Variant Annotator — ClinVar, gnomAD & Predictor Evidence Card
Look up a variant by rsID, chrom:pos:ref:alt, or HGVS and get its ClinVar significance, gnomAD allele frequencies, and CADD/SIFT/PolyPhen2/REVEL scores in one card.
🌐 Sends the variant you enter to MyVariant.info's API to look up ClinVar/gnomAD/predictor data (and to Ensembl's API when bridging a transcript "c." description) — not processed on SeqBench's own server
Paste a variant in whatever notation you have on hand — an rsID, chrom:pos:ref:alt, genomic HGVS ("g."), or a transcript HGVS ("c.") description that gets bridged to genomic coordinates automatically via the HGVS Converter — and get back a single evidence card: ClinVar's clinical significance and submitted conditions, gnomAD exome and genome allele frequencies (overall and per-population), and CADD, SIFT, PolyPhen2 and REVEL pathogenicity predictor scores, all resolved from MyVariant.info in one call. A multi-allelic rsID returns every matching variant rather than silently picking one, and every section says plainly when a source has no data instead of leaving a blank.
rsID, chrom:pos:ref:alt, genomic HGVS (g.), or transcript HGVS (c. — bridged to genomic coordinates automatically).
How to use the Variant Annotator tool
- 1Paste a variant — an rsID ("rs1042522"), chrom:pos:ref:alt ("17:7676154:G:C"), genomic HGVS ("chr17:g.7676154G>C"), or transcript HGVS c. ("NM_000546.6:c.215C>G") — or load an example.
- 2Pick hg19 or hg38 (MyVariant.info's native default is hg19; transcript c. input is always bridged via hg38 regardless of this choice).
- 3Review the ClinVar significance, gnomAD frequencies, and CADD/SIFT/PolyPhen2/REVEL scores — and check the data-freshness caveats at the bottom, since gnomAD, CADD and ClinVar are each frozen snapshots, not live feeds.
Frequently asked questions
What variant formats are accepted?
An rsID ("rs1042522"), chrom:pos:ref:alt for a simple single-base substitution ("17:7676154:G:C"), genomic HGVS ("chr17:g.7676154G>C" or "17:g.7676154G>C"), or transcript HGVS c. ("NM_000546.6:c.215C>G" or "TP53:c.215C>G") — the last is resolved to genomic coordinates first via the same live-Ensembl pipeline behind the HGVS Converter tool. Multi-base indels given as chrom:pos:ref:alt are refused rather than guessed at, since del/ins/delins need proper HGVS notation to describe unambiguously.
Why does a section say "no data"?
ClinVar, gnomAD exome, gnomAD genome and the predictor scores (CADD/SIFT/PolyPhen2/REVEL) are each independent fields on MyVariant.info's record — plenty of real variants simply have no ClinVar submission, or fall outside gnomAD's exome/genome capture regions, or predate a predictor's own training set. A missing section is reported explicitly rather than omitted, so it's never ambiguous whether the tool looked and found nothing versus didn't look at all.
How current is the underlying data?
Not live. As surfaced in every result's caveats: gnomAD frequencies are frozen at v2.1.1 (downloaded 2019-05-20, an older and smaller cohort than gnomAD's current release), CADD scores are frozen at a 2019-07-25 upload, and ClinVar is a periodic snapshot (dated 2025-05 as of this writing) — recent ClinVar submissions in particular may be missing. Treat this as a fast first-pass check, not a substitute for querying ClinVar/gnomAD directly for anything clinically actionable.
Is my input stored, and can I use this from code?
The variant you enter is sent to MyVariant.info (and, for transcript "c." input, to Ensembl's REST API to resolve genomic coordinates first); nothing is stored by SeqBench. The same stateless variant_annotate tool is available via the REST API and the MCP server.
Related tools
Type or paste a sequence and edit it directly — every feature remaps live as you insert, delete, or replace bases, with undo/redo and GenBank import/export.
Per-base quality, GC and length distributions, duplication levels, overrepresented sequences and adapter content, each with a warn/fail verdict.
Align several DNA or protein sequences and view a colored alignment with a consensus.