<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
</head>
<body>
<p>Hi Amandine,</p>
<p> The IMPACT column is a subjective classification of the severity
of the variant consequence. It is a separate rating given for
compatibility with other variant annotation tools e.g. snpEff. As
this rating is subjective, you can always get the full set of
consequences for each allele and make your own severity judgement.</p>
<p>Information on all of our consequences can be found here: <a
rel="nofollow"
href="https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html">https://www.ensembl.org/info/genome/variation/prediction/predicted_data.html</a></p>
<p><br>
</p>
<p>Best wishes,</p>
<p>Diana <br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 28/10/2021 08:44, AMANDINE SEPTIER
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:20211028074636.71A5762A233_17A555CB@hh-mx3.ebi.ac.uk">
<meta http-equiv="content-type" content="text/html; charset=UTF-8">
<div style="font-family: arial, helvetica, sans-serif; font-size:
12pt; color: #000000">
<div data-marker="__QUOTED_TEXT__">
<div style="font-family:'arial' , 'helvetica' ,
sans-serif;font-size:12pt;color:#000000">
<div>
<div>
<div style="font-family: 'arial', 'helvetica',
sans-serif; font-size: 12pt; color: #000000;"
data-mce-style="font-family: 'arial', 'helvetica',
sans-serif; font-size: 12pt; color: #000000;">
<div>Hello VEP team,<br>
<br>
Thank you very much for your tool.<br>
I send you this mail because I'm analyzing Exome
data and making CNV calls on a patients cohort.<br>
When I annotate SVs with VEP, it returns "MODIFIER"
hits for CNVs covering several exons/introns without
covering the entire impacted gene(s).(details below)<br>
Some of them are experimentally validated, so it is
a pity that VEP doesn't send back these CNVs. (ex :
CFAP251)<br>
Is it possible to put more weight on the
'feature_truncation' or 'feature_elongation'
variants consequences so that they have a greater
impact?<br>
This is just a discussion I'm opening up.<br>
Thanks in advance for your future return.<br>
Regards.<br>
<div>-- <br>
</div>
<div>
<div><span style="font-family: 'arial',
'helvetica', sans-serif; font-size: 11pt;
color: #000000;" data-mce-style="font-family:
'arial', 'helvetica', sans-serif; font-size:
11pt; color: #000000;">----------------------------------------------------------------------<br>
</span></div>
<div><span style="font-family: 'arial',
'helvetica', sans-serif; font-size: 11pt;
color: #000000;" data-mce-style="font-family:
'arial', 'helvetica', sans-serif; font-size:
11pt; color: #000000;">Amandine SEPTIER</span><br>
</div>
<div><span style="font-size: 11pt; font-family:
'arial', 'helvetica', sans-serif; color:
#000000;" data-mce-style="font-size: 11pt;
font-family: 'arial', 'helvetica', sans-serif;
color: #000000;">Doctorante</span><br>
<span style="font-family: 'arial', 'helvetica',
sans-serif; font-size: 11pt; color: #000000;"
data-mce-style="font-family: 'arial',
'helvetica', sans-serif; font-size: 11pt;
color: #000000;">Laboratoire TIMC-IMAG/MAGe,
CNRS UMR 5525</span><br>
<span style="font-family: 'arial', 'helvetica',
sans-serif; font-size: 11pt; color: #000000;"
data-mce-style="font-family: 'arial',
'helvetica', sans-serif; font-size: 11pt;
color: #000000;">Pavillon Taillefer, Faculté
de Médecine</span><br>
<span style="font-family: 'arial', 'helvetica',
sans-serif; font-size: 11pt; color: #000000;"
data-mce-style="font-family: 'arial',
'helvetica', sans-serif; font-size: 11pt;
color: #000000;">38700 La Tronche, France </span><br>
---------------------------------------------------------------</div>
</div>
<br>
VCF INPUT:<br>
##fileformat=VCFv4.3<br>
##fileDate=20211027<br>
##ALT=<ID=DEL,Description="Deletion"><br>
##ALT=<ID=DUP,Description="Duplication"><br>
##ALT=<ID=CNV,Description="Copy number variable
region"><br>
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of
structural variant"><br>
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the
variant described in this record"><br>
##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype"><br>
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number
genotype for imprecise events"><br>
#CHROM POS ID REF ALT QUAL
FILTER INFO FORMAT S1 S2 S3<br>
<span class="Object" role="link"
id="OBJ_PREFIX_DWT472_com_zimbra_phone"><a
href="callto:4 146867498"
onclick="window.top.Com_Zimbra_Phone.unsetOnbeforeunload()"
data-mce-href="callto:4 146867498"
moz-do-not-send="true">4 146867498</a></span>
TTC29_HetDEL . <DEL> . .
