NCBI Genome Remapping Service- clinical remap result difference with UCSC hg19

Question

[Sudhir Jadhao]

Hello Everyone

I have cDNA variant of LRG (Refseq) sequences (e.g. NM_020469.2:c.467C>T) want to convert to hg19 genomic co-ordinate. For the same I am using "NCBI Genome Remapping Service- clinical remap " online service.

Parameter selected: I have data on : LRG I want to map to:hg19

my Input;

NM_020469.2:c.467C>T
NM_020469.2:c.318C>T
NM_020469.2:c.220C>T
NM_020469.2:c.189C>T
NM_020469.2:c.188G>A
NM_020469.2:c.106G>T

output(vcf format):

Problem is in vcf output when I go to UCSC hg19 same genome position it shows me different basepair(136136770=> A [but the output given by clinical remap is G for same postion]) than clinical remap output .

So from the vcf output, all reference base pairs are not matching with UCSC hg19 genome base pair. for example

Can anyone please tell me the reason and help to convert my cDNA LRG variant to hg19 genomic coordinate.

Thank you In advance,

Best Regards,
Sudhir

[GenoMax]

@Sudhir: it is not a good practice to create multiple questions that address similar content. Has your previous question been addressed (NCBI Genome Remapping Service- clinical remap ) satisfactorily? At first glance it seems to be what you are asking again in this question.

[Sudhir Jadhao]

Both questions are completely different

[finswimmer]

No, I believe these questions are the result of the same problem. See my comment in the other thread.

[Sudhir Jadhao]

I agree with you @fin.

I just wanted to make this question more understandable to Biostar community