Data sources
We collated all previously reported deafness-causing variants as described in Shearer AE, et al 2014 and Azaiez H, et al 2018. Annotation is based on data from the following sources:
ClinVar
- Release
- 2020 September 2
- Reference
- Landrum MJ, et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res 44, D862–D868 (2016).
- Release
- dbNSFP v4.1
- References
-
Liu X, Jian X, and Boerwinkle E. 2011. dbNSFP: a lightweight database of human non-synonymous SNPs and their functional predictions. Human Mutat., 32, 894-899.
Liu X, Jian X, and Boerwinkle E. 2013. dbNSFP v2.0: A Database of Human Non-synonymous SNVs and Their Functional Predictions and Annotations. Human Mutat., 34, E2393-E2402.
Liu X, Wu C, Li C, and Boerwinkle E. 2013. dbNSFP v3.0: A One-Stop Database of Functional Predictions and Annotations for Human Non-synonymous and Splice Site SNVs. Human Mutat., 37, 235-241.
Liu, X., Li, C., Mou, C. et al. dbNSFP v4: a comprehensive database of transcript-specific functional predictions and annotations for human nonsynonymous and splice-site SNVs. Genome Med 12, 103 (2020). https://doi.org/10.1186/s13073-020-00803-9 - Release
- Version 2.1.1
- Reference
- gnomAD Website: gnomAD browser gnomAD Flagship Publication: Karczewski, K.J., et al., Variation across 141,456 human exomes and genomes reveals the spectrum of loss-of-function intolerance across human protein-coding genes. bioRxiv, 2019: p. 531210.
- Release
- Version 101
- References
- Ensembl Website
- Release
- v1.6
- References
-
Rentzsch P, Witten D, Cooper GM, Shendure J, Kircher M.
CADD: predicting the deleteriousness of variants throughout the human genome.
Nucleic Acids Res. 2018 Oct 29. doi: 10.1093/nar/gky1016.
PubMed PMID: 30371827. -
Kircher M, Witten DM, Jain P, O'Roak BJ, Cooper GM, Shendure J.
A general framework for estimating the relative pathogenicity of human genetic variants.
Nat Genet. 2014 Feb 2. doi: 10.1038/ng.2892.
PubMed PMID: 24487276. - Release
- Build 146
- Reference
- Sherry ST, et al. dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001 Jan 1;29(1):308-11.
- We collated all previously reported deafness-causing variants as described in the following publication:
-
Shearer AE, et al. Utilizing ethnic-specific differences in minor allele frequency
to re-categorize reported pathogenic deafness variants. Am J Hum Genet
2014. -
Jesaitis, A. Variant Notation: In simplicity we find complexity. Our 2 SNPs... ®
(2014).