ClinVar Miner

Submissions for variant NM_003640.5(ELP1):c.3876T>G (p.Thr1292=) (rs61749202)

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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 RCV000297833 SCV000476540 uncertain significance Familial dysautonomia 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, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Invitae RCV000590763 SCV000563260 benign not provided 2019-12-31 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000590763 SCV000698213 benign not provided 2017-08-22 criteria provided, single submitter clinical testing Variant summary: The c.3876T>G (p.Thr1292=) in IKBKAP gene is a synonymous change that involves a non-conserved nucleotide. 4/5 programs in Alamut predict that this variant does not affect splicing, however no functional studies supporting this notion were published at the time of evaluation. The variant is present in control dataset of ExAC at a frequency of 0.01362 (1653/121382 chrs tested, including 21 homozygotes), predominantly in individuals of European Ancestry descent (0.01845; 1231/66722 chrs tested, including 17 homozygotes). These frequencies exceed the estimated maximum allele frequency for a pathogenic allele in this gene (0.0018). The variant of interest has not, to our knowledge, been reported in affected individuals via published reports, but is cited as Benign by a reputable clinical laboratory. Taken together, the variant was classified as benign.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000297833 SCV001159187 benign Familial dysautonomia 2020-08-30 criteria provided, single submitter clinical testing

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