hi ,

I using snpEff for annotating the snp which downloded form clinVAR database .

Input file is :

GeneSymbol  AlleleID    Type    Name    Chromosome  Start   Stop    ReferenceAllele AlternateAllele
ABCA4   858976  single nucleotide variant   NM_000350.3(ABCA4):c.560G>A (p.Arg187His)   1   94568581    94568581    C   T
ABCA4   858975  single nucleotide variant   NM_000350.3(ABCA4):c.573C>T (p.Phe191=) 1   94564545    94564545    G   A
ABCA4   858973  single nucleotide variant   NM_000350.3(ABCA4):c.3050+1G>A  1   94510168    94510168    C   T
ABCA4   858971  single nucleotide variant   NM_000350.3(ABCA4):c.4253+7G>A  1   94496545    94496545    C   T

I fetch the column Chromosome Start Stop RefenceAllele AlternatedAllele and make one new file for a input to snpEFF.

Using assembly hg37

Output Are :

CHROM   POS REF ALT ANN[*].GENE ANN[*].EFFECT   ANN[*].IMPACT   ANN[*].BIOTYPE  ANN[*].HGVS_P
Chromosome  0   REFERENCEALLELE ALTERNATEALLELE .   .   MODIFIER    .   .
1   94568581    C   T   ABCA4   missense_variant    MODERATE    protein_coding  p.Arg187His
1   94568581    C   T   ABCA4   missense_variant    MODERATE    protein_coding  p.Arg187His
1   94564545    G   A   ABCA4   splice_region_variant&synonymous_variant    LOW protein_coding  p.Phe191Phe
1   94564545    G   A   ABCA4   splice_region_variant&synonymous_variant    LOW protein_coding  p.Phe191Phe
1   94510168    C   T   ABCA4   splice_donor_variant&intron_variant HIGH    protein_coding  .
1   94496545    C   T   ABCA4   splice_region_variant&intron_variant    LOW protein_coding  .
1   94495157    C   T   ABCA4   stop_gained HIGH    protein_coding  p.Trp1461*
1   94487194    A   G   ABCA4   splice_donor_variant&intron_variant HIGH    protein_coding  .
1   94487194    A   G   ABCA4   splice_donor_variant&intron_variant HIGH    processed_transcript    .
1   94486866    C   T   ABCA4   missense_variant    MODERATE    protein_coding  p.Glu1650Lys
1   94486866    C   T   ABCA4   non_coding_transcript_exon_variant  MODIFIER    processed_transcript    .
1   94486866    C   T   ABCA4   non_coding_transcript_exon_variant  MODIFIER    processed_transcript    .
1   94474389    T   A   ABCA4   missense_variant    MODERATE    protein_coding  p.Asp1918Val
1   94474389    T   A   ABCA4   missense_variant    MODERATE    protein_coding  p.Asp37Val
1   94474389    T   A   ABCA4   missense_variant    MODERATE    protein_coding  p.Asp188Val

for the particular position it giving me multiple results. Is this relevant or not ? some of the example i have seen in which all column have same information but biotype are showing two different type.