Hi community!,

I'm annotating variants with the VEP software and I'm finding some unexpected transcript data of the type:

- NM_014938.4_dupl16
- NM_001170637.2_dupl3

```
    1       206516261       .       C       T       47      PASS CSQ=T|non_coding_transcript_exon_variant|MODIFIER|SRGAP2|23380|Transcript|NM_001170637.2_dupl3|mRNA|1/20||NM_001170637.2_dupl3.1:n.65C>T||65|||||||1||SNV|EntrezGene|||||||||||C|C||||||||||||||||||||||||||||||||||||||||||||||||||||||||||1:206516261-206516261|0.4996565||||,
    T|missense_variant|MODERATE|SRGAP2|23380|Transcript|NM_001170637.3|protein_coding|1/20||NM_001170637.3:c.65C>T|NP_001164108.1:p.Arg289Trp|864|865|289|R/W|Cgg/Tgg|||1||SNV|EntrezGene||||||NP_001164108.1|||||C|C|OK|||||||||||||||||||||||||||||||||||0.63580||||T|T||||||||||2|||||||1:206516261-206516261|0.4996565||||,
    T|missense_variant|MODERATE|SRGAP2|23380|Transcript|NM_001300952.1|protein_coding|1/18||NM_001300952.1:c.65C>T|NP_001287881.1:p.Arg289Trp|864|865|289|R/W|Cgg/Tgg|||1||SNV|EntrezGene||||||NP_001287881.1|||||C|C|OK|||||||||||||||||||||||||||||||||||0.63580||||T|T||||||||||2|||||||1:206516261-206516261|0.4996565||||,
    T|non_coding_transcript_exon_variant|MODIFIER|SRGAP2|23380|Transcript|NM_015326.3_dupl3|mRNA|1/20||NM_015326.3_dupl3.1:n.65C>T||65|||||||1||SNV|EntrezGene||YES|||||||||C|C||||||||||||||||||||||||||||||||||||||||||||||||||||||||||1:206516261-206516261|0.4996565||||,
    T|missense_variant|MODERATE|SRGAP2|23380|Transcript|NM_015326.4|protein_coding|1/20||NM_015326.4:c.65C>T|NP_056141.2:p.Arg289Trp|864|865|289|R/W|Cgg/Tgg|||1||SNV|EntrezGene||YES||||NP_056141.2|||||C|C|OK|||||||||||||||||||||||||||||||||||0.63580||||T|T||||||||||2|||||||1:206516261-206516261|0.4996565||||       GT:DP:VD:AD:AF:RD:ALD   0/1:9:3:6,3:0.3333:6,0:3,0
```

Searching on the VEP webpage or in the internet I can't find any reference to this kind of "dupl" suffix. Has anyone faced this? I don't know if they are alternatives of the transcript or explain why they are not transcripts on its own.

Thanks in advance!

Cristian.


Edit: Added example of variant with the vep annotation of dup (NM_015326.3_dupl3)

Edit2: Using VEP ensembl version 91.1 with cache v91

We are investigating these. It looks like some RefSeq transcripts (eg NM_001170637.3) have been duplicated in Ensembl's other_features database with a lower version number and this dupl suffix (eg NM_001170637.2_dupl3). This has been propagated across to the VEP cache, which is why you're seeing them. We don't currently know why, but we believe that you can just ignore them from your analyses for now.