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unknown severity: splice_polypyrimidine_tract_variant & splice_donor_region_variant

Open ToonRosseel opened this issue 1 year ago • 0 comments

When using Ensembl VEP version 105 we get following vcf2db warnings:

[2022-07-07T10:19Z] WARNING: unknown severity for 'C|splice_donor_region_variant&intron_variant|LOW|NOC2L|ENSG00000188976|Transcript|ENST00000327044|protein_coding||8/18|ENST00000327044.7:c.888+4C>G|||||||rs13303056|1||-1||SNV|HGNC|HGNC:24517|YES|NM_015658.4||1|P1|CCDS3.1|ENSP00000317992|Q9Y3T9.182||UPI000041820C|||Ensembl||G|G|||||||chr1:g.953778G>C||0.829|0.9135|0.9365|0.9523|0.9172|0.8238|0.9333|0.9321|0.8235|0.9508|0.9351|0.9215|0.9599|0.9413|0.9357|0.9192|0.9599|gnomAD_FIN||||||||||NOC2L:K296int|1&1&4||NOC2L&NM_015658.3&c.888+4C>G|||||INTRON_END:953781&DONOR_ESS:4&DONOR_ISS:4&EXON_END:953892&DONOR_GERP_DIFF:NA&DONOR_ESE:45&MUTANT_DONOR_MES:8.46099459345687&EXON_START:953782&DONOR_ISE:20&BRANCHPOINT_DISTANCE:NA&INTRON_START:953289&DONOR_MES_DIFF:-0.0169218360392236|8.461|-0.017|8.444|splice_donor_region_variant' with effect 'splice_donor_region_variant'
[2022-07-07T10:19Z] Please report this on github with the effect-string above
[2022-07-07T08:07Z] WARNING: unknown severity for 'A|splice_polypyrimidine_tract_variant&intron_variant|LOW|PKD1|ENSG00000008710|Transcript|ENST00000262304|protein_coding||12/45|ENST00000262304.9:c.2986-15C>T|||||||rs2855349&COSV51915841|1||-1||SNV|HGNC|HGNC:9008|YES|NM_001009944.3||1|A2|CCDS32369.1|ENSP00000262304|P98161.246||UPI00001B0454|P98161-1||Ensembl||G|G||1|||||chr16:g.2112978G>A|0.1016|0.0212|0.0346|0.2589|0.0199|0.18|0.01959|0.01593|0.05527|0.02214|0.04355|0.01434|0.2355|0.006574|0.01323|0.03884|0.168|0.2589|EAS|benign|0&1|1&1|25741868||||||-15|-38|-47|-32|0.00|0.00|0.00|0.00|PKD1||||ACCEPTOR_ESS:4&MUTANT_ACCEPTOR_MES:9.72629935165179&INTRON_START:2112964&EXON_START:2112788&EXON_END:2112963&ACCEPTOR_ESE:34&ACCEPTOR_GERP_DIFF:NA&INTRON_END:2113160&ACCEPTOR_MES_DIFF:0.0275745470020006&ACCEPTOR_ISS:11&BRANCHPOINT_DISTANCE:20&ACCEPTOR_ISE:9|9.726|0.028|9.754|splice_polypyrimidine_tract_variant' with effect 'splice_polypyrimidine_tract_variant'
[2022-07-07T08:07Z] Please report this on github with the effect-string above

We use geneimpacts v0.3.7. Could this been fixed?

Thank you in advance

ToonRosseel avatar Jul 08 '22 07:07 ToonRosseel