cornstalk-handprint.yml

unique-id: cornstalk-handprint
phe-label: V-21MAR-01
alternate-names:
- VUI202103/01
- B.1.324.1
belongs-to-lineage:
- PANGO: B.1.623
description: First detected in the UK in a traveller from Antigua.
information-sources:
- https://assets.publishing.service.gov.uk/government/uploads/system/uploads/attachment_data/file/968581/Variants_of_Concern_VOC_Technical_Briefing_7_England.pdf
- https://github.com/cov-lineages/pango-designation/issues/25
variants:
- amino-acid-change: G76S
  codon-change: GGC-AGC
  gene: ORF1ab
  one-based-reference-position: 2945
  predicted-effect: non-synonymous
  protein: nsp3
  protein-codon-position: 76
  reference-base: G
  type: SNP
  variant-base: A
- codon-change: GAT-GAC
  gene: ORF1ab
  one-based-reference-position: 8704 
  predicted-effect: synonymous
  protein: nsp4
  protein-codon-position: 50
  reference-base: T
  type: SNP
  variant-base: C
- codon-change: GAC-GAT
  gene: ORF1ab
  one-based-reference-position: 8986
  predicted-effect: synonymous
  protein: nsp4
  protein-codon-position: 144
  reference-base: C
  type: SNP
  variant-base: T
- codon-change: AAG-AAA
  gene: ORF1ab
  one-based-reference-position: 13617
  predicted-effect: synonymous
  protein: nsp12
  protein-codon-position: 59
  reference-base: G
  type: SNP
  variant-base: A 
- amino-acid-change: G206C
  codon-change: GGT-TGT
  gene: ORF1ab
  one-based-reference-position: 16852
  predicted-effect: non-synonymous
  protein: nsp13
  protein-codon-position: 206
  reference-base: G
  type: SNP
  variant-base: T
- codon-change: CTA-TTA
  gene: S
  one-based-reference-position: 22388
  predicted-effect: synonymous
  protein: surface glycoprotein
  protein-codon-position: 276
  reference-base: C
  type: SNP
  variant-base: T
- amino-acid-change: E484K
  codon-change: GAA-AAA
  gene: S
  one-based-reference-position: 23012
  predicted-effect: non-synonymous
  protein: surface glycoprotein
  protein-codon-position: 484
  reference-base: G
  type: SNP
  variant-base: A
- gene: ORF8
  one-based-reference-position: 27922
  protein: ORF8 Protein
  reference-base: TCACAACTGTAGCTGCATTTCACCAAGAATGTAGT
  type: deletion
  variant-base: A
- gene: .
  one-based-reference-position: 28272
  predicted-effect: synonymous
  protein: .
  reference-base: A
  type: SNP
  variant-base: T
calling-definition:
  confirmed:
    mutations-required: 8
    indels-required: 0
    allowed-wildtype: 0
  low-qc:
    mutations-required: 0
    indels-required: 0
    allowed-wildtype: 0
acknowledgements:
curators:
- Natalie Groves
- Ulf Schaefer
- Nick Loman
- Nick Ellaby