ClinVar Miner

Submissions for variant NM_012434.5(SLC17A5):c.1111+7G>A

gnomAD frequency: 0.01982  dbSNP: rs146729568
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Total submissions: 10
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001095190 SCV000464775 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 RCV000285760 SCV000464776 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.
Counsyl RCV000285760 SCV000789959 likely benign Salla disease 2017-04-26 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV001201293 SCV001372422 benign not specified 2020-06-08 criteria provided, single submitter clinical testing Variant summary: SLC17A5 c.1111+7G>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. 4/4 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 0.022 in 251238 control chromosomes in the gnomAD database, including 106 homozygotes. The observed variant frequency is approximately 9 fold of the estimated maximal expected allele frequency for a pathogenic variant in SLC17A5 causing Sialic Acid Storage Disorder phenotype (0.0024), strongly suggesting that the variant is benign. To our knowledge, no occurrence of c.1111+7G>A in individuals affected with Sialic Acid Storage Disorder and no experimental evidence demonstrating its impact on protein function have been reported. Three ClinVar submitters (evaluation after 2014) cite the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as benign.
Invitae RCV000285760 SCV001728614 benign Salla disease 2024-02-01 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV000285760 SCV001762889 benign Salla disease 2021-07-10 criteria provided, single submitter clinical testing
Genome-Nilou Lab RCV001095190 SCV001762890 benign Sialic acid storage disease, severe infantile type 2021-07-10 criteria provided, single submitter clinical testing
GeneDx RCV000675824 SCV001833564 benign not provided 2015-03-03 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000675824 SCV000801546 likely benign not provided 2017-04-19 no assertion criteria provided clinical testing
Natera, Inc. RCV000285760 SCV002076727 benign Salla disease 2019-11-26 no assertion criteria provided clinical testing

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