ClinVar Miner

Submissions for variant NM_001003841.3(SLC6A19):c.887+9G>A

gnomAD frequency: 0.00004  dbSNP: rs762018842
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Fulgent Genetics, Fulgent Genetics RCV002486486 SCV002791534 uncertain significance Hyperglycinuria; Neutral 1 amino acid transport defect; Iminoglycinuria 2021-12-15 criteria provided, single submitter clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV001357408 SCV001552875 uncertain significance not provided no assertion criteria provided clinical testing The SLC6A19 c.887+9G>A variant was not identified in the literature nor was it identified in the ClinVar, Cosmic or LOVD 3.0 databases. The variant was identified in dbSNP (ID: rs762018842) and in control databases in 4 of 280578 chromosomes at a frequency of 0.000014 (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 3 of 24826 chromosomes (freq: 0.000121) and European (non-Finnish) in 1 of 127236 chromosomes (freq: 0.000008), but was not observed in the Latino, Ashkenazi Jewish, East Asian, European (Finnish), Other, and South Asian populations. The variant occurs outside of the splicing consensus sequence however 3 of 4 in silico or computational prediction software programs (MaxEntScan, NNSPLICE, and GeneSplicer) predict a greater than 10% difference in splicing and the creation of a new 5' splice site. However, this information is not predictive enough to assume pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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