Just to give my thoughts:
- The missing information is the actual sequence
- Is this a conflict in the change in position of the insert?
- Could it simply be a consequence of down stream numbering, either a logical error (coding stuff), or lab artefact.
My bet is its point 2, but really we don't know except for the OP because we don't know the sequence.
Sources of error, Point 2
- Sanger sequencing was traditionally known for "frame-shift" errors if there were mono-mers, e.g. AAAA -> AAAAA, it can mess up over the number of bases in a mono-mer.
- PCR amplification can also cause slippage against monomers, same thing as the above point - but it's real.
- 1 vs 0 ... this is because in a Pythonic list or any C/Perl-based array numbering starts at 0 (not 1) - hence @terdon's comments.
If upstream mono-mers are present that might be the source of the confusion here and given the amount of sequence data thats very likely.
What I'd do:
- Just Blast the new sequence and see what emerges: if it is genuinely novel - they'll be zero 100% identity hits.
- VCFs ... I think this is VarSome's stuff (forget).
If there are Blast hits it will identify whether there is any upstream lab artefacts.
If this was any other situation in human genetics, or even mammalian genetics I'd be excited. However, in this case - I think its a routine result. Firstly, the chance of finding a new "driver" mutation are slim. Secondly, I've looked at this chromosome in a cancer patient (only once) and it was nuts (and thats an under statement) - I've a fairly good memory for numerical patterns, and I'd never seen a pathogenic species behaving like that. I think this insert is just a consequence of the entire mutational chaos that are cancer cells.
Just to make it clear: I don't do cancer but if you want an authoritative assessment and think you've something major I'd contact (or your PI) the Broad Institute via Geraldine A. Van der Auwera who also has an account on this site via @Geraldine_VdAuwera. Sanger sequencing is not what they do, but they'd know at the drop of a hat what the significance and if they don't respond - thats your answer ;-). Alternatively, VarSome would know, albeit they're commercial enterprise offering freeware.