ClinVar Miner

Submissions for variant NM_012434.5(SLC17A5):c.246G>A (p.Ala82=)

gnomAD frequency: 0.10691  dbSNP: rs472294
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Total submissions: 12
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins NTD LLC (GA) RCV000118354 SCV000203575 benign not specified 2013-12-11 criteria provided, single submitter clinical testing
PreventionGenetics,PreventionGenetics RCV000118354 SCV000311929 benign not specified criteria provided, single submitter clinical testing
Illumina Laboratory Services,Illumina RCV001095271 SCV000464781 benign Sialic acid storage disease, severe infantile type 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.
Illumina Laboratory Services,Illumina RCV000297962 SCV000464782 benign Salla disease 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 RCV000118354 SCV000514634 benign not specified 2015-11-09 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.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000590335 SCV000699338 benign not provided 2017-02-08 criteria provided, single submitter clinical testing Variant summary: The SLC17A5 c.246G>A (p.Ala82Ala) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a polymorphism outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 11883/121310 control chromosomes (671 homozygotes) at a frequency of 0.0979557, which is approximately 41 times the estimated maximal expected allele frequency of a pathogenic SLC17A5 variant (0.0023717), strong evidence that this variant is a benign polymorphism. In addition, multiple clinical diagnostic laboratories/reputable databases classified this variant as benign. The variant of interest has not, to our knowledge, been reported in affected individuals via publications nor evaluated for functional impact by in vivo/vitro studies. Due to the synonymous nature of the variant, the lack of predicted effect on splicing and the high frequency in the contol population, this variant is classified as benign.
Invitae RCV000297962 SCV001719101 benign Salla disease 2021-12-18 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000297962 SCV001762580 benign Salla disease 2021-07-10 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001095271 SCV001762581 benign Sialic acid storage disease, severe infantile type 2021-07-10 criteria provided, single submitter clinical testing
Genetic Services Laboratory,University of Chicago RCV000118354 SCV000152754 likely benign not specified no assertion criteria provided clinical testing Likely benign based on allele frequency in 1000 Genomes Project or ESP global frequency and its presence in a patient with a rare or unrelated disease phenotype. NOT Sanger confirmed.
Mayo Clinic Laboratories,Mayo Clinic RCV000590335 SCV000801550 benign not provided 2017-04-19 no assertion criteria provided clinical testing
Natera, Inc. RCV000297962 SCV001453517 benign Salla disease 2020-09-16 no assertion criteria provided clinical testing

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