SNPeff result interpretation
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6.5 years ago
Pascal ▴ 250

Hi,

I am using SNPeff to annotate my somatic mutations. That works well, however I am not sure how to interpret the result. Below is the annotation added to the INFO field by SNPeff. I get many times the exact same annotation, except the Rank is different. All I found in the documentation is that the Rank is the exon/intron number. Since this is a single location, I cannot make sense out of it. How can the same mutation be at different ranks? I seem to get this very often for "sequence_feature" annotations.

Thanks,

Pascal

Allele | Annotation | Annotation_Impact | Gene_Name | Gene_ID | Feature_Type | Feature_ID | Transcript_BioType | Rank | HGVS.c | HGVS.p | cDNA.pos / cDNA.length | CDS.pos / CDS.length | AA.pos / AA.length | Distance | ERRORS / WARNINGS / INFO

A|synonymous_variant|LOW|FAT2|ENSG00000086570|transcript|ENST00000261800|protein_coding|9/23|c.7380C>T|p.Val2460Val|7393/14534|7380/13050|2460/4349||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|12/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|10/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|19/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|14/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|18/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|21/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|17/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|16/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|13/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|22/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|7/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|8/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|3/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|1/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|11/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|6/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|2/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|15/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|9/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|5/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|20/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|topological_domain:Extracellular|ENST00000261800|protein_coding|4/23|c.7380C>T||||||
A|sequence_feature|LOW|FAT2|ENSG00000086570|domain:Cadherin_21|ENST00000261800|protein_coding|9/23|c.7380C>T||||||
SNPeff Cancer WES Variant Annotation • 2.8k views
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Hello, this is almost 3 years late, but were you able to interpret the meaning of this finally? Please do share what you learnt, if you did. Thanks!