If your daughter has CF then, yes, she definitely has two mutations (R1162L being one and the other???). As far as classifications go, there are five classes, "benign" isn't one of them.
Class I mutations lead to defects in the synthesis of stable CFTR mRNA transcripts resulting in absence of the CFTR protein. About half of all mutations in CFTR (encompassing premature termination, exon skipping, aberrant mRNA splicing, and frameshifts) are thought to fall into this class and result in complete loss of CFTR protein/function.
Class II mutations complete protein translation but produce an abnormal protein that fails to escape the endoplasmic reticulum. Little or no CFTR reaches the plasma membrane, and the absence of all surface CFTR results in a severe phenotype. It is being increasingly recognized that mutations in unrelated genes can create defective proteins, which fail to traffic properly through the cell. Classically, missense mutations creating an abnormal protein were thought to be relatively benign or less consequential than nonsense mutations (null) or large deletions. This is no longer strictly the case because examples from CF and other inherited disorders demonstrate that a synthesized protein that fails to mature along the normal biosynthetic pathway often becomes quite destructive.
Class III mutations disrupt activation and regulation of CFTR at the plasma membrane. Thus biosynthesis, trafficking, and processing are undisturbed, but the channel may be defective with respect to ATP binding and hydrolysis, or phosphorylation.
Class IV mutations affect chloride conductance or channel gating and thus result in reduced chloride current.
Class V mutations reduce the level of normal CFTR protein by alterations in the promoter or by altering splicing. Currently it is thought that a reduction in mRNA to less than 10% of normal results in disease in CF.
I tried to find some info on the R1162L with regard to what class it may fall in. So far, the only thing I've found is the "definition" which is, the replacement of arginine at codon 1162 (CGA) by leucine (CTA) [Arg1162Leu (R1162L)]. I believe this is a Class IV type mutation but your best bet is to check with Steve under the Ambry Genetics thread/sticky in the families section.
Also note that the class of the second gene is important. Class interactions do play a part in clinical outcome along with environment, compliance, quality of care, and luck. If you know the other gene, I may be able to provide you with input on that as well.