ClinVar Miner

Submissions for variant NM_007078.3(LDB3):c.1422G>A (p.Ser474=) (rs142625982)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine,Partners HealthCare Personalized Medicine RCV000038726 SCV000062404 likely benign not specified 2015-02-18 criteria provided, single submitter clinical testing p.Ser474Ser in exon 12 of LDB3: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue, is not located with in the splice consensus sequence, and has been identified in 0.1% (91/66282) of European chromosomes by the Exome Aggregation Consortium (ExAC, http://exac.broa dinstitute.org; dbSNP rs142625982).
Invitae RCV000231484 SCV000289617 benign Myofibrillar myopathy, ZASP-related 2016-03-10 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000038726 SCV000698753 benign not specified 2017-06-19 criteria provided, single submitter clinical testing Variant summary: The LDB3 c.1422G>A (p.Ser474Ser) variant involves the alteration of a non-conserved nucleotide causing a synonymous change that 4/5 splice prediction tools predict change of a cryptic splicing acceptor site. ESE finder predicts that this variant may alter ESE binding. However, these predictions have yet to be confirmed by functional studies. This variant was found in 301/264076 control chromosomes (gnomAD) at a frequency of 0.0011398, which is approximately 46 times the estimated maximal expected allele frequency of a pathogenic LDB3 variant (0.000025), suggesting this variant is likely a benign polymorphism. In addition, multiple clinical diagnostic laboratories classified this variant as likely benign/benign. Therefore, due to the nature and location of this variant, control population frequency, and additional clinical diagnostic laboratories classifying the variant as "likely benign/benign," the variant of interest has been classified as Benign.
Ambry Genetics RCV000619945 SCV000736503 likely benign Cardiovascular phenotype 2015-12-15 criteria provided, single submitter clinical testing Lines of evidence used in support of classification: Synonymous alterations with insufficient evidence to classify as benign
Invitae RCV000860874 SCV001001046 benign not provided 2019-02-22 criteria provided, single submitter clinical testing

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