SVTYPE=DEL;END=146867583 GT:CN 0/1:1
./.:2 ./.:2<br>
<span class="Object" role="link"
id="OBJ_PREFIX_DWT473_com_zimbra_phone"><a
href="callto:12 121908103"
onclick="window.top.Com_Zimbra_Phone.unsetOnbeforeunload()"
data-mce-href="callto:12 121908103"
moz-do-not-send="true">12 121908103</a></span>
CFAP251_AllGene . <DEL> . .
SVTYPE=DEL;END=122003919 GT:CN 1/1:0
1/1:0 1/1:0<br>
<span class="Object" role="link"
id="OBJ_PREFIX_DWT474_com_zimbra_phone"><a
href="callto:12 121999716"
onclick="window.top.Com_Zimbra_Phone.unsetOnbeforeunload()"
data-mce-href="callto:12 121999716"
moz-do-not-send="true">12 121999716</a></span>
CFAP251_HomoDEL . <DEL> . .
SVTYPE=DEL;END=122001598 GT:CN 1/1:0
1/1:0 1/1:0<br>
<span class="Object" role="link"
id="OBJ_PREFIX_DWT475_com_zimbra_phone"><a
href="callto:12 121999716"
onclick="window.top.Com_Zimbra_Phone.unsetOnbeforeunload()"
data-mce-href="callto:12 121999716"
moz-do-not-send="true">12 121999716</a></span>
CFAP251_exon20/22 . <DEL> . .
SVTYPE=DEL;END=121999944 GT:CN 1/1:0
1/1:0 1/1:0<br>
<span class="Object" role="link"
id="OBJ_PREFIX_DWT476_com_zimbra_phone"><a
href="callto:12 122001497"
onclick="window.top.Com_Zimbra_Phone.unsetOnbeforeunload()"
data-mce-href="callto:12 122001497"
moz-do-not-send="true">12 122001497</a></span>
CFAP251_exon21/22 . <DEL> . .
SVTYPE=DEL;END=122001598 GT:CN 1/1:0
1/1:0 1/1:0<br>
<br>
COMMAND LINE:<br>
vep -i VEPtest_211027.vcf --cache --offline
--force_overwrite --format vcf --vcf -o
OutVEP_211027.csv<br>
<br>
OUTPUT<br>
##fileformat=VCFv4.3<br>
##fileDate=20211027<br>
##ALT=<ID=DEL,Description="Deletion"><br>
##ALT=<ID=DUP,Description="Duplication"><br>
##ALT=<ID=CNV,Description="Copy number variable
region"><br>
##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of
structural variant"><br>
##INFO=<ID=END,Number=1,Type=Integer,Description="End position of the
variant described in this record"><br>
##FORMAT=<ID=GT,Number=1,Type=Integer,Description="Genotype"><br>
##FORMAT=<ID=CN,Number=1,Type=Integer,Description="Copy number
genotype for imprecise events"><br>
##VEP="v104" time="<span class="Object" role="link"
id="OBJ_PREFIX_DWT477_com_zimbra_phone"><a
href="callto:2021-10-27 11"
onclick="window.top.Com_Zimbra_Phone.unsetOnbeforeunload()"
data-mce-href="callto:2021-10-27 11"
moz-do-not-send="true">2021-10-27 11</a></span>:56:04"
cache="/home/septiera/.vep/homo_sapiens/104_GRCh38"
ensembl-funcgen=104.59ae779
ensembl-variation=104.6154f8b ensembl=104.1af1dce
ensembl-io=104.1d3bb6e 1000genomes="phase3"
COSMIC="92" ClinVar="20210102" ESP="V2-SSA137"
HGMD-PUBLIC="20204" assembly="GRCh38.p13"
dbSNP="154" gencode="GENCODE 38" genebuild="2014-07"
gnomAD="r2.1.1" polyphen="2.2.2" regbuild="1.0"
sift="sift5.2.2"<br>
##INFO=<ID=CSQ,Number=.,Type=String,Description="Consequence
annotations from Ensembl VEP. Format:
Allele|Consequence|IMPACT|SYMBOL|Gene|Feature_type|Feature|BIOTYPE|EXON|INTRON|HGVSc|HGVSp|cDNA_position|CDS_position|Protein_position|Amino_acids|Codons|Existing_variation|DISTANCE|STRAND|FLAGS|SYMBOL_SOURCE|HGNC_ID"><br>
#CHROM POS ID REF ALT QUAL
FILTER INFO FORMAT S1 S2 S3<br>
<span class="Object" role="link"
id="OBJ_PREFIX_DWT478_com_zimbra_phone"><a
href="callto:4 146867498"
onclick="window.top.Com_Zimbra_Phone.unsetOnbeforeunload()"
data-mce-href="callto:4 146867498"
moz-do-not-send="true">4 146867498</a></span>
TTC29_HetDEL . <DEL> . .
