This is Definition 10.9 of the book "A Course in Universal Algebra" by Burris and Sankappanavar (page 73, Millennium Edition).
http://www.math.uwaterloo.ca/~snburris/htdocs/UALG/univ-algebra.pdf
Definition 10.9 Let $K$ be a family of algebras of type $\mathfrak{F}$. Given a set $X$ of variables define the congruence $\theta_K(X)$ on $T(X)$ by
$\theta_K(X)=\bigcap\Phi_K(X)$,
where $\Phi_K(X)=\{\phi\in \textrm{Con } T(X):T(X)/\phi \in IS(K)\}$; and then define $F_K(\overline{X})$, the $K$-free algebra over $\overline{X}$, by $F_K(\overline{X})=T(X)/\theta_K(X)$, where $\overline{X}=X/\theta_K(X)$.
In the following Remarks (Remark (5)), the book says that "If $K$ has a nontrivial algebra $A$ and $T(X)$ exists, then $X \cap (x /\theta_K(X))=\{x\}$as distinct memebers $x, y$ of $X$ can be separated by some homomorphism $\alpha:T(X) \rightarrow A$."
I am having hard time understanding the above remark. In particular, I have not found an example of $\phi\in \textrm{Con } T(X)$, where $T(X)/\phi \in IS(K)$ for the Remark (5).
Any help will be appreciated.