Variant annotation & evidence
Functional, population, and clinical annotation of each variant, assembling the evidence needed to interpret it.
Core Bioinformatics
Biomarker & Variant Interpretation
From a variant list to a defensible interpretation. We annotate, gather evidence, and classify variants—germline under ACMG/AMP, somatic by clinical-actionability tier—then prioritise against your phenotype or biomarker question, and hand back documented tables and figures for research and clinical research.
VCF · raw reads in
Classified · tiered · prioritized out
Typical turnaround 3–7 days
Individual pricing from $149
Illustrative sample output
Pathogenic
VUS
Benign
Overview
Rigorous interpretation, without the in-house curation overhead
Variant interpretation turns a long list of calls into a short list of answers—which variants matter, how confident we are, and why. The hard part is rarely running a single tool; it is assembling the population, clinical, computational, and phenotype evidence for each variant, applying a recognised framework consistently, and documenting every criterion so the classification is defensible and reproducible.
We build and run that workflow for you. Working from your called variants, we annotate against curated knowledge bases, classify germline variants under ACMG/AMP and somatic variants by actionability tier, and prioritise toward your biological or biomarker question—using established, peer-reviewed tools and returning results with every tool and database version recorded. This is research and clinical-research support, not a diagnostic service—final clinical reporting stays with your accredited lab.
Capabilities
What we analyse
One service spanning interpretation end to end—from annotation and evidence to classification, prioritization, and biomarker reporting.
ACMG/AMP germline classification
Systematic five-tier classification (pathogenic to benign) with each ACMG/AMP evidence criterion applied and documented.
Somatic tier classification
Tumor-variant tiering by clinical actionability under AMP/ASCO/CAP, linked to therapies, trials, and cancer knowledge bases.
Phenotype-driven prioritization
Ranking candidate variants against patient phenotype (HPO terms) to surface the most likely causal ones.
CNV & SV interpretation
Interpretation of copy-number and structural variants under ACMG/ClinGen CNV guidance, annotated to affected genes.
ctDNA & liquid biopsy
Error-corrected, UMI-aware detection and interpretation of low-frequency variants for tumor profiling and residual-disease research.
Pharmacogenomics
Star-allele calling and drug–gene interpretation to connect genotype to medication response in a research context.
Biomarker discovery & reporting
An evidence-documented shortlist of candidate biomarkers for your question, with clear tables and a reviewable report.
The Pipeline
How a variant interpretation runs
A transparent, best-practice sequence—each variant's evidence assembled and each call documented in the final report. Nothing is a black box.
Steps are adapted to your case: germline vs. somatic, panel vs. exome vs. genome, tissue vs. ctDNA, phenotype-led vs. biomarker-led. We confirm the plan with you before any compute begins.
Intake & QC
We take your called variants (VCF), normalise and left-align them, and check quality—or call variants first from raw reads.
Tools: bcftools · vt · VCF QC
Annotation
Each variant is annotated for consequence, population frequency, and known clinical significance.
Tools: VEP · ANNOVAR · SnpEff
Evidence gathering
Population, clinical, computational, and splicing evidence is assembled per variant from curated resources.
Sources: ClinVar · gnomAD · AlphaMissense · SpliceAI
Classification & tiering
Germline variants are classified under ACMG/AMP; somatic variants tiered by actionability—each criterion recorded.
Tools: InterVar · OncoKB · CIViC
Phenotype prioritization
Candidates are ranked against your phenotype (HPO) or biomarker question to surface the most relevant.
Tools: Exomiser · Phen2Gene · HPO
Review & research reporting
A documented, evidence-linked shortlist is compiled for your team's review—research and clinical-research use, not a diagnosis.
Outputs: classified table · evidence · rationale
Delivery
Classified tables, prioritised shortlist, figures, and reproducible methods with every tool and database version.
Tools: R / ggplot2 · versioned methods manifest
Tools & Technologies
Established, peer-reviewed tools—matched to your data
We select from the field's standard toolkit rather than forcing every dataset through one pipeline. A representative set of what we work with:
Annotation
VEP
ANNOVAR
SnpEff
bcftools
dbNSFP
Germline classification
InterVar
VarSome
Franklin
TAPES
CharGer
Somatic / cancer interpretation
OncoKB
CIViC
PCGR
Cancer Genome Interpreter
COSMIC
Computational predictors
AlphaMissense
REVEL
CADD
SIFT
PolyPhen-2
SpliceAI
Phenotype prioritization
Exomiser
Phen2Gene
LIRICAL
HPO
ctDNA / liquid biopsy
fgbio
UMI-tools
VarDict
smCounter2
Pharmacogenomics
PharmCAT
PharmGKB
CPIC
Stargazer
Reporting & review
R / ggplot2
IGV
cBioPortal
MultiQC
Reference Resources
Public knowledge behind every call
A classification is only as good as the evidence behind it. We build on the community's authoritative, versioned knowledge bases.
