Null Variant classified as Benign

[ding-lab]

Null Variant classified as Benign

[NTNguyen13]

Hi, thank you for clarification. Github doesn't support vcf so I changed the extension to .txt
I will try to remove AF info before using CharGer, but I still wonder why the null variant is not listed in PVS1 evidence.

VEP_annotated.txt

[NTNguyen13]

For more information: this variant falls in RB1 gene, which is presence in PP2 gene list and inheritance table with autosomal dominant mode

[ccwang002]

Thanks for reporting this to us. This is a known issue we want to address in the new release. CharGer v0.5 will sometimes use the wrong AF as the population allele frequency if it cannot find gnomAD_AF, ExAC_MAF, and ExAC_AF. More specifically, it should be using the AF inside CSQ rather than the one directly in the INFO. For example, the following VCF will likely get the same problem as yours (AF being 1.00):

##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##VEP="v95" time="2019-08-20 15:52:03" cache="~/.vep/homo_sapiens/95_GRCh38" ensembl-funcgen=95.94439f4 ensembl-variation=95.858de3e ensembl=95.4f83453 ensembl-io=95.78ccac5 1000genomes="phase3" COSMIC="86" ClinVar="201810" ESP="V2-SSA137" HGMD-PUBLIC="20174" assembly="GRCh38.p12" dbSNP="151" gencode="GENCODE 29" genebuild="2014-07" gnomAD="170228" polyphen="2.2.2" regbuild="1.0" sift="sift5.2.2"
##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|VARIANT_CLASS|SYMBOL_SOURCE|HGNC_ID|CANONICAL|TSL|APPRIS|CCDS|ENSP|SWISSPROT|TREMBL|UNIPARC|GENE_PHENO|SIFT|PolyPhen|DOMAINS|miRNA|HGVS_OFFSET|AF|AFR_AF|AMR_AF|EAS_AF|EUR_AF|SAS_AF|AA_AF|EA_AF|ExAC_AF|ExAC_Adj_AF|ExAC_AFR_AF|ExAC_AMR_AF|ExAC_EAS_AF|ExAC_FIN_AF|ExAC_NFE_AF|ExAC_OTH_AF|ExAC_SAS_AF|gnomAD_AF|gnomAD_AFR_AF|gnomAD_AMR_AF|gnomAD_ASJ_AF|gnomAD_EAS_AF|gnomAD_FIN_AF|gnomAD_NFE_AF|gnomAD_OTH_AF|gnomAD_SAS_AF|MAX_AF|MAX_AF_POPS|CLIN_SIG|SOMATIC|PHENO|PUBMED|MOTIF_NAME|MOTIF_POS|HIGH_INF_POS|MOTIF_SCORE_CHANGE">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
1       69270   .       A       G       269.77  .       AC=2;AF=1.00;AN=2;DP=10;CSQ=G|synonymous_variant|LOW|OR4F5|ENSG00000186092|Transcript|ENST00000335137|protein_coding|1/1||ENST00000335137.4:c.180A>G|ENSP00000334393.3:p.Ser60%3D|216|180|60|S|tcA/tcG|rs201219564||1||SNV|HGNC|HGNC:14825|YES||P1|CCDS30547.1|ENSP00000334393|Q8NH21||UPI0000041BC1||||Gene3D:1.20.1070.10&Pfam_domain:PF13853&Prints_domain:PR00237&PROSITE_profiles:PS50262&hmmpanther:PTHR26451&hmmpanther:PTHR26451:SF179&Superfamily_domains:SSF81321&Transmembrane_helices:TMhelix&Conserved_Domains:cd15226&Low_complexity_(Seg):seg||||||||||||||||||||0.8327|0.3603|0.7916|0.8434|0.9983|0.877|0.9112|0.8481|0.9018|0.9983|gnomAD_EAS||||||||

The current workaround is to remove the AF INFO field before running CharGer. Using the same example the input becomes:

##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|E
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO
1       69270   .       A       G       269.77  .       AC=2;AN=2;DP=10;CSQ=...(same)...

If your VCF has the same format, please try this approach and see it works for you. By the way, if you can also share your de-identified VCF that will help us debug and build up our test case. CharGer 0.5 doesn't rely on any sample-level information so feel free to remove all the sample columns.