Thank you for the wonderful tool! I have used it for years and it helped me a lot!
However, When I used Name-checker to search NM_031431.3:c.2474_2475invTG, I found that the reference nucleotides of position 13:46108853-46108854 are "CA" instead of "TG". I have checked the reference nucleotides in these positions on UCSC and NCBI, and results are both "TG". I have also checked gnomAD and found that the frequencies of these two variants were very high.
I may have some mistakes in checking the reference, but it does confuse me. It would be nice if someone can show me the reason for it. Thank you!
It looks to me that the sequence in NM_031431.3 is different than the one in NC_000013.10.
You can see that in Mutalyzer NM vs NC as well as when using the NCBI viewer:
mihailefter
commented
4 years ago 
Hi Mutalyzer,
Thank you for the wonderful tool! I have used it for years and it helped me a lot!
However, When I used Name-checker to search NM_031431.3:c.2474_2475invTG, I found that the reference nucleotides of position 13:46108853-46108854 are "CA" instead of "TG". I have checked the reference nucleotides in these positions on UCSC and NCBI, and results are both "TG". I have also checked gnomAD and found that the frequencies of these two variants were very high.
I may have some mistakes in checking the reference, but it does confuse me. It would be nice if someone can show me the reason for it. Thank you!
Sam