Different position converter result?

[xiucz]

Hi, I use different position converter to get my HGVS format data:

NM_173651.2:c.11438G>T

https://mutalyzer.nl/position-converter?assembly_name_or_alias=GRCh37&description=NM_173651.2%3Ac.11438G%3ET gives result :NC_000002.11:g.186665204G>T

However, ucsc genome brewer gives : chr2:186,665,466, which seems very weird to me for this type of analysis.

Can you help me ? Thanks.

[zwdzwd]

Hi I think TransVar agrees with mutalyzer.

transvar canno -i 'NM_173651.2:c.11438G>T' --refseq input transcript gene strand coordinates(gDNA/cDNA/protein) region info NM_173651.2:c.11438G>T NM_173651 (proteincoding) FSIP2 + chr2:g.186665204G>T/c.11438G>T/p.R3813I inside[cds_in_exon_17] CSQN=Missense;reference_codon=AGA;alternative_codon=ATA;dbxref=GeneID:401024,HGNC:21675;aliases=NP_775922;source=RefSeq

Can you show me how you used UCSC genome browser to get 186,665,466?

Thanks,

[xiucz]

Hi, I just use Genome Browser to get my position, see this link, the yellow part shows ucsc's position.

Searching for "NM_173651.2:c.11438G>T" in Genome Browser, and it gives an error. But searching for "NM_173651:c.11438G>T" works.

In UCSC's reply letter, they tell me

The difference you are seeing between mutalyzer and the UCSC Genome Browser is due to transcript differences. As you may have noticed, searching for "NM_173651.2:c.11438G>T" gives an error about how we don't have NM_173651.2 sequence.

It seems UCSC will return the latest version transcript's information if I give the the identifer without the extension? So, UCSC gives NM_1735651.3 's information. However, if I give "NM_173651.3:c.11438G>T"(version 3) to UCSC, it returns me a quite different position.

Is TransVar based on mutalyzer? And what's your opinion about UCSC's difference?

Thank you.

[xiucz]

Hi, I confirmed my question. Searching for a transcript identifier without the extension will give you the latest transcript.

Thank you.