ClinVar Miner

Submissions for variant NM_007078.3(LDB3):c.689+9C>T (rs727503124)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine, Partners HealthCare Personalized Medicine RCV000150919 SCV000198545 likely benign not specified 2014-03-14 criteria provided, single submitter clinical testing 689+9C>T in intron 4 of LDB3: This variant is not expected to have clinical sign ificance because it is not located within the splice consensus sequence. 689+9 C>T in intron 4 of LDB3 (allele frequency = n/a)
GeneDx RCV000150919 SCV000520033 likely benign not specified 2015-10-29 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.
Invitae RCV000639883 SCV000761466 likely benign not provided 2018-12-26 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000150919 SCV000917575 benign not specified 2017-10-02 criteria provided, single submitter clinical testing Variant summary: The LDB3 c.689+9C>T variant causes a missense change involving the alteration of a non-conserved intronic nucleotide. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant was found in the control population dataset of gnomAD in 0.0000675, which is approximately 3 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/reputable databases classified this variant as likely benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as benign.

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