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pcingola / SnpEff

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Error in start_codon_gain_variant? #130

Closed pcingola closed 3 years ago

pcingola commented 8 years ago

I am trying to annotate the snp chr5:138609638 C>G (gene: MATR3, transcript: NM_199189.2, strand +). I use snpEff 4.2 on hg19 database but the issue also arises on GRCh37.75.

The command line: 

java -jar snpEff.jar -v hg19  snp.vcf

SnpEff annotates the variant as "5_prime_UTR_premature start_codon_gain_variant" but the snp does not produce an ATG (see flanking sequences below).

GACCCCAGCCCTTCT [C>G] TCCTCTAAGAAGCAG

Input VCF line

chr5    138609638       .       C       G       5728.77 on_target       AC=1;
pcingola commented 3 years ago

Closing old issues.