How to match Clinvar.vcf database by CHROM+POS+REF+ALT

Question

[merobin8]

I have got Clinvar,vcf database and uploaded to SQL Sever . This database have field CHROM , POS, REF , ALT .

Now I want to use CHROM , POS, REF , ALT AS key to match the record to get CLNSIG .

For 'del' and 'ins' case ,how to get the correct REF , ALT from MutationCallRelativeToCDS to match the database ? Is there any rules ?

Below are some examples :

c.3285-15delA
c.3659+19delA
c.3811+60_3811+61insT
c.3811+60delT
c.4229-33delT
c.357-36_357-35insC
c.866+33_866+34insT
c.866+47delC
c.2017-27_2017-26insC
c.358+44_358+46delTCT
c.358+44_358+46delTCT
c.358+44_358+46delTCT
c.866+33_866+34insT
c.866+47delC
c.2017-29_2017-28insC
c.823+33delG
c.3235+44_3235+50delAGGAGCC
c.3235+44_3235+50delAGGAGCC
c.3235+44_3235+50delAGGAGCC
c.3235+44_3235+50delAGGAGCC
c.3235+44_3235+50delAGGAGCC
c.3235+44_3235+50delAGGAGCC
c.3235+44_3235+50delAGGAGCC
c.409-50delG
c.866+48_866+49insAGGCAACC
c.1114+36_1114+37insA

Below are how the datebase looks like :

POS ID  REF ALT QUAL    FILTER
949422  475283  G   A   .   .
949502  542074  C   T   .   .
949523  183381  C   T   .   .
949559  542075  C   T   .   .
949597  475278  C   T   .   .
949608  402986  G   A   .   .
949696  161455  C   CG  .   .
949739  161454  G   T   .   .
949781  542076  G   A   .   .

[cpad0112]

Either you back calculate and match or calculate csyntax and match

[finswimmer]

Hello,

I don't know the program MutationCallRelativeToCDS. Can you link to it?

I hope you have at least gene names, but better transcript id's, to your c. variants. Otherwise there is no chance to convert them to genomic position.

The most easiest way to convert hgvs variants to genomic positions is to use VEP. If you use gene names instead of transcript id's be aware that the result might be ambiguous.

fin swimmer