{"action":"created","issue":{"url":"https://api.github.com/repos/hammerlab/varcode/issues/168","repository_url":"https://api.github.com/repos/hammerlab/varcode","labels_url":"https://api.github.com/repos/hammerlab/varcode/issues/168/labels{/name}","comments_url":"https://api.github.com/repos/hammerlab/varcode/issues/168/comments","events_url":"https://api.github.com/repos/hammerlab/varcode/issues/168/events","html_url":"https://github.com/hammerlab/varcode/issues/168","id":173489496,"number":168,"title":"Synonimous FrameShift over stop codon not annotated as silent ","user":{"login":"joaoe","id":461983,"avatar_url":"https://avatars.githubusercontent.com/u/461983?v=3","gravatar_id":"","url":"https://api.github.com/users/joaoe","html_url":"https://github.com/joaoe","followers_url":"https://api.github.com/users/joaoe/followers","following_url":"https://api.github.com/users/joaoe/following{/other_user}","gists_url":"https://api.github.com/users/joaoe/gists{/gist_id}","starred_url":"https://api.github.com/users/joaoe/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/joaoe/subscriptions","organizations_url":"https://api.github.com/users/joaoe/orgs","repos_url":"https://api.github.com/users/joaoe/repos","events_url":"https://api.github.com/users/joaoe/events{/privacy}","received_events_url":"https://api.github.com/users/joaoe/received_events","type":"User","site_admin":false},"labels":[],"state":"closed","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":2,"created_at":"2016-08-26T16:13:35Z","updated_at":"2016-09-13T16:46:15Z","closed_at":"2016-09-13T16:46:15Z","body":"Testcase, using genome GRCm38, over transcript ENSMUST00000086738\r\n```\r\n##fileformat=VCFv4.1\r\n#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO\tFORMAT\r\n\r\n# The coding sequence at chr1/99772765 has transcript ID ENSMUST00000086738\r\n# and the end looks like:\r\n# TTC ATC TGA ACT ATT GTG TGG TCA TCT GGT CCT CTT TTT (...)\r\n#         ^ stop codon\r\n\r\n# Synonymous FrameShift over the stop codon: TGA -> TAG AAC ...\r\nchr1\t100484699\t.\tT\tTA\t5000\t.\t.\t.\r\n```\r\n\r\nThis is annotated as\r\n```\r\nStopLoss(variant=chr1 g.100484699_100484700insA, transcript_name=Cntnap5b-001, transcript_id=ENSMUST00000086738, effect_description=p.*1293 (stop-loss))\r\n* aa_ref = \"*\"\r\n* aa_alt = \"\"\r\n* modifies_protein_sequence = True\r\n```\r\n\r\nI think this should be annotated as `Silent(...)`"},"comment":{"url":"https://api.github.com/repos/hammerlab/varcode/issues/comments/246745893","html_url":"https://github.com/hammerlab/varcode/issues/168#issuecomment-246745893","issue_url":"https://api.github.com/repos/hammerlab/varcode/issues/168","id":246745893,"user":{"login":"iskandr","id":48441,"avatar_url":"https://avatars.githubusercontent.com/u/48441?v=3","gravatar_id":"","url":"https://api.github.com/users/iskandr","html_url":"https://github.com/iskandr","followers_url":"https://api.github.com/users/iskandr/followers","following_url":"https://api.github.com/users/iskandr/following{/other_user}","gists_url":"https://api.github.com/users/iskandr/gists{/gist_id}","starred_url":"https://api.github.com/users/iskandr/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/iskandr/subscriptions","organizations_url":"https://api.github.com/users/iskandr/orgs","repos_url":"https://api.github.com/users/iskandr/repos","events_url":"https://api.github.com/users/iskandr/events{/privacy}","received_events_url":"https://api.github.com/users/iskandr/received_events","type":"User","site_admin":false},"created_at":"2016-09-13T16:46:15Z","updated_at":"2016-09-13T16:46:15Z","body":"Fixed by https://github.com/hammerlab/varcode/pull/173"}}
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