In VCF, column 4 is REF and 5 contains the ALT alleles - while Pierre's example doesn't contain the other columns that would be needed to make it valid VCF, I would assume that is what he is intending.

In which case the first variant (CATA to C) would represent a three base deletion (the ATA are not present in the ALT, and the second (AAGT to A) also represents a three base deletion of AGT. This is a good example that illustrates the difficulties when working with VCF. Notice:

• The "overlapping" A base at 13462 is not actually altered by the second variant, so semantically there isn't really an overlap, the A base that is in common in the REF and ALT alleles is only there because the VCF spec says that you cannot have either REF or ALT be empty -- it's commonly called a padding or anchor base.
• In the human reference, the base at 13466 is an A, so the second variant could equivalently be represented as 1 13463 rs1441058751 AGTA A, so there isn't even any syntactic overlap if that representation were used.
• If these two variants occurred in the same haplotype, you could also represent the variation as (for example) 1 13459 rs1315857414 CAGAAGT CA, (and conversely, you could represent each of your variants as separate single base deletions)

When you are matching and comparing VCF variants you really need to be comparing at the level of the underlying haplotypes rather than at the syntactic level of what is in the REF and ALT fields of the VCF. For this I recommend a tool such as vcfeval from RTG Tools (which I help develop).