AlphaMissense has "benign" in GRCh37 data files and "likely_benign" in GRCh38

[davmlaw]

The plugin documentation says:

'am_class' is the classification of the variant into one of three discrete categories:
'Likely pathogenic', 'Likely benign', or 'ambiguous'. These are derived using the following
thresholds of am_pathogenicity:
'Likely benign' if am_pathogenicity < 0.34;
'Likely pathogenic' if am_pathogenicity > 0.564;
'ambiguous' otherwise.

This appears to be documenting the GRCh38 file, while the GRCh37 data file has "benign" in it.

If the results are supposed to be consistent:

• Can you please get AlphaMissense to re-generate the data files
• We could either modify plugin to do conversion, or add a sed script to convert GRCh37 file?

If it is supposed to be different - please update docs to reflect the different values across different builds. Thanks

[nuno-agostinho]

Hi @davmlaw,

Thanks for reporting this issue. I am going to discuss this with the team.

Best regards,
Nuno