I have genomic coordinate of iCLIP data. I want the coordinate of this proteine at the transcript level. I know that transcript are spliced and I want the coordinate on every transcript if the binding site doesn't occure in intron.

It should be very simple

1. download the gtf file and install bedtools
2. convert it to bed using gtf2bed
3. grep -wi 'exon' bed_file_converted_from_gtf > exons.bed
4. intersectBed -a your_iCLIP_coordinates -b exons.bed > your_protein_binding_transcripts.bed

hth

Tools like Ensembl VEP can do this, and will output things like cDNA position and CDS position (e.g. with or without counting the UTR)

The https://mutalyzer.nl/ tool also looks interesting

These may not be the most lightweight or purpose built, and only may work on certain organisms

I think the reason for not having such a purpose built tool is that it can be a complex task given the nature of things like overlapping genes or similar phenomenon, so VEP and other tools make best-attempt efforts to report all possible results

Transvar webserver can handle this task.

As you said, there will likely be multiple hits for each genomic positions.