Panel or whole exome sequencing is often utilized in the diagnostic work-up of ALS, increasing the need for accurate variant interpretation and reporting.  

To assess the utility of the American College of Medical Genetics (ACMG) guidelines for ALS (amyotrophic lateral sclerosis)-associated genes and propose recommendations to minimize the number of variants of unknown significance (VOUS). 

Variants in ALS-associated genes (ANXA11, ALS2, CCNF, CHCHD10, FUS, OPTN, NEK1, PFN1, SOD1, TARDBP, TBK1, UBQLN2, VAPB, and VCP) were sourced from public databases and reviewed using ACMG guidelines.  Consensus classifications were achieved using a modified Delphi approach.  Inter-rater reliability was assessed (k-alpha statistic).  ‘Meta’ in silico prediction algorithms – integrative “ensemble” prediction scores - were evaluated.  ALS-specific and gene-specific criteria were identified and utilized to estimate whether VOUS were more likely benign or pathogenic.

Final mean k-alpha was 0.91 (95% CI 0.87-0.95).  Only 19% of reported ALS variants met criteria for Pathogenic/Likely Pathogenic.  78% of variants were VOUS using ACMG criteria.  Criteria most relevant to pathogenicity were i) absence of variant from population databases, ii) novel missense variant, iii) computational evidence of pathogenicity.  Many criteria were only rarely applicable in ALS.  Gene-specific criteria included: i) identification of null variants (ALS2, OPTN, TBK1), iii) mutational hotspots (FUS, TARDBP, UBQLN2, VCP), iii) co-segregation of variant with disease (PFN1, VCP).  Relaxing the ACMG criteria with ALS-specific or gene-specific information allowed us to reclassify 77% of VOUS toward ‘Likely Pathogenic’ or ‘Likely Benign’.  

While ACMG criteria are a good starting point for the classification of variants in ALS genes, they leave many variants as VOUS.   We outline a set of disease and gene-specific issues for common ALS genes that guide variant interpretation beyond those provided by ACMG criteria and provide additional diagnostic interpretation of variants to help inform patients and families.