Predict what a variant does,
per transcript, with scores.
The Variant Effect Predictor tells you the consequence of a change — missense, stop-gained, splice — for every affected transcript, with SIFT and PolyPhen impact scores. vep_consequences takes an rsID or HGVS and returns it all, pinned to source. Research use only.
What the instrument does
Ensembl VEP annotates a variant with its predicted molecular consequences across all overlapping transcripts, the most severe consequence, and pathogenicity predictions from SIFT and PolyPhen.
On the console, vep_consequences accepts an rsID or HGVS notation and returns per-transcript consequence terms, impact levels, and SIFT/PolyPhen scores — a prediction, clearly labelled as such.
Tools this powers on the console
vep_consequences
Research use only. Service names belong to their owners; no partnership or endorsement is implied.
How Perslis integrates Ensembl VEP
VEP is prediction, and the console keeps that boundary sharp. It returns SIFT and PolyPhen scores as computed estimates, distinct from ClinVar's expert clinical classification — an agent sees the algorithmic call and the curated call as two different kinds of evidence, never merged into one confident verdict.
Keyed to the same coordinates as dbSNP and Ensembl, VEP completes the variant triangle: dbSNP says the variant exists, VEP predicts its effect, ClinVar reports what clinicians concluded. Every call is stamped research use only.
Ask
One question at the console — no per-service query language, no tab-hopping.
Route
Lois calls this instrument alongside the others and gathers what returns.
Pin
Every field keeps its source: database, accession, URL. A result that cannot name its source is refused by construction.
Admit
The PEEL gate decides what enters the lab record. Reported values stay verbatim; unsupported claims stay out.
A real, source-pinned result
Pulled live from the service and pinned to its identifier — the same contract every answer on the console is held to.
| Most severe consequence | missense_variant |
|---|---|
| Gene / transcript | F5 · ENST00000367796 |
| Impact | MODERATE |
| SIFT | deleterious (0) |
| PolyPhen | probably_damaging (0.936) |
| Assembly | GRCh38 · 1:169,549,811 |
Source: ensembl vep · rs6025 · retrieved 2026-09-18 · research use only
Why route VEP through one console
Consequence, callable
An agent predicts a variant's effect per transcript from an rsID — no VEP web form.
Prediction kept separate
SIFT/PolyPhen scores stay distinct from ClinVar's clinical classification — two kinds of evidence, not one.
Labelled research-use
Every result is stamped research use only, so a prediction is never mistaken for medical advice.
Instruments VEP talks to
A variant has three questions. VEP predicts effect beside dbSNP's record and ClinVar's clinical read.
