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Global annotations |
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Data source |
Version hg19 |
Version hg38 |
Citations / link |
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VEP |
111 |
111 |
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. The Ensembl Variant Effect Predictor. Genome Biology Jun 6;17(1):122. (2016) doi:10.1186/s13059-016-0974-4 |
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ClinVar |
20/11/2024 |
20/11/2024 |
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Gnomad |
2.1.1 4.1.0 (liftover) |
3.1.2 4.1.0 |
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dbscSNV |
v1.1 |
v1.1 |
Jian X, Boerwinkle E and Liu X. 2014. In silico prediction of splice-altering single nucleotide variants in the human genome . Nucleic Acids Research 42(22):13534-13544. |
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PhyloP |
Pollard KS, Hubisz MJ, Siepel A. Detection of non-neutral substitution rates on mammalian phylogenies. Genome Res. 2009 Oct 26. [Epub ahead of print] ( |
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PhastCons |
Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005 Aug;15(8):1034-50. ( |
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AION Classification (circe predictions) |
v1 |
lifted over v1 |
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Refseq |
Ensembl 111 |
- |
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Grantham scores |
From paper |
From paper |
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BLOSUM62 |
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Canonical transcript definition |
v9 updated(gnomAD v2.1.1 + APPRIS 2022_02.v47) |
v9 (MANE Select v1.3 + MANE Clinical v1.3) |
https://academic.oup.com/nar/article/41/D1/D110/1054030 |
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Internal annotations |
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Data source |
Nostos internal versioning hg19 |
Nostos internal versioning hg38 |
Citations |
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Repeat definition |
RepeatMasker from UCSC 20/02/2020 |
RepeatMasker from UCSC 18/10/2022 (hg38) |
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Hotspot definition |
v9 (based on Clinvar 31/03/2024) |
v9 (based on Clinvar 31/03/2024) |
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NMD |
v9 |
v9 |
https://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/ensGene.txt.gz |
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Uniprot functional domains |
UniProt Release 06/2020 |
Uniprot release Release 06/2023 |
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Global frequent artifact blacklist |
v2 |
v1 native hg38 |
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Whitelist of variants to keep with high gnomad freq |
v1 |
v1 liftover |
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PP2 gene list |
v9 (Clinvar - 31/03/2024) |
v9 (Clinvar - 31/03/2024) |
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BP1 gene list |
v9 (Clinvar - 31/03/2024) |
v9 (Clinvar - 31/03/2024) |
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PVS1 gene list |
v9 (Clinvar - 31/03/2024) |
v9 (Clinvar - 31/03/2024) |
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Coding region BED file |
hg19.ensGene.gtf.gz 10-01-2020 + ClinVar 31/03/2024 |
MANE v1 + ClinVar 31/03/2024 |
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CNV annotations |
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Data source |
Version hg19 |
Version hg38 |
Citations |
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AnnotSV |
3.3.6 |
3.3.6 |
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Exomiser data |
2202 |
2202 |
https://data.monarchinitiative.org/exomiser/data/2202_phenotype.zip |
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gnomAD-SV |
v2.1.1 |
v4.1.0 |
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ExAC |
v0.3.1 |
v0.3.1 |
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ClinVar |
31/03/2024 |
31/03/2024 |
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ClinGen |
01/12/2024 |
01/12/2024 |
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dbVar |
05/09/2023 |
05/09/2023 |
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DDD |
09/2015 (v9.2) |
09/2015 (v9.2) |
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DGV |
25/02/2020 |
25/02/2020 |
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1000 genomes |
21/05/2017 |
21/05/2017 |
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Ira M. Hall’s lab |
31/12/2018 Static paper https://www.biorxiv.org/content/10.1101/508515v1.supplementary-material (liftdown) |
31/12/2018 Static paper https://www.biorxiv.org/content/10.1101/508515v1.supplementary-material |
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Children’s Mercy Research Institute |
Liftdown 27/10/2021 Static GitHub VCF file |
27/07/2021 Static GitHub VCF file (in GRCh38) |
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RefSeq |
2020-08-17 |
2020-08-17 |
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Ensembl |
2014-02-07 |
2022-06-04 |
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Breakpoints |
20/03/2009 |
20/03/2014 |
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Repeats (*) |
05/09/2023 |
05/09/2023 |
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Segmental duplications |
15/10/2021 |
15/10/2021 |
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ENCODE blacklist |
04/05/2011 |
16/10/2016 |
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GAP |
15/10/2021 |
15/10/2021 |
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Cytoband |
14/06/2009 (GRCh37) |
11/03/2019 (GRCh38) |
http://hgdownload.cse.ucsc.edu/goldenpath/hg19/database/cytoBand.txt.gz |
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TAD boundaries |
15/04/2024 |
21/11/2017 |
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ACMG |
Static paper (https://pubmed.ncbi.nlm.nih.gov/35802134/) v3.1 78 genes |
Static paper (https://pubmed.ncbi.nlm.nih.gov/35802134/) v3.1 78 genes |
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Disease annotations |
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Data source |
Version |
- |
Citations / link |
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HPO |
Downloaded 02/05/2024 |
- |
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Mondo |
Downloaded 02/05/2023 |
- |
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GenCC |
Downloaded on 02/05/2024 |
- |
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HGNC |
Downloaded on 02/05/2024 |
- |
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DDG2P |
Downloaded 02/05/2024 |
- |
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PanelApp |
Downloaded 02/05/2024 |
- |
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Data Sources
gnomAD