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The AUDIT questionnaire is designed to screen for hazardous alcohol use by measuring both alcohol consumption and the problematic consequences of drinking. We performed a genome-wide association study of AUDIT scores in the UK Biobank and the 23andMe cohorts and find several genetic loci that are significantly associated with AUDIT scores. We show that the problem drinking is genetically correlated with psychopathology whereas alcohol consumption shares a genetic profile with a more favourable health profile, i.e. higher HDL cholesterol and lower triglycerides. Our findings show that, while alcohol consumption and problem drinking have overlapping genetic architecture, some of the genes which associate with each trait are distinct. The last 7 questions of the AUDIT questionnaire are important to detect genetic variation which is specific to problem drinking and therefore these items should be retained when attempting to uncover the genetic basis of alcohol use disorders. Finally, we make recommendations about which AUDIT cut-offs to use when trying to create a phenotype that mirrors Alcohol Use Disorders when performing genetic studies.