I am using bootstrap-4 in my Vue webapp, But I am not able to customise this as is explained here.
I have my index.html which uses Bootstrap CDN, like following:
<!DOCTYPE html>
<html lang="en">
  <head>
    <meta charset="utf-8">
    <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
    <meta http-equiv="x-ua-compatible" content="ie=edge">
    <title>Sample</title>
    <meta name="viewport" content="initial-scale=1, maximum-scale=1, user-scalable=no, minimal-ui">
    <link rel="stylesheet" href="/static/custom.scss" type="text/x-scss">  ==> where I am overwriting variable
    <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0-alpha.5/css/bootstrap.min.css" integrity="sha384-AysaV+vQoT3kOAXZkl02PThvDr8HYKPZhNT5h/CXfBThSRXQ6jW5DO2ekP5ViFdi" crossorigin="anonymous">
    <script src="//cdnjs.cloudflare.com/ajax/libs/jquery/3.1.1/jquery.js"></script>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/tether/1.3.7/js/tether.min.js" integrity="sha384-XTs3FgkjiBgo8qjEjBk0tGmf3wPrWtA6coPfQDfFEY8AnYJwjalXCiosYRBIBZX8" crossorigin="anonymous"></script>
    <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0-alpha.5/js/bootstrap.min.js" integrity="sha384-BLiI7JTZm+JWlgKa0M0kGRpJbF2J8q+qreVrKBC47e3K6BW78kGLrCkeRX6I9RoK" crossorigin="anonymous"></script>
  </head>
  <body>
    <div id="app"></div>
    <script src="/dist/client-vendor-bundle.js"></script>
    <script src="/dist/client-bundle.js"></script> -->
  </body>
</html>
I also tried changing the order of custom.scss and bootstrap.css in index.html as well.
Following is custom.scss, where I am overwriting variables:
$body-bg:    #f5f5f5;
$body-color: #f5f5f5;
$enable-flex: true;
But this is not working.
I also tried importing this in my app component, like following:
<style lang="scss">
  @import 'custom.scss';
  // Following also did not work
  $body-bg: #333;
  $body-color: #999;  
</style>
How do I overwrite these variable to customise my webapp.

cdnuse the npm version where you get access to bootstrap's.scssfiles and compile it with your custom.scssso you can overwrite those values.