PS1 and PM5 also can't be assigned

[tiehan]

I run some snps by InerVar, but PS1 and PM5 can't be assigned.

function check_PS1(): try: if aa_changes_dict[keys_tmp2]: PS1_t2=0 except KeyError: for nt in ACGTs: if nt != cls[Allels_flgs['Alt']]: keys_tmp3=cls[Allelsflgs['Chr']]+""+cls[Allelsflgs['Start']]+""+cls[Allelsflgs['End']]+""+nt try: if aa_changes_dict[keys_tmp3] == aa_last: PS1_t2=1 except KeyError: pass

I wonder if keys_tmp2 in aa_changes_dict, why not PS1_t2=1?

[quanliustc]

here, PS1_t2 must be 0 firstly, it means this variant has the same allele change and also the same amino acid change in the pathogenic databank, so it cannot assign PS1, if it is not the same allele change but the same amino acid change, PS1 will apply.

[quanliustc]

Also, maybe you can give me the list, I will track the details in the pathogenic allele change databset.

[tiehan]

I see . I wonder that some variants in your aa_changes_dict will not be assigned PS1 and maybe be assigned to VUS.

[quanliustc]

The dataset of amino acid change was based on pathogenic variants in clinvar, so it could miss some real pathogenic variants. And for the reported non-conflit pathogenic variants in disease variant dataset(such as clinvar), we will assign PP5. PS1 only can be assigned when there are other nt change(not in the dataset we built ) with the same amino acid change. Also the same evidence we cannot use > twice.

[tiehan]

Thanks. I understand