ClinVar Miner

Submissions for variant NM_000030.3(AGXT):c.165+16A>G (rs66494441)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics,PreventionGenetics RCV000252777 SCV000301565 benign not specified criteria provided, single submitter clinical testing
Integrated Genetics/Laboratory Corporation of America RCV000589389 SCV000693976 benign not provided 2017-06-26 criteria provided, single submitter clinical testing Variant summary: The AGXT c.165+16A>G variant involves the alteration of a non-conserved intronic nucleotide at a position not widely known to affect splicing. Mutation taster predicts a benign outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. This variant was found in 19192/117856 control chromosomes (1649 homozygotes) from ExAC at a frequency of 0.1628428, which is approximately 69 times the estimated maximal expected allele frequency of a pathogenic AGXT variant (0.0023717), thus this variant is a common benign polymorphism. This variant, as a part of a haplotype, has been reported in patients with primary hyperoxaluria type 1 in whom another pathogenic variant (p.Ile244Thr) in homozygosity explained the phenotype, further supporting the benign nature (Kanoun_2013). One clinical diagnostic laboratory (via ClinVar) has classified it as benign. Taken together, this variant is classified as benign.
Clinical Biochemistry Laboratory,Health Services Laboratory RCV000186225 SCV000239549 uncertain significance Primary hyperoxaluria, type I 2014-11-27 no assertion criteria provided research

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