MyVariant Data Updates

by Yao Yao

We're excited to announce the latest MyVariant.info updates! The number of our hg19 variant annotation documents has increased from 969 millions to 1.42 billion, and hg38 from 887 millions to 1.45 billion.

Here's what's new in build version 20220205 (hg19) .

  • CIViC variant annotation was updated in January by querying the API.
  • ClinVar data was updated from release 2021-04 to 2022-01, adding ~265,000 new records.
  • dbNSFP data was updated from version 4.1a to 4.2a, with new annotation fields such as BayesDel meta-scores, CADD scores, LINSIGHT scores, LIST-S2 scores, Altai Neanderthal genotypes, and Denisova genotypes.
  • dbSNP data was updated from release 154 to 155, which augmented our service with 431 millions of new records. (1.2 billion in total.)
  • Geno2MP made a new VCF release last September and we updated our data accordingly.
  • We continued to use gnomAD version 2.1.1 for our hg19 annotation services but we managed to enrich them with 77 new fields of site quality metrics (e.g. Random Forest prediction of true variants, VQSLOD scores) and population frequencies (e.g. allele frequencies in East Asian or Latino American populations).
  • Proudly from the Scripps Research Translational Institute, Wellderly data was updated to version 2 with 75 millions of records.
  • All newly-introduced variant records were also annotated by SnpEff version 4.3k.

Here's what's new in build version 20220207 (hg38).

  • ClinVar data was updated from release 2021-04 to 2022-01, adding ~265,000 new records.
  • dbNSFP data was updated from version 4.1a to 4.2a, with new annotation fields such as BayesDel meta-scores, CADD scores, LINSIGHT scores, LIST-S2 scores, Altai Neanderthal genotypes, and Denisova genotypes.
  • dbSNP data was updated from release 154 to 155, which augmented our service with 448 millions of new records. (1.2 billion in total.)
  • gnomAD version 3.1.1 was newly adopted for our hg38 genome annotation service, adding 498 millions of new records. (Meanwhile version 2.1.1 was still used for exomes.) We also enriched both services with 77 new fields of site quality metrics (e.g. Random Forest prediction of true variants, VQSLOD scores) and population frequencies (e.g. allele frequencies in East Asian or Latino American populations).
  • All newly-introduced variant records were also annotated by SnpEff version 4.3k.

Please read our release notes for more details of the data updates. For issues or suggestions, please feel free to contact us on Github.