The Clinical Genome Resource (ClinGen) Sequence Variant Interpretation Working Group set out to refine the American College of Medical Genetics and Genomics and the Association of Molecular Pathologists (ACMG/AMP) variant pathogenicity recommendations for stand‐alone rule BA1 (a variant with minor allele frequency MAF > 0.05 is benign), by clarifying how it should be used and specifying a set of variants that should be exempted from this rule. We cross‐referenced ClinVar and Exome Aggregation Consortium data to identify variants for which there was a plausible argument for pathogenicity and the variant exists in one or more population data sets at MAF > 0.05. We identified nine such variants that were present in these data sets that may not be benign. The ACMG/AMP criteria were applied to these variants that resulted in four pathogenic and five variants of uncertain significance. We have refined benign rule BA1 by clarifying terms used to describe its use, which databases we recommend using, and assumptions made about this rule. We also recognized an initial list of nine variants for which there was some evidence of pathogenicity even though the MAF was high for these variants. We specify processes whereby individuals can petition ClinGen for amendments to our variant‐specific assertions and the criteria experts should use when setting a numerically lower threshold for BA1 for specific genes. The ACMG/AMP variant pathogenicity recommendations include a stand‐alone rule BA1 (variant with MAF >0.05 is benign). We cross‐referenced ClinVar and ExAC for variants with MAF >0.05 and reasonable evidence for pathogenicity, identifying nine (four pathogenic and five VOUS) variants as a part of an initial exclusion list. We specify how individuals can amend this list. Additionally, we clarified terms, criteria and assumptions about rule BA1 and specify the criteria that experts should use when setting lower gene‐specific BA1 thresholds.