Snpeff annotation question

Question

[rajeshpn]

When I annotated a human genome using reference genome with snpeff, at each genomic position, there are more than one annotation results in the same gene and also other genes appearing and they are separated by ",". Here is an example below at a genomic position of 204,688,055 on chromosome number NC_000001.11. Same is the case with the genomes of other organisms as well.

Can anyone explain the reason?

Thanks

G|upstream_gene_variant|MODIFIER|exon-NM_006338.3-1|GENE_exon-NM_006338.3-1|transcript|rna-NM_006338.3|protein_coding||c.-3090T>C|||||2317|,G|upstream_gene_variant|MODIFIER|exon-NM_201630.2-1|GENE_exon-NM_201630.2-1|transcript|rna-NM_201630.2|protein_coding||c.-2962T>C|||||2317|,G|upstream_gene_variant|MODIFIER|exon-XM_005244827.3-1|GENE_exon-XM_005244827.3-1|transcript|rna-XM_005244827.3|protein_coding||c.-3065T>C|||||2219|,G|downstream_gene_variant|MODIFIER|LRRN2|gene-LRRN2|transcript|NM_006338.3|protein_coding||c.*2317A>G|||||2317|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|LRRN2|gene-LRRN2|transcript|NM_201630.2|protein_coding||c.*2317A>G|||||2317|WARNING_TRANSCRIPT_NO_START_CODON,G|downstream_gene_variant|MODIFIER|LRRN2|gene-LRRN2|transcript|XM_005244827.3|protein_coding||c.*2219A>G|||||2219|WARNING_TRANSCRIPT_NO_START_CODON,G|intragenic_variant|MODIFIER|LOC100418822|LOC100418822|gene_variant|LOC100418822|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|RPL23AP15|RPL23AP15|gene_variant|RPL23AP15|||n.204688055T>C||||||,G|intragenic_variant|MODIFIER|ST13P19|ST13P19|gene_variant|ST13P19|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|H2BU2P|H2BU2P|gene_variant|H2BU2P|||n.204688055T>C||||||,G|intragenic_variant|MODIFIER|SEPTIN14P21|SEPTIN14P21|gene_variant|SEPTIN14P21|||n.204688055T>C||||||,G|intragenic_variant|MODIFIER|CICP21|CICP21|gene_variant|CICP21|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|RPS21P1|RPS21P1|gene_variant|RPS21P1|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|RNASEH1P3|RNASEH1P3|gene_variant|RNASEH1P3|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|RNU6-747P|RNU6-747P|gene_variant|RNU6-747P|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|OR2AS2P|OR2AS2P|gene_variant|OR2AS2P|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|RNU5A-8P|RNU5A-8P|gene_variant|RNU5A-8P|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|MTCYBP14|MTCYBP14|gene_variant|MTCYBP14|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|MTND6P14|MTND6P14|gene_variant|MTND6P14|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|MTND5P19|MTND5P19|gene_variant|MTND5P19|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|MTND4P10|MTND4P10|gene_variant|MTND4P10|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|MTND4LP21|MTND4LP21|gene_variant|MTND4LP21|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|MTND3P8|MTND3P8|gene_variant|MTND3P8|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|MTCO3P46|MTCO3P46|gene_variant|MTCO3P46|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|DUSP5P1|DUSP5P1|gene_variant|DUSP5P1|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|RNA5SP18|RNA5SP18|gene_variant|RNA5SP18|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|BPNT2P1|BPNT2P1|gene_variant|BPNT2P1|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|FTH1P2|FTH1P2|gene_variant|FTH1P2|||n.204688055A>G||||||,G|intragenic_variant|MODIFIER|FCF1P7|FCF1P7|gene_variant|FCF1P7|||n.204688055T>C||||||,G|intragenic_variant|MODIFIER|FABP7P1|FABP7P1|gene_variant|FABP7P1|||n.204688055A>G||||||

Answer 1

[Pierre Lindenbaum]

Can anyone explain the reason?

LIFE

[rajeshpn]

Thanks. Your response explains transcripts of NM_006338.3-1, NM_201630.2-1, XM_005244827.3-1. But this does not explain the presence of intragenic variants in LOC100418822, RPL23AP15, ST13P19, CICP21 and more. Any additional suggestions? Thanks