SVTYPE=DEL;END=146867583;CSQ=deletion|frameshift_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000325106|protein_coding|8/13||||1009-1093|800-884|267-295|||||-1||HGNC|HGNC:29936,deletion|frameshift_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000504425|protein_coding|8/13||||1027-1111|800-884|267-295|||||-1||HGNC|HGNC:29936,deletion|frameshift_variant&NMD_transcript_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000508306|nonsense_mediated_decay|8/14||||978-1062|800-884|267-295|||||-1||HGNC|HGNC:29936,deletion|frameshift_variant&feature_truncation|HIGH|TTC29|ENSG00000137473|Transcript|ENST00000513335|protein_coding|9/14||||1078-1162|878-962|293-321|||||-1||HGNC|HGNC:29936
GT:CN 0/1:1 ./.:2 ./.:2<br>
<span class="Object" role="link"
id="OBJ_PREFIX_DWT479_com_zimbra_phone"><a
href="callto:12 121908103"
onclick="window.top.Com_Zimbra_Phone.unsetOnbeforeunload()"
data-mce-href="callto:12 121908103"
moz-do-not-send="true">12 121908103</a></span>
CFAP251_AllGene . <DEL> . .
SVTYPE=DEL;END=122003919;CSQ=deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000261817|protein_coding|5-6/6|4-5/5||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding||||||||||||1||HGNC|HGNC:28506,deletion|transcript_ablation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000361485|retained_intron||||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000397454|protein_coding||||||||||||1||HGNC|HGNC:28506,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&feature_truncation|MODIFIER|RNU7-170P|ENSG00000239082|Transcript|ENST00000459303|snRNA|1/1||||2-?|||||||1||HGNC|HGNC:45704,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000535257|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000535293|nonsense_mediated_decay|4-5/5|3-4/4||||||||||1||HGNC|HGNC:9567,deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000537407|nonsense_mediated_decay|5-7/7|4-6/6||||||||||1||HGNC|HGNC:9567,deletion|downstream_gene_variant|MODIFIER||ENSG00000255856|Transcript|ENST00000538710|lncRNA|||||||||||3515|-1|||,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000540779|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000540962|nonsense_mediated_decay|4-5/5|3-4/4||||||||||1||HGNC|HGNC:9567,deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000541212|protein_coding|5-6/6|4-5/5||||||||||1||HGNC|HGNC:9567,deletion|stop_lost&coding_sequence_variant&3_prime_UTR_variant&intron_variant&feature_truncation|HIGH|PSMD9|ENSG00000110801|Transcript|ENST00000542602|protein_coding|3-4/4|2-3/3||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000543211|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000543699|nonsense_mediated_decay|5-6/6|4-5/5||||||||||1||HGNC|HGNC:9567,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000544254|retained_intron|2-3/3|1-2/2||||||||||1||HGNC|HGNC:9567,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|PSMD9|ENSG00000110801|Transcript|ENST00000544724|retained_intron|3-4/4|2-3/3||||||||||1||HGNC|HGNC:9567,deletion|transcript_ablation|HIGH||ENSG00000256950|Transcript|ENST00000544911|retained_intron||||||||||||1|||,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000545752|processed_transcript||||||||||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|1-2/2|1/1|||?-484|||||||1||HGNC|HGNC:28506,deletion|transcript_ablation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000546044|retained_intron||||||||||||1||HGNC|HGNC:28506,deletion|3_prime_UTR_variant&intron_variant&NMD_transcript_variant&feature_truncation|MODIFIER||ENSG00000256950|Transcript|ENST00000546333|nonsense_mediated_decay|4/4|3/3||||||||||1|||
GT:CN 1/1:0 1/1:0 1/1:0<br>
<span class="Object" role="link"
id="OBJ_PREFIX_DWT480_com_zimbra_phone"><a
href="callto:12 121999716"
onclick="window.top.Com_Zimbra_Phone.unsetOnbeforeunload()"
data-mce-href="callto:12 121999716"
moz-do-not-send="true">12 121999716</a></span>
CFAP251_HomoDEL . <DEL> . .
