ClinVar Miner

Submissions for variant NM_003640.5(ELP1):c.2855A>T (p.Lys952Ile) (rs2230798)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000249304 SCV000309751 benign not specified criteria provided, single submitter clinical testing
Invitae RCV000857357 SCV000563267 benign not provided 2019-12-31 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory,University Medical Center Utrecht RCV000465354 SCV000743224 benign Familial dysautonomia 2014-10-09 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000465354 SCV001329066 likely benign Familial dysautonomia 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
Integrated Genetics/Laboratory Corporation of America RCV000249304 SCV001363974 benign not specified 2019-02-22 criteria provided, single submitter clinical testing Variant summary: IKBKAP c.2855A>T (p.Lys952Ile) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.016 in 276918 control chromosomes in the gnomAD database, including 53 homozygotes. The observed variant frequency is approximately 8.5 fold of the estimated maximal expected allele frequency for a pathogenic variant in IKBKAP causing Familial Dysautonomia phenotype (0.0018), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.2855A>T in individuals affected with Familial Dysautonomia and no experimental evidence demonstrating its impact on protein function have been reported. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, and classified the variant as benign. Based on the evidence outlined above, the variant was classified as benign.
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV000465354 SCV001474251 benign Familial dysautonomia 2020-06-19 criteria provided, single submitter clinical testing

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