ClinVar Miner

Submissions for variant NM_000155.4(GALT):c.564+15G>A (rs111033732)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000270166 SCV000330958 likely benign not specified 2015-09-25 criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000588771 SCV000695696 likely benign not provided 2016-02-19 criteria provided, single submitter clinical testing Variant summary: The GALT c.564+15G>A variant affects a non-conserved intronic nucleotide not widely known to impact normal splicing. Mutation Taster predicts a benign outcome for this variant, and 4/5 Alamut algorithms predict no change to the splice donor site, however these in silico predictions have not been verified with functional studies. This variant is found in 48/121384 control chromosomes at a frequency of 0.0003954, which does not significantly exceed maximal expected frequency of a pathogenic allele (0.0028868). This variant has been cited in one Hispanic classic GALT patient (Yang_HM_2002), authors did not provide co-segregation data, and the allele frequency in Latinos from the ExAC project is 2-fold greater (48/11576 alleles; 0.00415), thus this variant is likely a benign polymorphism found in Latinos. Additionally, multiple clinical labs/databases classify the variant as benign/likely benign without providing evidence to independently evaluate. Taken together, the variant was classified as Likely Benign until additional information becomes available.
Research and Development, ARUP Laboratories RCV000022152 SCV000042832 benign Deficiency of UDPglucose-hexose-1-phosphate uridylyltransferase 2012-12-04 no assertion criteria provided clinical testing Converted during submission to Benign.

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