mRNA positions from vcf

Question

[jindal.aashi21]

Hi everyone,

I am processing a vcf file from ExAC browser (release 1.0) with hg19 as human reference genome. I want to identify only those mutations which occur at mRNA positions. Is there any field/column in vcf that can give me that information.

For now, I tried to use "BIOTYPE" field from vcf. I selected only those positions for which "BIOTYPE=Protein_coding". However, when cross-checking these positions with exon start/stop positions from USCS browser, some of these are marked as non-coding RNA. How is this possible or "BIOTYPE=protein_coding" does not give me the right information about RNA type?

Example: 138593 position in chr1 in vcf is marked with BIOTYPE=protein_coding. This position is part of LOC729737 gene. When I look for this position in ucsc file, it is marked as non-coding RNA (as per ucsc kgXref table).

[ATpoint]

See here:

ID: C9J4L2_HUMAN
DESCRIPTION: SubName: Full=Uncharacterized protein;
CAUTION: The sequence shown here is derived from an Ensembl automatic analysis pipeline and should be considered as preliminary data.

[jindal.aashi21]

Hi,

Thanks for your response. May you please explain this more.

[ATpoint]

What is unclear? The page summarizing LOC729737 and there you see that based on Ensembl automatic analysis pipeline there is some yet not verified evidence for a protein-coding gene.

[benformatics]

Also check the Ensembl genome browser to see if there are any other annotated transcripts in your location of interest. UCSC and/or other sources sometime exclude potential isoforms that don't have as much supporting data.