You need to call Fn1 before Fn2 to access it's value, so let's wrap Fn1 into Promise:

App = {
    st: null,//st is number value

    Fn1: function() {
        return new Promise((resolve, reject) => {
            App.contracts.contractName.deployed().then(function(instance){
                return instance.getST();
            }).then(function(result){      
                App.st = result;
                resolve();
            }).catch(function(err){
                reject(err);
            })
        })
    },
    Fn2: function() {
        alert(App.st)
    }    
}

or better with async/await:

App = {
    st: null,//st is number value

    Fn1: async function() {
        try {
            const instance = await App.contracts.contractName.deployed();
            const result = await instance.getST();
            App.st = result;
        } catch(err) {
            throw err;
        }
    },
    Fn2: function() {
        alert(App.st)
    }    
}

Now you can wait until Fn1 exec before calling Fn2:

App.Fn1().then(function() {
  App.Fn2()
})

or using async/await:

await App.Fn1()
App.Fn2()