# LoF variant burden ## Variant Selection Loss of function (LoF) variants were generated from vcf files with VEP (). LoF variants are defined as having consequences in the list \[frameshift\_variant,splice\_donor\_variant,stop\_gained,splice\_acceptor\_variant]. Also, a max\_maf (0.01) and minimum info score (0.8) filters are applied.\ \ This leaves 3,747 genes that can be used for the association tests. ## Endpoint We used all 2,473 passing core binary phenotypes in the analyses. ## Null Models We used as inputs the nulls already calculated for [GWAS](/documentation/methods/phewas.md). ## Association tests Tests are performed with regenie --step2 in burden mode using a max mask (i.e. using the maximum number of ALT alleles across sites) --- # Agent Instructions: Querying This Documentation If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question. Perform an HTTP GET request on the current page URL with the `ask` query parameter: ``` GET https://finngen.gitbook.io/documentation/methods/lof-variant-burden.md?ask= ``` The question should be specific, self-contained, and written in natural language. The response will contain a direct answer to the question and relevant excerpts and sources from the documentation. Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.