SVTYPE=DEL;END=122001598;CSQ=deletion|coding_sequence_variant&intron_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding|20-21/22|20/21|||3132-3461|3008-3337|1003-1113|||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&intron_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron|1-2/3|1/2|||2832-3161|||||||1||HGNC|HGNC:28506,deletion|upstream_gene_variant|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|||||||||||106|1||HGNC|HGNC:28506
GT:CN 1/1:0 1/1:0 1/1:0<br>
<span class="Object" role="link"
id="OBJ_PREFIX_DWT481_com_zimbra_phone"><a
href="callto:12 121999716"
onclick="window.top.Com_Zimbra_Phone.unsetOnbeforeunload()"
data-mce-href="callto:12 121999716"
moz-do-not-send="true">12 121999716</a></span>
CFAP251_Corrpad_exon20/22 . <DEL>
. .
SVTYPE=DEL;END=121999944;CSQ=deletion|inframe_deletion&feature_truncation|MODERATE|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding|20/22||||3132-3359|3008-3235|1003-1079|||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron|1/3||||2832-3059|||||||1||HGNC|HGNC:28506,deletion|upstream_gene_variant|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|||||||||||1760|1||HGNC|HGNC:28506
GT:CN 1/1:0 1/1:0 1/1:0<br>
<span class="Object" role="link"
id="OBJ_PREFIX_DWT482_com_zimbra_phone"><a
href="callto:12 122001497"
onclick="window.top.Com_Zimbra_Phone.unsetOnbeforeunload()"
data-mce-href="callto:12 122001497"
moz-do-not-send="true">12 122001497</a></span>
CFAP251_Corrpad_exon21/22 . <DEL>
. .
SVTYPE=DEL;END=122001598;CSQ=deletion|frameshift_variant&feature_truncation|HIGH|CFAP251|ENSG00000158023|Transcript|ENST00000288912|protein_coding|21/22||||3361-3461|3237-3337|1079-1113|||||1||HGNC|HGNC:28506,deletion|non_coding_transcript_exon_variant&feature_truncation|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000428465|retained_intron|2/3||||3061-3161|||||||1||HGNC|HGNC:28506,deletion|upstream_gene_variant|MODIFIER|CFAP251|ENSG00000158023|Transcript|ENST00000545988|processed_transcript|||||||||||106|1||HGNC|HGNC:28506
GT:CN 1/1:0 1/1:0 1/1:0<br>
<br>
<div>
<h3>System</h3>
<ul>
<li>VEP version: 104.3</li>
<li>VEP Cache version:
homo_sapiens_vep_104_GRCh38</li>
<li>Perl version: perl-5.16.3-299.el7_9.x86_64</li>
<li>OS: centos 7</li>
<li>tabix installed ? yes</li>
</ul>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
</div>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<pre class="moz-quote-pre" wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
Posting guidelines and subscribe/unsubscribe info: <a class="moz-txt-link-freetext" href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
</body>
</html>