Abstract: Methods for reporting clinically-actionable potential germline pathogenic variants identified in nucleic acid sequencing data are described. The methods may comprise, for example, receiving variant sequence data for a sample from a subject; filtering the variant sequence data to identify variant sequences located in a gene locus known to comprise clinically-actionable germline variants; filtering the variant sequences identified as being located in such a gene locus to identify those that are potentially germline pathogenic; filtering the resulting list of potentially germline pathogenic variant sequences to identify those that have an allele frequency greater than a first predetermined threshold; and based on a determination that a potentially germline pathogenic variant sequence has an allele frequency greater than the first predetermined threshold, reporting the variant sequence as a clinically-actionable potential germline pathogenic variant.