From Genome Analysis Wiki
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SYNONYMOUS_CODING=BARD1(uc002veu.2):His506His[-] means the SNP is synonymous coding at the 506th codon in gene BARD1 with a minus strand and it keeps amino-acid His unchanged.
NON_SYNONYMOUS_CODING=BARD1(uc002veu.2):Arg658Cys[-] means the SNP is non_synonymous coding at the 658th codon in gene BARD1 (ucsc gene name uc002veu.2)with a minus strand and it changes amino-acid from Arg to Cys.
NCAPH2[+] means the SNP is in the SPLICE_SITE (5 bp within exon start or end positions in the coding region) of gene MCAPH2 with a plus strand. STOP_GAINED= MAPK12: Trp49035685stop[-] means the SNP is at position 49035685 in gene MAPK12 with a minus strand and it changes amino-acid Trp to a stop codon.
The annotating result will be added to the entry "INFO" of the input VCF SNP file and outputted together with other information. Here is an example of output VCF file headlines: