<html><body><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">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">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">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">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">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">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">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">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">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">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">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></body></html>