Conflicting annotations between HGVSp, HGVSp_Short, and Genomic_Change

[ibrahimkurt]

Example 1:

When we run this BRAF entry with an insertion mutation in this MAF file via mafannotator.pyscript, -q HGVSp, -q HGVSp_Short, and -q Genomic_Change returns conflicting different results:

Annotation by Genomic_Change returns Unknown. Annotation by HGVSp returns Likely Oncogenic. Annotation by HGVSp_Short returns Likely Oncogenic.

It seems like the correct call is Likely Oncogenic w/ drug recommendations as shown here: https://www.oncokb.org/gene/BRAF/G506_S507insISQ

The question is what is the reason for the conflict between annotations by HGVSp, HGVSp_Short and Genomic_Change?

[ibrahimkurt]

Example 2:

When we run this another BRAF entry with a missense mutation in this MAF file via mafannotator.pyscript, -q HGVSp, -q HGVSp_Short, and -q Genomic_Change returns conflicting different results:

Annotation by Genomic_Change returns Likely Oncogenic. Annotation by HGVSp returns Unknown. Annotation by HGVSp_Short returns Unknown.

It seems like the correct call is Likely Oncogenic w/ drug recommendations as shown here: https://www.oncokb.org/gene/BRAF/L505F

The question is what is the reason for the conflict between annotations by HGVSp, HGVSp_Short and Genomic_Change?