laboratory Corporation of America RCV000589974 SCV000698565 benign not provided 2017-06-26 criteria provided, single submitter clinical testing Variant summary: The c.1218G>A (p.Ala406=) in SMAD4 gene is a synonymous change that involves a non-conserved nucleotide. 3/5 programs in Alamut predict that this variant may have some mild effect normal splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in the control population datasets of ExAC and gnomAD at a similar frequencies 0.000036 (4/121400 and 10/ 277190 chrs tested, respectively). However, the possibility of the variant to be derived from pseudogene cannot be completely ruled out. The variant has not, to our knowledge, been reported in affected individuals via published reports but is cited as Benign/Likely Benign by reputable databases/clinical laboratories. Taking together, the variant was classified as Benign.
Invitae RCV000468651 SCV000556143 likely benign Juvenile polyposis syndrome 2017-12-18 criteria provided, single submitter clinical testing
PreventionGenetics RCV000589974 SCV000806691 likely benign not provided 2017-12-11 criteria provided, single submitter clinical testing
Quest Diagnostics Nichols Institute San Juan Capistrano RCV000589974 SCV000889840 benign not provided 2017-11-17 criteria provided, single submitter clinical testing

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