Submit variants

Consistent with the goals of the LRG collaboration, we offer the opportunity to submit information about variants to dbSNP or dbVar/DGVa, as appropriate, and obtain an accession number for each variant. The results will be returned to you as outlined in the instructions.

Required information

The minimum information you need to report for each variant is:

  • The variant description in HGVS nomenclature, preferably using a LRG record as reference sequence. The NCBI Clinical remap tool can be used to convert the coordinates of your variants from other reference sequences to the LRG reference system. Mutalyzer and VariantValidator may be used to ensure that your HGVS expression is correct. Read http://www.HGVS.org/varnomen to learn more about HGVS guidelines.

  • The number of independent observations (defaults to one).

  • Whether the variant is somatic, germline or unknown.


We would encourage you to also submit the following information:

  • The type of phenotype ID (OMIM, MeSH, UMLS, HPO or SNOMED)

  • Phenotype ID value

  • Clinical interpretation of the level of pathogenicity associated with this variant

  • PubMed ID(s)

  • Local ID - the identifier your organization uses to uniquely identify this variant

  • OMIM allelic variant ID

  • The gender and ethnicity of the individuals in which this variant was identified

  • A URL that points to this variant on your organization’s website

  • Alternate designations or common names for this variant

  • The assay method that was used to identify this variant


Submission procedure

Below is a general outline of the submission procedure:

  1. Download and read the instructions for submission and the submission template so you understand the procedure and the steps involved.

  2. Fill in your submission data in the template.

  3. Request a “handle” from dbSNP and enter this in the submission template.

  4. Email the submission and “handle” to contact@lrg-sequence.org
    Alternatively, if the submission is large, request an upload account on our FTP server by sending an email to contact@lrg-sequence.org and upload the submission via FTP.

Any questions can be sent to contact@lrg-sequence.org as well.