Using \rule
Use a zero-width \rule as a "strut" at the start of the second line:
\documentclass{article}
\usepackage{amsmath}
\begin{document}
\begin{align*}
x &= 1 \\
\rule[-1.3\baselineskip]{0pt}{3\baselineskip} y &= 2
\end{align*}
\end{document}
It looks like this:
The syntax of \rule is \rule[raise]{width}{height}.
The way I arrived at the -1.3\baselineskip and 3\baselineskip values is by checking the definition for a \strut, which is \rule[-0.3\baselineskip]{0pt}{\baselineskip}, and subtracting 1\baselineskip from the raise and adding twice that to the height.
We can visualize the effect of the rule by temporarily setting its width to 1pt:
Using \vphantom
If instead of setting a height value, you want to reserve the amount of space that some specific formula would take, you can use \vphantom instead of \rule. The \vphantom macro creates a zero-width box with as much height as its contents.
For example, this code reserves as much space as a summation sign would take:
\documentclass{article}
\usepackage{amsmath}
\begin{document}
\begin{align*}
x &= 1 \\
\vphantom{\sum_0^x} y &= 2
\end{align*}
\end{document}