If your study is focused on a specific transcript variant then use NM but if your measuring all transcripts use NG.

Use NM if your primers measure that certain transcript

As long as your consisted 

Hi

I also agree with the answer above. The 'Transcript assemblies' that include the different transcript covering various regions of a bigger transcript are put together as one group. These are different than the 'splice variants/ alternative transcripts' generated due to splicing...use if carefully

bye

Dear Tina:

You can use any database entry to design primers and thus you should refer to that particular entry (in your case, an NG_ file) when explaining which primers you used.

For variant annotation involving specific defects you MUST use NM_ transcript files, as some exons do not appear in specific transcripts and therefore the effects are transcript-specific. Use Mutalyzer software (recommended by The Human Genome Variation Society) for that. Available at: https://mutalyzer.nl

Best regards

Thank you all for taking time to respond to my question. Your answers have been very helpful.