ClinVar Miner

Submissions for variant NM_000192.3(TBX5):c.309C>T (p.Leu103=) (rs28730763)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV000329123 SCV000376508 benign Holt-Oram syndrome 2018-01-13 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.
Invitae RCV000468582 SCV000562257 benign Aortic valve disease 2 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000587262 SCV000695950 benign not provided 2016-06-27 criteria provided, single submitter clinical testing Variant summary: The TBX5 c.309C>T (p.Leu103Leu) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a polymorphism outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. ESE finder predicts that this variant may affect ESE sites. This variant was found in 1592/121410 control chromosomes (111 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.1429258 (1487/10404). This frequency significantly exceeds the estimated maximal expected allele frequency of a pathogenic TBX5 variant (0.0000013), suggesting this is likely a benign polymorphism found primarily in the populations of African origin. This variant has been reported in multiple affected individuals as a polymorphism. Some patient also carried a pathogenic variant, further supporting the benign classification of this variant. In addition, one clinical diagnostic laboratory classified this variant as benign. Taken together, this variant is classified as benign.
Ambry Genetics RCV000621453 SCV000735167 benign Cardiovascular phenotype 2015-07-15 criteria provided, single submitter clinical testing

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