CAVA csn missing the "="

[rohandavidg]

Hi,

We are seeing a truncated CAVA_CSN for a synonymous variant, where the '=' is missing. We were wondering if this issue has been seen before?
For example CAVA_CSN=CAVA_CSN=c.3786C>T_p. instead of CAVA_CSN=c.3786C>T_p.=

chr12 2721137 . C T . . CAVA_TYPE=Substitution;CAVA_ENST=NM_000719.6;CAVA_GENE=CACNA1C;CAVA_GENEID=775;CAVA_TRINFO=+/644.7kb/47/13.5kb/2138;CAVA_LOC=Ex29;CAVA_CSN=c.3786C>T_p.;CAVA_PROTPOS=1262;CAVA_PROTREF=F;CAVA_PROTALT=F;CAVA_CLASS=SY;CAVA_SO=synonymous_variant;CAVA_IMPACT=3;CAVA_ALTANN=.;CAVA_ALTCLASS=.;CAVA_ALTSO=. GT:AD:DP 0/1:3501,3455:6966
chr12 2788879 . G A . . CAVA_TYPE=Substitution;CAVA_ENST=NM_000719.6;CAVA_GENE=CACNA1C;CAVA_GENEID=775;CAVA_TRINFO=+/644.7kb/47/13.5kb/2138;CAVA_LOC=Ex42;**CAVA_CSN=c.5361G>A_p.;**CAVA_PROTPOS=1787;CAVA_PROTREF=T;CAVA_PROTALT=T;CAVA_CLASS=SY;CAVA_SO=synonymous_variant;CAVA_IMPACT=3;CAVA_ALTANN=.;CAVA_ALTCLASS=.;CAVA_ALTSO=. GT:AD:DP 0/1:3762,3506:7269

[marton-munz]

Hi, thanks very much for your feedback.
We were not able to reproduce the issue and we have never seen this problem before.
I have noticed that you are using RefSeq transcripts (e.g. CAVA_ENST=NM_000719.6). RefSeq transcripts are currently not supported in CAVA and we haven't released RefSeq transcript database. What transcript database have you used for annotating with CAVA? I suspect this may be behind the issue you encountered.