ClinVar Miner

Submissions for variant NM_007078.3(LDB3):c.1014A>G (p.Thr338=)

gnomAD frequency: 0.00452  dbSNP: rs150209221
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Total submissions: 9
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Laboratory for Molecular Medicine,Mass General Brigham Personalized Medicine RCV000038714 SCV000062392 benign not specified 2012-04-11 criteria provided, single submitter clinical testing Thr338Thr in Exon 10 of LDB3: This variant is not expected to have clinical sign ificance because it does not alter an amino acid residue, is not located within the splice consensus sequence and has been identified in 1.2% (43/3736) of Afric an American chromosomes from a broad population by the NHLBI Exome Sequencing Pr oject (; dbSNP rs150209221).
PreventionGenetics,PreventionGenetics RCV000038714 SCV000311687 likely benign not specified criteria provided, single submitter clinical testing
Invitae RCV001085854 SCV000557550 benign Myofibrillar myopathy 4 2021-12-07 criteria provided, single submitter clinical testing
Ambry Genetics RCV000620086 SCV000736317 benign Cardiovascular phenotype 2016-09-23 criteria provided, single submitter clinical testing General population or subpopulation frequency is too high to be a pathogenic mutation based on disease/syndrome prevalence and penetrance
Athena Diagnostics Inc RCV000712208 SCV000842646 benign not provided 2018-03-15 criteria provided, single submitter clinical testing
CHEO Genetics Diagnostic Laboratory,Children's Hospital of Eastern Ontario RCV000769283 SCV000900661 benign Cardiomyopathy 2016-07-27 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000038714 SCV000917574 benign not specified 2018-08-06 criteria provided, single submitter clinical testing Variant summary: LDB3 c.1014A>G alters a non-conserved nucleotide resulting in a synonymous change. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0014 in 276194 control chromosomes, predominantly at a frequency of 0.015 within the African subpopulation in the gnomAD database, including 4 homozygotes. The observed variant frequency within African control individuals in the gnomAD database is approximately 600-fold of the estimated maximal expected allele frequency for a pathogenic variant in LDB3 causing Cardiomyopathy phenotype (2.5e-05), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.1014A>G in individuals affected with Cardiomyopathy and no experimental evidence demonstrating its impact on protein function have been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. Both laboratories classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
GeneDx RCV000712208 SCV001939651 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000712208 SCV002544443 benign not provided 2022-04-01 criteria provided, single submitter clinical testing

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