INFO

https://mp.weixin.qq.com/s/ixsqg306nwLHGTqVvR6Stw

gnomAD

https://gnomad.broadinstitute.org/faq

LOFTEE

https://github.com/konradjk/loftee

LoF

LoF variants (i.e. does not fail any filters) | | LC | low-confidence, failing at least one filter | | OS | Other splice (beta) |

LoF_filter

variant falls in the last filter_position of the transcript (default = 0.05) | | INCOMPLETE_CDS | The LoF falls in a transcript whose start or stop codons are not known. | | EXON_INTRON_UNDEF | The LoF falls in a transcript whose exon/intron boundaries are undefined in the EnsEMBL API | | SMALL_INTRON | The LoF falls in a splice site of a small (biologically unlikely; default < 15 bp) intron | | ANC_ALLELE | The alternate allele of the LoF reverts the sequence back to the ancestral state | | NON_DONOR_DISRUPTING | An essential splice donor variant’s DISRUPTION_PROB fails to exceed the donor_disruption_cutoff | | NON_ACCEPTOR_DISRUPTING | An essential splice acceptor variant’s DISRUPTION_PROB fails to exceed the acceptor_disruption_cutoff | | RESCUE_DONOR | A splice donor-disrupting variant (either essential or extended with sufficient DONOR_DISRUPTION_PROB) is rescued by an alternative splice site (less than max_scan_distance bp away) with an MES score above donor_rescue_cutoff. The variant in question, which was formerly determined to disrupt an existing splice site, gets downgraded to an LC LoF | | RESCUE_ACCEPTOR | Ditto for splice acceptor-disrupting variants | | GC_TO_GT_DONOR | Essential donor splice variant creates a more canonical splice site (strengthening the site if anything, thus unlikely to disrupt splicing) | | 5UTR_SPLICE and 3UTR_SPLICE | Essential splice variant LoF occurs in the UTR of the transcript |

LoF_flags

in a single exon transcript | | NAGNAG_SITE | The LoF is a splice variant that falls into a NAGNAG sequence, which may indicate a frame-restoring splice site | | PHYLOCSF_WEAK | The LoF falls in an exon that does not exhibit a pattern of conservation typical of a protein-coding exon | | PHYLOCSF_UNLIKELY_ORF | The LoF falls in an exon that exhibits a pattern of conservation typical of a protein-coding exon, but the reading frame is likely offset | | NON_CAN_SPLICE | The LoF is a splice variant that falls in a non-canonical splice site (not GT..AG) |