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3.8 years ago
乙
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210
Hello,
I have annotated my VCF
files using VEP
from Ensembl. I have obtained the following lines (please copy paste them in a file for a better view):
CHROM POS REF ALT QUAL DP Consequence IMPACT SYMBOL Gene Feature_type Transcript Transcript_version BIOTYPE EXON INTRON HGVSc HGVSp cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation
chr7 44145448 C T 2539.77 180 intron_variant MODIFIER GCK 2645 Transcript NM_000162 NM_000162.5 protein_coding - 9/9 NM_000162.5:c.1253+49G>A - - - - - - rs13306387
chr7 44146057 G T 3229.77 323 intron_variant MODIFIER GCK 2645 Transcript NM_000162 NM_000162.5 protein_coding - 8/9 NM_000162.5:c.1020-327C>A - - - - - - rs887688&COSV56267186
chr7 44146206 C G 1619.77 145 intron_variant MODIFIER GCK 2645 Transcript NM_000162 NM_000162.5 protein_coding - 8/9 NM_000162.5:c.1019+257G>C - - - - - - rs887687
chr7 44146619 C G 4788.77 431 splice_acceptor_variant HIGH GCK 2645 Transcript NM_000162 NM_000162.5 protein_coding - 7/9 NM_000162.5:c.864-1G>C - - - - - - CS001424&CS109126
chr7 44149675 T C 1305.77 116 intron_variant MODIFIER GCK 2645 Transcript NM_000162 NM_000162.5 protein_coding - 6/9 NM_000162.5:c.679+85A>G - - - - - - rs2268575
chr7 44149722 A G 6190.77 217 intron_variant MODIFIER GCK 2645 Transcript NM_000162 NM_000162.5 protein_coding - 6/9 NM_000162.5:c.679+38T>C - - - - - - rs2268574&COSV60787932
Clearly, those mutations are located in introns but there's one found in a splice site by looking at the Consequence
column. I would like to know if there are any tools available (or any means necessary) to provide the Codons
information for these mutations.
For example, the Codons
column in the following lines where the impacted nucleotide is shown in uppercase:
CHROM POS REF ALT QUAL DP Consequence IMPACT SYMBOL Gene Feature_type Transcript Transcript_version BIOTYPE EXON INTRON HGVSc HGVSp cDNA_position CDS_position Protein_position Amino_acids Codons Existing_variation
chr1 952421 A G 4279.77 146 synonymous_variant LOW NOC2L 26155 Transcript NM_015658 NM_015658.4 protein_coding 10/19 - NM_015658.4:c.1182T>C NP_056473.3:p.Thr394= 1198 1182 394 T acT/acC rs3828047
chr1 953259 T C 1984.77 69 synonymous_variant LOW NOC2L 26155 Transcript NM_015658 NM_015658.4 protein_coding 9/19 - NM_015658.4:c.918A>G NP_056473.3:p.Glu306= 934 918 306 E gaA/gaG rs3748596
chr1 953279 T C 1769.77 61 missense_variant MODERATE NOC2L 26155 Transcript NM_015658 NM_015658.4 protein_coding 9/19 - NM_015658.4:c.898A>G NP_056473.3:p.Ile300Val 914 898 300 I/V Atc/Gtc rs3748597
Thank you in advance
Hello badredda!
It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/13449/is-it-possible-to-get-the-codons-for-an-intron-splice-mutation-given-the-chromos
This is typically not recommended as it runs the risk of annoying people in both communities.
@Pierre thanks for the note, I deleted the post there.