I routinely use Mutation Taster to predict functional impact of a mutation in silico. However the input on MT is either ORF position, cDNA (transcript: ORF with UTRs) or genomic location on the gene (not the genomic location on chromosome). It is extremely complicated to identify the exact position from cDNA to transcript esp when there is an intronic mutation. Is there an easy online tool which can do this?
If the mutations are only in your introns, you can design PCR primers using the intron spanning sequences. Then amplify the intron region and sequence your samples. On the other hand, using the same principle, using a qPCR thermocycler you can do high resolution melting point analysis to detect differences between your samples without sequencing.
ANNOVAR is popular for variant annotation, and they have an online version at http://wannovar.wglab.org/ . It requires essentially the first 8 columns that you would see in a VCF file, in tab-delimited format. I.e. you can just provide the genomic coordinates and the base pair change, and you can fill the rest of the columns in with dummy data. E.g.:
chr1 22313024 . G A . PASS TEST=1
The tool will annotate the variant with the MutationTaster score as well as dozens of others, Sift, PolyPhen2, CADD, gene name, allele frequency in various populations, etc.
Perhaps I misunderstand your question, but maybe Mutalyzer could help to convert postions to the format you need.
https://mutalyzer.nl/position-converter
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