[ensembl-dev] Exon info missing for indels

[Konrad Karczewski]

Hi dev team,

I'm getting some strange behavior when using VEP to annotate certain indels. In particular, the EXON field doesn't get populated for some reason. See below: a SNP at the same position looks fine (exon 39/91), while an indel doesn't get the same annotation. Any ideas about this?

Thanks!
-Konrad

2       141459861       .       C       A       2       VQSRTrancheINDEL99.50to99.90    AC=1;CSQ=A|ENSG00000168702|ENST00000389484|Transcript|stop_gained&splice_region_variant|7123|6151|2051|E/*|Gaa/Taa||1||-1|LRP1B|HGNC|6693|protein_coding|YES|CCDS2182.1|ENSP00000374135|LRP1B_HUMAN|Q8WY27_HUMAN&Q8WY26_HUMAN&Q580W7_HUMAN&Q53TB8_HUMAN&Q53S76_HUMAN&Q53S73_HUMAN&Q53S26_HUMAN&Q53RL0_HUMAN&Q53RG4_HUMAN&Q53RA0_HUMAN&Q53QP5_HUMAN&Q53QM8_HUMAN&Q4ZG53_HUMAN&Q4ZFV5_HUMAN|UPI00001B045B|||39/91||PROSITE_profiles:PS51120&SMART_domains:SM00135&Superfamily_domains:SSF63825|ENST00000389484.3:c.6151G>T|ENSP00000374135.3:p.Glu2051Ter|||||||||||||||POSITION:0.445724637681159|||HC
2       141459861       .       C       CATAAGTATTTGAGT 363.89  VQSRTrancheINDEL99.50to99.90    AC=1;CSQ=ATAAGTATTTGAGT|ENSG00000168702|ENST00000389484|Transcript|frameshift_variant&splice_region_variant&feature_elongation|7122-7123|6150-6151|2050-2051|-/TQILX|-/ACTCAAATACTTAT||1||-1|LRP1B|HGNC|6693|protein_coding|YES|CCDS2182.1|ENSP00000374135|LRP1B_HUMAN|Q8WY27_HUMAN&Q8WY26_HUMAN&Q580W7_HUMAN&Q53TB8_HUMAN&Q53S76_HUMAN&Q53S73_HUMAN&Q53S26_HUMAN&Q53RL0_HUMAN&Q53RG4_HUMAN&Q53RA0_HUMAN&Q53QP5_HUMAN&Q53QM8_HUMAN&Q4ZG53_HUMAN&Q4ZFV5_HUMAN|UPI00001B045B|||||PROSITE_profiles:PS51120&SMART_domains:SM00135&Superfamily_domains:SSF63825|ENST00000389484.3:c.6151-1_6151insACTCAAATACTTAT|ENSP00000374135.3:p.Glu2051ThrfsTer19|||||||||||||||POSITION:0.445652173913043||EXON_INTRON_UNDEF|LC