Multiple identical mutations in SnpEff result: ex1.genes.txt

Question

[Maya]

Hi, I am new here and struggling to get exome sequencing data in VCF format annotated. I ran

java -Xmx8g -jar snpEff.jar -v -stats ex1.html hg38 P2.vcf > out/P2.ann.vcf 

and among the output I got was the list of mutated genes (ex1.genes.txt). There are multiple identical mutation listed on the ex1.genes.txt as A1CF gene seen below. How did this happen and could I just ignore the overlapping ones? Thanks in advance for any help!

The following table is formatted as tab separated values

#GeneName   GeneId  TranscriptId    BioType variants_impact_HIGH    variants_impact_LOW variants_impact_MODERATE    variants_impact_MODIFIER    variants_effect_3_prime_UTR_variant variants_effect_5_prime_UTR_premature_start_codon_gain_variant  variants_effect_5_prime_UTR_variant variants_effect_conservative_inframe_deletion   variants_effect_conservative_inframe_insertion  variants_effect_disruptive_inframe_deletion variants_effect_disruptive_inframe_insertion    variants_effect_downstream_gene_variant variants_effect_exon_loss_variant   variants_effect_frameshift_variant  variants_effect_initiator_codon_variant variants_effect_intron_variant  variants_effect_missense_variant    variants_effect_non_coding_transcript_exon_variant  variants_effect_non_coding_transcript_variant   variants_effect_splice_acceptor_variant variants_effect_splice_donor_variant    variants_effect_splice_region_variant   variants_effect_start_lost  variants_effect_start_retained_variant  variants_effect_stop_gained variants_effect_stop_lost   variants_effect_stop_retained_variant   variants_effect_synonymous_variant  variants_effect_upstream_gene_variant
A1BG    A1BG    NM_130786.4 protein_coding  0   7   8   44  2   0   0   0   0   0   0   7   0   0   0   12  8   0   0   0   0   0   0   0   0   0   0   7   23
A1BG-AS1    A1BG-AS1    NR_015380.2     0   0   0   50  0   0   0   0   0   0   0   19  0   0   0   7   0   6   0   0   0   0   0   0   0   0   0   0   18
A1CF    A1CF    NM_001198818.1  protein_coding  0   0   6   30  0   0   0   0   1   0   0   4   0   0   0   26  5   0   0   0   0   0   0   0   0   0   0   0   0
A1CF    A1CF    NM_001198819.1  protein_coding  0   0   6   30  0   0   0   0   1   0   0   4   0   0   0   26  5   0   0   0   0   0   0   0   0   0   0   0   0
A1CF    A1CF    NM_001198820.1  protein_coding  0   0   6   30  0   0   0   0   1   0   0   4   0   0   0   26  5   0   0   0   0   0   0   0   0   0   0   0   0
A1CF    A1CF    NM_001370130.1  protein_coding  0   0   6   30  0   0   0   0   1   0   0   4   0   0   0   26  5   0   0   0   0   0   0   0   0   0   0   0   0
A1CF    A1CF    NM_001370131.1  protein_coding  0   0   6   30  0   0   0   0   1   0   0   4   0   0   0   26  5   0   0   0   0   0   0   0   0   0   0   0   0
A1CF    A1CF    NM_014576.4 protein_coding  0   0   6   30  0   0   0   0   1   0   0   4   0   0   0   26  5   0   0   0   0   0   0   0   0   0   0   0   0
A1CF    A1CF    NM_138932.2 protein_coding  0   0   6   30  0   0   0   0   1   0   0   4   0   0   0   26  5   0   0   0   0   0   0   0   0   0   0   0   0
A1CF    A1CF    NM_138933.2 protein_coding  0   0   6   30  0   0   0   0   1   0   0   4   0   0   0   26  5   0   0   0   0   0   0   0   0   0   0   0   0
A2M A2M NM_000014.5 protein_coding  2   21  24  45  0   0   0   0   0   0   0   1   0   0   0   43  24  0   0   0   0   2   0   0   2   0   0   20  2

Answer 1

[Ram]

The same nucleotide change can impact multiple transcripts of a gene in distinct ways. All variant annotation software have options to list each such per-transcript effects separately and that's what's happening here. The various NM_s are protein coding transcripts of the A1CF gene.

Sometimes, the same variant can have multiple "effect"s on the same transcript as a single region can serve multiple purposes. For example, a splice site exonic variant can also be a missense or synonymous variant. That could be what's going on in entries with duplicated GeneID and TranscriptID columns,