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dandelion-marshy.yml
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unique-id: dandelion-marshy
phe-label: V-21MAY-01
alternate-names:
-
belongs-to-lineage:
- PANGO: AV.1
description: This variant has been observed in a growing cluster in the UK
information-sources:
- https://github.com/cov-lineages/pango-designation/issues/73
variants:
- codon-change: GTT-GTC
gene: ORF1ab
one-based-reference-position: 772
predicted-effect: synonymous
protein: nsp1
protein-codon-position: 169
reference-base: T
snp-codon-position: 3
type: SNP
variant-base: C
- amino-acid-change: G339S
codon-change: GGT-AGT
gene: ORF1ab
one-based-reference-position: 1820
predicted-effect: non-synonymous
protein: nsp2
protein-codon-position: 339
reference-base: G
type: SNP
variant-base: A
- amino-acid-change: A411V
codon-change: GCT-GTT
gene: ORF1ab
one-based-reference-position: 2037
predicted-effect: non-synonymous
protein: nsp2
protein-codon-position: 411
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: H342Y
codon-change: CAT-TAT
gene: ORF1ab
one-based-reference-position: 3743
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 342
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: P822L
codon-change: CCT-CTT
gene: ORF1ab
one-based-reference-position: 5184
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 822
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: N1587S
codon-change: AAT-AGT
gene: ORF1ab
one-based-reference-position: 7479
predicted-effect: non-synonymous
protein: nsp3
protein-codon-position: 1587
reference-base: A
type: SNP
variant-base: G
- amino-acid-change: A446V
codon-change: GCT-GTT
gene: ORF1ab
one-based-reference-position: 9891
predicted-effect: non-synonymous
protein: nsp4
protein-codon-position: 446
reference-base: C
type: SNP
variant-base: T
- gene: ORF1ab
one-based-reference-position: 11287
protein: nsp6
reference-base: GTCTGGTTTT
type: deletion
variant-base: G
- codon-change: GGT-GGC
gene: ORF1ab
one-based-reference-position: 11503
predicted-effect: synonymous
protein: nsp6
protein-codon-position: 177
reference-base: T
snp-codon-position: 3
type: SNP
variant-base: C
- amino-acid-change: S434A
codon-change: TCT-GCT
gene: ORF1ab
one-based-reference-position: 14740
predicted-effect: non-synonymous
protein: nsp12
protein-codon-position: 434
reference-base: T
type: SNP
variant-base: G
- amino-acid-change: A119V
codon-change: GCT-GTT
gene: ORF1ab
one-based-reference-position: 18395
predicted-effect: non-synonymous
protein: nsp14
protein-codon-position: 119
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: D80G
codon-change: GAT-GGT
gene: S
one-based-reference-position: 21801
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 80
reference-base: A
type: SNP
variant-base: G
- amino-acid-change: T95I
codon-change: ACT-ATT
gene: S
one-based-reference-position: 21846
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 95
reference-base: C
type: SNP
variant-base: T
- amino-acid-change: G142D
codon-change: GGT-GAT
gene: S
one-based-reference-position: 21987
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 142
reference-base: G
type: SNP
variant-base: A
- gene: S
one-based-reference-position: 21990
protein: surface glycoprotein
reference-base: TTTA
type: deletion
variant-base: T
- codon-change: TCC-TCT
gene: S
one-based-reference-position: 22687
predicted-effect: synonymous
protein: surface glycoprotein
protein-codon-position: 375
reference-base: C
snp-codon-position: 3
type: SNP
variant-base: T
- amino-acid-change: N439K
codon-change: AAC-AAG
gene: S
one-based-reference-position: 22879
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 439
reference-base: C
type: SNP
variant-base: G
- 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
- amino-acid-change: P681H
codon-change: CCT-CAT
gene: S
one-based-reference-position: 23604
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 681
reference-base: C
type: SNP
variant-base: A
- amino-acid-change: I1130V
codon-change: ATA-GTA
gene: S
one-based-reference-position: 24950
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 1130
reference-base: A
type: SNP
variant-base: G
- amino-acid-change: D1139H
codon-change: GAT-CAT
gene: S
one-based-reference-position: 24977
predicted-effect: non-synonymous
protein: surface glycoprotein
protein-codon-position: 1139
reference-base: G
type: SNP
variant-base: C
- gene: ORF3a
one-based-reference-position: 26157
protein: ORF3a protein
reference-base: TGTTA
type: deletion
variant-base: T
- amino-acid-change: A63T
codon-change: GCT-ACT
gene: M
one-based-reference-position: 26709
predicted-effect: non-synonymous
protein: membrane glycoprotein
protein-codon-position: 63
reference-base: G
type: SNP
variant-base: A
- codon-change: ATC-ATT
gene: ORF6
one-based-reference-position: 27297
predicted-effect: synonymous
protein: ORF6 protein
protein-codon-position: 32
reference-base: C
snp-codon-position: 3
type: SNP
variant-base: T
- gene: .
one-based-reference-position: 28270
protein: .
reference-base: TAA
type: deletion
variant-base: T
- amino-acid-change: I157V
codon-change: ATC-GTT
gene: N
one-based-reference-position: 28742
predicted-effect: non-synonymous
protein: nucleocapsid phosphoprotein
protein-codon-position: 157
reference-base: ATC
type: MNP
variant-base: GNT
calling-definition:
confirmed:
mutations-required: 22
indels-required: 0
allowed-wildtype: 0
probable:
mutations-required: 7
indels-required: 0
allowed-wildtype: 0
low-qc:
mutations-required: 0
indels-required: 0
allowed-wildtype: 0
acknowledgements:
- Matthew Parker
curators:
- Natalie Groves