- ClinVar
- Aggregated clinical significance of variants with review status.
- gnomAD
- Population allele frequencies for assessing rarity and filtering.
- COSMIC
- Catalogue of somatic mutations in cancer for tumour interpretation.
- OncoKB
- Precision-oncology knowledge base linking variants to therapies.
- CIViC
- Open, expert-curated clinical interpretations of cancer variants.
- HPO
- Human Phenotype Ontology for phenotype-driven prioritization.
- OMIM
- Curated gene–disease relationships for Mendelian conditions.
- PharmGKB
- Pharmacogenomic knowledge linking genotype to drug response.
- dbNSFP
- Aggregated functional predictions and conservation scores.
Choosing a Framework
Germline vs. somatic vs. pharmacogenomic
Different questions call for different interpretation frameworks. A quick orientation; we will help you decide.
| Dimension | Germline | Somatic | Pharmacogenomic |
|---|---|---|---|
| Framework | ACMG/AMP five-tier | AMP/ASCO/CAP tiers I–IV | CPIC / PharmGKB levels |
| Question | Is this variant disease-causing? | Is this variant actionable in this tumour? | How may genotype affect drug response? |
| Key evidence | Population, functional, segregation | Therapy, trial, prognostic knowledge | Star alleles & drug–gene guidelines |
| Typical output | Pathogenic → benign call | Tiered, therapy-linked variants | Metaboliser status & flags |
| Best suited to | Rare / inherited disease research | Oncology & tumour profiling | Drug-response research |
What You Receive
A complete, documented deliverable
Not just a spreadsheet of variants dropped in a folder—every output you need to review, act on, and reproduce the interpretation.
- Annotated variant table with all evidence fields
- ACMG/AMP classifications with the criteria applied
- Somatic tier assignments linked to knowledge bases
- Prioritized candidate shortlist for your question (TSV / XLSX)
- Phenotype-match ranking, where applicable
- Clear figures (lollipop plots, evidence summaries)
- Reproducible methods with tool & database versions
Built for reproducibility, not just a result
Every interpretation follows documented best practices—each ACMG/AMP criterion or somatic tier recorded with the evidence behind it, against pinned database versions—so a classification is transparent and defensible rather than a black-box label. This is research and clinical-research support that your team reviews; it is not a clinical diagnostic service and not a medical diagnosis, and final clinical reporting remains with an accredited laboratory and qualified professionals.
The practical payoff: your methods section writes itself, a reviewer can re-run the analysis, and a result from today can be reproduced a year from now. We will also tell you honestly when a design or sample size won't support the conclusion you're after.
FAQ
Variant interpretation questions
What researchers and project leads most often ask before starting an interpretation project.
A called variant file (VCF) from your genomics pipeline — or we can call variants first from your raw reads. We annotate, gather evidence, and classify from there, and can work with germline, somatic, panel, exome, or genome data.
Yes. For germline variants we apply the ACMG/AMP classification framework and its evidence criteria; for somatic variants we use AMP/ASCO/CAP tiering. We document which criteria were applied and the evidence behind each call.
Germline interpretation classifies inherited variants (pathogenic to benign) under ACMG/AMP; somatic interpretation tiers tumor variants by clinical actionability under AMP/ASCO/CAP, drawing on cancer knowledge bases like OncoKB and CIViC. We handle both.
Yes. We run error-corrected, UMI-aware workflows for low-frequency variant detection from ctDNA, suitable for tumor profiling and residual-disease research, and interpret the resulting variants.
No. We provide research and clinical-research bioinformatics support — annotation, classification, and prioritization that your team reviews. We are not a clinical diagnostic laboratory, and results are not a medical diagnosis; clinical reporting stays with an accredited lab and qualified professionals.
Annotated, classified variant tables with the evidence and criteria behind each call, a prioritized shortlist for your question, phenotype-matched candidates where applicable, clear figures, and reproducible methods with every tool and database version recorded.
Related
Where interpretation fits
Have variants that need interpreting?
Tell us your organism, data type, and question—we'll scope it honestly, including if a different design would serve you better.