When generating BIP39 seed by hand, you will need this script to fix last 4 bits (12th word) with a correct checksum.

checksum_12_words.js

// We expect array of 12 words as human readable indexes (1-2048)
function checksum_12_words(data) {
  if (data.length != 12) return console.log("ERROR: Need 12 words numbers as input")
  
  let binstr = (s,l =8) => s.toString(2).padStart(l,'0') // convert to binary `0011...` string
  let tohex = (bytes) => bytes.map( x => x.toString(16).padStart(2,0) ).join('')
                                   
  let bytes = data.map( x => binstr(x - 1, 11)) // convert to 0-index, then to binary `0011...` 
                .join('').match(/.{1,8}/g) 	// split 8 bits	
                .map( x => parseInt(x, 2))	// convert to UInt8 
  // Now we got 17 UInt8 bytes. Last 4 bits (the 17th byte) are wrong and need to be fixed
  
  if (bytes.length != 17) return console.log("ERROR: Something is wrong, check your input")
  
  bytes.pop() // remove wrong 17th byte of checksum
  // You can comment out next line if you dont want to print the entropy
  console.log("Entropy is :",tohex(bytes))  
  
  // This function works only if your browser is pointing to TLS website or
  // on Firefox and Safari you can use http://localhost/. On Chrome you can
  // use raw view of any gist since it has no running scripts: https://bit.ly/2YJILYN
  window.crypto.subtle.digest("SHA-256", new Uint8Array(bytes).buffer).then( x => {
    if (x.byteLength != 32) return console.log("ERROR: Wrong SHA256")
    let hash = new Uint8Array(x)
    let cs = binstr(hash[0]).match(/.{1,4}/g)[0]	// Thats our checksum
    
    // Take byte 15 for first 7 bits our final word and we add checksum bits
    let bits = [binstr(bytes[15]),cs].join('')
    if (bits.length != 12) return console.log("ERROR: Wrong final word bits")
    
    //console.log(bits)
    console.log("Your 12th word index is: " + (1+parseInt(bits.substr(1),2)))
  })
  return "OK"
}

// Test vector of human readable 1-index words: arrive, dirt, join, ...
// https://vault12.s3-us-west-1.amazonaws.com/bip39-words.pdf
// Try your own! 

data = [101, 502, 962, 1400, 1607, 1817, 1090, 1827, 820, 1334, 156, 1073]
checksum_12_words(data)

// Entropy is : 0c87d5e0d77c8dc6220f226674d44dc3
// "OK"
// Your 12th word index is: 1078
// This is human readable 1-index of word `mammal`