ClinVar Miner

Submissions for variant NM_024312.5(GNPTAB):c.1986G>A (p.Ala662=) (rs112000802)

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Integrated Genetics/Laboratory Corporation of America RCV000586492 SCV000699476 uncertain significance not provided 2017-04-24 criteria provided, single submitter clinical testing Variant summary: The GNPTAB c.1986G>A (p.Ala662Ala) variant involves the alteration of a non-conserved nucleotide, resulting in a synonymous change. One in silico tool predicts a damaging outcome for this variant. 5/5 splice prediction tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. This variant was found in 23/121332 control chromosomes, predominantly observed in the African subpopulation at a frequency of 0.001832 (19/10372). This frequency is about slightly lower than the estimated maximal expected allele frequency of a pathogenic GNPTAB variant (0.0022361), suggesting this is possibly a benign polymorphism found primarily in the populations of African origin. The variant of interest has not, to our knowledge, been reported in affected individuals via publications and/or reputable databases/clinical diagnostic laboratories; nor evaluated for functional impact by in vivo/vitro studies. Taken together, this variant is classified as VUS-possibly benign.

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