ClinVar Miner

Submissions for variant NM_003060.4(SLC22A5):c.1451-16G>A

gnomAD frequency: 0.00371  dbSNP: rs140988771
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000440075 SCV000525456 likely benign not specified 2017-06-21 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000440075 SCV001360660 benign not specified 2019-03-11 criteria provided, single submitter clinical testing Variant summary: SLC22A5 c.1451-16G>A alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 0.0017 in 277110 control chromosomes, predominantly at a frequency of 0.011 within the African subpopulation in the gnomAD database, including 2 homozygotes. The observed variant frequency within African control individuals in the gnomAD database is approximately 2.41 fold of the estimated maximal expected allele frequency for a pathogenic variant in SLC22A5 causing Systemic Primary Carnitine Deficiency phenotype (0.0046), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. To our knowledge, no occurrence of c.1451-16G>A in individuals affected with Systemic Primary Carnitine Deficiency and no experimental evidence demonstrating its impact on protein function have been reported. A ClinVar submission from a clinical diagnostic laboratory (evaluation after 2014) cites the variant as likely benign. Based on the evidence outlined above, the variant was classified as benign.
Invitae RCV001511362 SCV001718592 benign Renal carnitine transport defect 2024-01-31 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001511362 SCV002055881 benign Renal carnitine transport defect 2021-07-15 criteria provided, single submitter clinical testing

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