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

Total submissions: 3

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.