Hi all,
I have a problem with interpretation of one variant annotation. It is multipleks result. Here is an a variant and annotations:
chr1 169519049 169519049 T/C exonic F5gene
F5:NM_000130:exon10:c.A1601G:p.Q534R ClinVar=pathogenic rs=6025
I see this variant annotated the same way in all 24 samples. Moreover I checked this variant by Sanger - no confirmation. I also checked the 1000g2014 for "all" and "eur" frequency for this variant = 99% of population have it! So I am very confused what just have happened here.
Firstly, I was thinking about pseudogene, but I didn't find any pseudogenes for fragment occurring this variant in blast results.
Second I found in 1000g database that for this RS number there can be a lot of different genotypes where one is pathogenic, rest are not. So I would suggest to have not pathogenic annotation since there is information about frequency bigger that 1%. So,why there is information about non-pathogenic in 1000g database and pathogenic in ClinVar database?
Third, this gene is on reverse strand, also I am working on hg19 reference which differ in that location from hg38 reference. In hg19 there is forward/reverse T/A, in hg38 there is G/C. Sanger sequencing is showing G.
Please, could anybody me tell me where is the mistake? This is complicated.
PS. I am using annovar for variant annotation.
Best,
Agata
This is coming from ClinVar, so have a look at the output there.
Ok, so there is pathogenic allel T, not C (in my results), so why clinvar annotated that as pathogenic? Ad do you know how to deal with multiple genotype annotation? Can annovar do something like that?
Someone submitted it as pathogenic, perhaps they just swapped the alleles when they did that. You might find out the ClinVar contact and see if they can have a look. Regarding multiple alleles, I'm not a good person to answer that, I don't do much work in this particular area.
Too bad, thanks anyway. I am also wondering why I have C while Sanger cinfirm G, any clue?
The mutation is A to G (or T to C). Sanger is showing G, so it is confirming the mutation.
Depending on how you designed your PCR primers and how you are analyzing the reads, either strand could be showing up.
You know what, I think this is the inconsistency between references. If I map this to hg38 no variant will be reported, because I have C and G/C as reference.
Looks like the population mutation frequency is over 95%, so it makes sense that they changed the reference.
Yes, but I have T/C as a result...annotated as pathogenic. Sanger is showing G.