I have 24 LoF suspected variants which I'm trying to annotate using LOFTEE. For 14 out of 24 variants, there is LoF annotation for at least one transcript in the "Extra" column like follows.
[In the case of NM_013266.4:c.1219delC]
Feature "ENST00000494580" is annotated as "IMPACT=HIGH;STRAND=-1;FLAGS=cds_start_NF;LoF=LC;LoF_filter=END_TRUNC;LoF_info=GERP_DIST:0--" in the Column "Extra".
However, for the rest of the variants (10 variants marked with stars* below), there is no LoF annotation for any of the transcripts, although the consequence is indeed LoF suspected (eg. frameshift).
Does anyone have an explanation for this?
the input command is "./vep --species homo_sapiens --assembly GRCh38 --database --plugin LoF,loftee_path:$HOME/ensembl-vep/loftee,human_ancestor_fa:$HOME/ensembl-vep/human_ancestor.fa -i $HOME/ensembl-vep/LoF_hgvs_c_info.txt -o $HOME/ensembl-vep/LoF_hgvs_c_LOFTEE_result".
Thanks.
*NM_001035.3:c.14217delT
NM_013266.4:c.1219delC
NM_004387.4:c.335-204delT
*NM_053025.4:c.1654C>T
NM_004572.4:c.148_151delACAG
NM_001267550.2:c.36364+1G>C
*NM_020778.5:c.2304delA
NM_000527.5:c.2431A>T
NM_001267550.2:c.44281+1G>C
*NM_001267550.2:c.4764_4765dupAT
*NM_000488.4:c.762+69dupT
*NM_020778.5:c.2304delA
NM_012186.3:c.432C>G
NM_013266.4:c.560dupT
NM_001267550.2:c.36364+1G>C
*NM_003476.5:c.583T>A
*NM_001267550.2:c.47208_47209delCA
NM_001267550.2:c.36364+1G>C
NM_032578.4:c.3796C>T
*NM_000256.3:c.890C>G
NM_004387.4:c.335-163_335-157dupCGGTGGC
*NM_174936.4:c.1284G>A
NM_020297.4:c.1659+1delG
NM_013266.4:c.560dupT
LoF_hgvs_c_info.txt
LoF_hgvs_c_LOFTEE_result.xlsx
I have 24 LoF suspected variants which I'm trying to annotate using LOFTEE. For 14 out of 24 variants, there is LoF annotation for at least one transcript in the "Extra" column like follows.
[In the case of NM_013266.4:c.1219delC]
Feature "ENST00000494580" is annotated as "IMPACT=HIGH;STRAND=-1;FLAGS=cds_start_NF;LoF=LC;LoF_filter=END_TRUNC;LoF_info=GERP_DIST:0--" in the Column "Extra".
However, for the rest of the variants (10 variants marked with stars* below), there is no LoF annotation for any of the transcripts, although the consequence is indeed LoF suspected (eg. frameshift).
Does anyone have an explanation for this?
the input command is "./vep --species homo_sapiens --assembly GRCh38 --database --plugin LoF,loftee_path:$HOME/ensembl-vep/loftee,human_ancestor_fa:$HOME/ensembl-vep/human_ancestor.fa -i $HOME/ensembl-vep/LoF_hgvs_c_info.txt -o $HOME/ensembl-vep/LoF_hgvs_c_LOFTEE_result".
Thanks.
*NM_001035.3:c.14217delT
NM_013266.4:c.1219delC
NM_004387.4:c.335-204delT
*NM_053025.4:c.1654C>T
NM_004572.4:c.148_151delACAG
NM_001267550.2:c.36364+1G>C
*NM_020778.5:c.2304delA
NM_000527.5:c.2431A>T
NM_001267550.2:c.44281+1G>C
*NM_001267550.2:c.4764_4765dupAT
*NM_000488.4:c.762+69dupT
*NM_020778.5:c.2304delA
NM_012186.3:c.432C>G
NM_013266.4:c.560dupT
NM_001267550.2:c.36364+1G>C
*NM_003476.5:c.583T>A
*NM_001267550.2:c.47208_47209delCA
NM_001267550.2:c.36364+1G>C
NM_032578.4:c.3796C>T
*NM_000256.3:c.890C>G
NM_004387.4:c.335-163_335-157dupCGGTGGC
*NM_174936.4:c.1284G>A
NM_020297.4:c.1659+1delG
NM_013266.4:c.560dupT
LoF_hgvs_c_info.txt
LoF_hgvs_c_LOFTEE_result.xlsx