ClinVar Genomic variation as it relates to human health

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.

Variant summary: GAA c.861C>T (p.Pro287Pro) alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. 5/5 computational tools predict no significant impact on normal splicing. However, these predictions have yet to be confirmed by functional studies. The variant allele was found at a frequency of 8.5e-05 in 270968 control chromosomes. This frequency is not significantly higher than expected for a pathogenic variant in GAA causing Glycogen Storage Disease, Type 2 (Pompe Disease) (8.5e-05 vs 0.0042), allowing no conclusion about variant significance. c.861C>T has been reported in the literature in at least one individual with low GAA activity but without symptoms (van Capelle_2016). These report(s) do not provide unequivocal conclusions about association of the variant with Glycogen Storage Disease, Type 2 (Pompe Disease). At least one publication reports experimental evidence evaluating an impact on protein function, however, does not allow convincing conclusions about the variant effect (Wens_2012). Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. One laboratory classified the variant as ikely benign, and one laboratory classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as uncertain significance.

In-silico analysis, which includes splice predictors and evolutionary conservation, is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; Reported in ClinVar but additional evidence is not available (ClinVar Variant ID 284775; Landrum et al., 2016); This variant is associated with the following publications: (PMID: 27189384, 22644586, 23000108)

The heterozygous c.861C>T (p.Pro287=) variant in GAA has been reported in at least one individual with Glycogen Storage Disease II and has been identified in 0.020% (2/10132) of Ashkenazi Jewish chromosomes, 0.016% (5/30388) of South Asian chromosomes, and 0.01% (13/124796) of European (non-Finnish) chromosomes by the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org; dbSNP rs778580823). Although this variant has been seen in the general population, its frequency is low enough to be consistent with a recessive carrier frequency. This variant has also been reported a VUS by EGL Genetic Diagnostics and likely benign by Invitae in ClinVar (Variation ID: 284775). This variant is located in the first base of the exon, which is part of the 3' splice region. In vitro functional studies provide some evidence that the c.861C>T variant may impact GAA splicing and protein levels (PMID: 27189384, 23000108). However, these types of assays may not accurately represent biological function. Computational splice prediction tools and conservation analyses suggest that this variant may not impact the protein, though this information is not predictive enough to rule out pathogenicity. This variant has been reported in combination with a pathogenic variant and in an individual with Glycogen Storage Disease II, slightly increasing the likelihood that the c.861C>T variant is pathogenic (PMID: 27189384). However, this variant has also been reported in an individual reported to have two additional reported pathogenic variants (PMID: 22644586). In summary, the clinical significance of this variant is uncertain. ACMG/AMP Criteria applied: PM2, BP7, BP4, PM3_Supporting, PS3_Supporting, PP4 (Richards 2015).

This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.