Dear Vitor,

I did not read all previous comments, but this is how I normally determine positions.

First I load my genomic and mRNA sequence in Spidey (http://www.ncbi.nlm.nih.gov/spidey/). This gives you the number of exons with relative position from each other. An other option is Blat (https://genome.ucsc.edu/cgi-bin/hgBlat?command=start). this program also gives you the number of exons, but with chromosomal numbering. However, do keep in mind two things. First, you need to know for sure what your reference sequence is. This is particularly important in case of multiple transcripts (splice variants). Second, from my own experience, you really need to have your literature up to date. In some cases, many because of the progress in genetics, insights change, which could result in a change of number of exons (eg. 9 in stead of 8). Be careful with this.

Now you are all set with interpreting your mutations.

My favorite is mutationtaster (http://www.mutationtaster.org/) a user friendly interface. However, there are many such tools available on the web each with there on strenghts and weaknesses. I like mutationtaster, as it gives you all kinds of info, such as, location (genomic, coding, chromosomal etc), and most importantly, if your mutation is known or not (eg HGMD, Exac, 1000G etc).

Hope this helps.

Good luck and if you have any questions please dont hesitate to contact me.

Kind regards,

René

Hello Vitor,

the best way to report a variant is to specify it in terms of genomic coordinates. I would avoid using exon numbering, unless its use for your gene/protein is very well standardized and common. The reason is that alternative splicing may transform exon numbering in a real nightmare. Same applies also for coding numbering.

If the sequence is known: you can try to identify its genomic position in many ways; for instance you can navigate to the genome browser (http://genome-euro.ucsc.edu/) -> Tools -> Blat (don't forget to specify Genome and Query type).

If the sequence is unknown: 711+1G>T refers to a specific isoform of your gene (e.g. NM_000492.3). If you know that reference name you can download the entire cDNA from Pubmed (http://www.ncbi.nlm.nih.gov/pubmed) by selecting 'nucleotide'  and writing the isoform name in your query.

http://www.ncbi.nlm.nih.gov/nuccore/568815591?report=graph

CFTR from Human chromosome 7.  110M-120M in the Find window at the above link to zoom in.

If you have gene sequences of about 25 nucleotides near the sites of interest, you can cut and paste these sequences into BLAST at the pubmed site (checking the Human Box) and get out position numbers of the best matches on chromosome 7.  The index numbers seem to change with each update of the genome but the sequences are constant.

The range numbers from BLAST can be cut and paste into the Find window at the above link and their nice program will zoom in on the narrow range and allow you to look nearby.

You can also type the sequence into the Find box, but it may be a little slower and I do not think that can easily find slight variants the way that BLAST can.

Dear Vitor,

I did not read all previous comments, but this is how I normally determine positions.

First I load my genomic and mRNA sequence in Spidey (http://www.ncbi.nlm.nih.gov/spidey/). This gives you the number of exons with relative position from each other. An other option is Blat (https://genome.ucsc.edu/cgi-bin/hgBlat?command=start). this program also gives you the number of exons, but with chromosomal numbering. However, do keep in mind two things. First, you need to know for sure what your reference sequence is. This is particularly important in case of multiple transcripts (splice variants). Second, from my own experience, you really need to have your literature up to date. In some cases, many because of the progress in genetics, insights change, which could result in a change of number of exons (eg. 9 in stead of 8). Be careful with this.

Now you are all set with interpreting your mutations.

My favorite is mutationtaster (http://www.mutationtaster.org/) a user friendly interface. However, there are many such tools available on the web each with there on strenghts and weaknesses. I like mutationtaster, as it gives you all kinds of info, such as, location (genomic, coding, chromosomal etc), and most importantly, if your mutation is known or not (eg HGMD, Exac, 1000G etc).

Hope this helps.

Good luck and if you have any questions please dont hesitate to contact me.

Kind regards,

René

Dear All, 

Thank you all, I really appreciated all the suggestions!