> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/annotation/introduction/readme.md). # Welcome **Illumina Connected Annotations** is a software tool that provides translational research-grade variant annotation from AI models and traditional sources for genomic data. It annotates SNVs, MNVs, insertions, deletions, indels, STRs, gene fusions, and structural variants, including CNVs. You can run it as a standalone package or embed it in larger workflows. Inputs are VCF files. Outputs are structured JSON or optional VCF. JSON is the default and most complete output format. VCF output supports a reduced annotation set. Illumina Connected Annotations supports multi-allelic and multi-sample VCFs. It is developed under a rigorous software development lifecycle (SDLC) process with continuous validation against large baseline annotation sets. {% hint style="info" %} **Start here** * [Quick start guidance on Illumina Connected Annotations v3.27.](/annotation/v3.27/introduction/readme.md) {% endhint %} ### What does Illumina Connected Annotations annotate? Illumina Connected Annotations uses Sequence Ontology consequences to describe transcript impact.
Variant consequence overview

Transcript consequences are reported using Sequence Ontology terms.

### Software Download Please visit [Illumina Connected Annotations](https://developer.illumina.com/illumina-connected-annotations). ### Reference genome support Illumina Connected Annotations supports `GRCh37.p13` and `GRCh38.p14`. We recommend using `GRCh38.p14` for any new work. See specific versioned user guides for details on supported reference genomes. ### Supplementary annotations Illumina Connected Annotations adds external data sources for variant and gene context. Content is available in two tiers: * **Basic** — available without a premium license * **Professional** — requires a license For licensing details, see [Licensed Content](/annotation/v3.27/introduction/licensedcontent.md). For access, contact `annotation_support@illumina.com`.
Data SourceAvailabilityLatest Supported Version (v3.27)
COSMICProfessional102
OMIMProfessional20250815
✨ PrimateAI-3DProfessional1.0
✨ PromoterAIProfessional1.0
✨ SpliceAIProfessional1.3
1000 Genomes ProjectBasicPhase 3 v3plus
ABraOMBasicSABE-WGS-1171
AlphaMissenseBasic1.0
Amino Acid ConservationBasic1.0
Cancer HotspotsBasic2017
ClinGenBasic20250815
ClinVarBasic20250806
ClinVar PreviewBasic20250601
DANNBasic20200205
dbSNPBasic156
DECIPHERBasic201509
FusionCatcherBasic1.33
GERPBasic20110522
GME VariomeBasic20160618
gnomADBasic

GRCh37 - v2.1

GRCh38 - v4.1

Mitochondrial HeteroplasmyBasic20180410
MITOMAPBasic20200819
MultiZ 100 WayBasic20171006
PhyloP PrimateBasic1.0
REVELBasic20200205
TOPMedBasicfreeze 5
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