ClinVar Miner

Submissions for variant NM_004304.5(ALK):c.3408C>T (p.Ser1136=) (rs56146053)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Clinical Services Laboratory,Illumina RCV001082897 SCV000429932 benign Neuroblastoma 3 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.
GeneDx RCV000438016 SCV000518941 benign not specified 2016-10-09 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 RCV001082897 SCV000554740 benign Neuroblastoma 3 2019-12-31 criteria provided, single submitter clinical testing
Ambry Genetics RCV000563653 SCV000664969 benign Hereditary cancer-predisposing syndrome 2017-02-08 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589663 SCV000698293 benign not provided 2016-08-24 criteria provided, single submitter clinical testing Variant summary: The ALK c.3408C>T (p.Ser1136Ser) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. 4/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 1019/121152 control chromosomes (44 homozygotes), predominantly observed in the African subpopulation at a frequency of 0.0932024 (968/10386). This frequency is about 223686 times the estimated maximal expected allele frequency of a pathogenic ALK variant (0.0000004), suggesting this is likely a common benign polymorphism found primarily in the populations of African origin. 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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