What do the transcript variant # mean in RefSeq?

Question

[curious]

I am looking at this file:

https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh38_latest/refseq_identifiers/GRCh38_latest_rna.fna.gz

I see there are transcript variant #'s

eg:

>NM_000014.6 Homo sapiens alpha-2-macroglobulin (A2M), **transcript variant 1**, mRNA

What do these correspond to? It does not seem to be the longest transcript. Is it the canonical transcript?

I spot checked BRCA1 and BRCA2

>NM_007294.4 Homo sapiens BRCA1 DNA repair associated (BRCA1), transcript variant 1, mRNA
>NM_000059.4 Homo sapiens BRCA2 DNA repair associated (BRCA2), transcript variant 1, mRNA

The NMs seem to match the ensembl canonical transcripts:

https://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000139618;r=13:32315086-32400268 https://useast.ensembl.org/Homo_sapiens/Gene/Summary?g=ENSG00000012048;r=17:43044295-43170245

[GenoMax]

What do these correspond to? It does not seem to be the longest transcript. Is it the canonical transcript?

Those are just different transcripts annotated in RefSeq for that particular gene.

Here is the example for gene you posted: https://www.ncbi.nlm.nih.gov/datasets/gene/id/2/products/

Click on Select Column button and add transcript name to the table to see the complete names.

If you are interested in one transcript per gene then take a look at the MANE project: https://www.ncbi.nlm.nih.gov/refseq/MANE/

[Ram]

It does not seem to be the longest transcript. Is it the canonical transcript?

Longest == canonical. If you're looking for the transcript deemed to be most relevant by researchers, look at MANE as suggested by GenoMax. MANE Select is an even better annotation for these transcripts.

With genes like BRCA1 and ESR1, you'll find that the MANE transcript does not match the canonical transcript and the common mutations you observe with match those annotated on the MANE transcripts.