ClinVar Miner

Submissions for variant NM_004304.5(ALK):c.1464C>T (p.Gly488=) (rs56165377)

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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 RCV000253215 SCV000310067 benign not specified criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV001084370 SCV000429960 benign Neuroblastoma 3 2018-01-12 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.
GeneDx RCV000253215 SCV000519045 benign not specified 2016-09-20 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 RCV001084370 SCV000554729 benign Neuroblastoma 3 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000567332 SCV000664981 benign Hereditary cancer-predisposing syndrome 2017-01-06 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;In silico models in agreement (benign);Synonymous alterations with insufficient evidence to classify as benign
Integrated Genetics/Laboratory Corporation of America RCV000588206 SCV000698266 benign not provided 2016-08-24 criteria provided, single submitter clinical testing Variant summary: The ALK c.1464C>T (p.Gly488Gly) variant involves the alteration of a conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 4/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 681/121400 control chromosomes (5 homozygotes) at a frequency of 0.0056096, which is approximately 13463 times the estimated maximal expected allele frequency of a pathogenic ALK variant (0.0000004), suggesting this variant is likely a benign polymorphism. The variant of interest has not, to our knowledge, been reported in affected individuals via publications. Taken together, this variant is classified as Benign.

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