Genevieve also invites you to create or edit shared notes, to augment ClinVar data. These notes are edited and stored in the GenNotes server, and are public domain.
Sometimes the database information for a reported effect is confusing or clearly incorrect. It might lack important details (e.g. "recessive or dominant?"). There might be literature that's helpful to know about. Notes are a simple supplement that help improve information about a variant.
Notes also create consensus. Notes are unified: there should only be one note for an effect, and everyone can see and edit the same note.
Each note relates to a reported effect. If a single variant is reported to have different effects, these should be different notes.
Each note contains the following fields:
| Name |
The name of the disease or trait. (required)
This might be identical to the condition name a ClinVar record has reported. If there is no "name" for an effect, this should be a brief description (e.g. "blue or gray eyes"). |
|---|---|
| Category |
Disease (default), Trait, or Other The default is to classify a new effect as a "disease", but some effects are not considered diseases. In reports this note field isn't separately reported. It affects how the "name" field is displayed (i.e. as a "disease" or "trait"). |
| Inheritance |
Dominant, Recessive, Additive, or Unknown or Other (Default) A dominant effect impacts all carriers. A recessive effect only occurs when all copies of the gene are affected (e.g. if someone is "homozygous"). X-linked diseases should be classified as recessive. An "additive" effect impacts all carriers, but the effect is stronger when both copies of the gene are affected. |
| Significance |
Causal (default), Risk factor, or Protective The default ("causal") describes effects that are typically considered hereditary genetic diseases, i.e. "this variant causes this disease". If a reported effect is instead a small or moderate increased risk, it's a "risk factor". A reported effect that decreases risk is "protective". |
| Evidence |
Well-established, Reported (default), Contradicted This category describes the strength of evidence for this effect. All effects are, by default, "reported". If an effect is clearly not true, then it may be re-classified as "contradicted". On the other hand, if an effect is clearly validated through numerous publications or reporting sources, it may be re-classified as "well-established". |
| ClinVar records |
ClinVar records related to this reported effect. (optional) All ClinVar records for this variant that relate to this reported effect. |
| Notes |
Additional notes about the effect. (optional) A Markdown-formatted free text field to add more information. For effects re-classified as "well-established" or "contradicted", this section would typically contain an explanation for this re-classification. |
To edit notes on GenNotes:
After a note is created or edited in GenNotes, you can reload a Genevieve report to see the updated information. You can also find more information within GenNotes, including the username associated with an edit, and historic versions of a note (like a wiki).
Defaults values are good. If you're not sure what to pick, the default is a safe choice. Almost every field has a default value.
It's fine to skip the text notes. For example, you might just want to note whether a reported effect is dominant or recessive.