DEAFNESS VARIATION DATABASE

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).

dbNSFP

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

gnomAD

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.

VEP

Release

Version 101

References

Ensembl Website

CADD

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.

dbSNP

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.

Population Analysis

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.

Other

Jesaitis, A. Variant Notation: In simplicity we find complexity. Our 2 SNPs... ®
  (2014).