A Promethease alternative that does not take a marketplace upload
Promethease-style reports match consumer rsIDs to literature and ClinVar, then return a readable packet. Historically that meant uploading a 23andMe or Ancestry file to a marketplace or paying for a generated report.
genome.sh does the match on disk. Public identifier lookup can still use HTTPS. The genotype file never needs to leave the machine. Promethease-style reports can be rebuilt locally without a marketplace upload.
This is not affiliated with SNPedia or Promethease. It is not a literature dump of every GWAS hit unless you add that work. It is local annotation plus an optional printable template.
- Input: a consumer export or VCF that stays on disk
- Match: rsIDs to ClinVar, gnomAD, dbSNP, PharmGKB, AlphaMissense
- Output: terminal, JSON, or a private A4 PDF template
The job people actually want from a 23andMe file
Take an export of about 600,000 rows. Look up the rsIDs that were called. Get a report you can read. Do not send the file to a stranger.
Most ClinVar pathogenic variants are not on the chip. A clean local report is not a clinical exome. Missing sites stay not called, not wild type.
APOE, HFE, and a handful of PharmGKB tags are the rsIDs people type first. They are public ids. The letters next to them are not.
People also want a single PDF they can file. The A4 template in the CLI repo is that artifact. Fill it from JSON, not from a marketplace HTML dump you do not control.
Local match: CLI, browser importer, agent PDF
CLI path: cargo install genome-sh, genome db install standard, then query rsIDs or annotate a converted file. JSON is the form an agent should read.
Browser path: /import parses supported files in the tab. The HTTP API still only accepts identifiers. There is no upload endpoint to abuse.
Agent path: copy the DNA report prompt, copy the A4 template from the CLI repo, keep the file local. The agent runs genome query --format json on your machine and fills the HTML, then PDF.
cargo install genome-sh genome db install standard genome query rs1800562 genome query rs429358 --format json | jq . genome query rs334
What you get, and what a SNPedia-style dump still adds
You get public annotations for sites that were called. That includes ClinVar significance and review status, gnomAD frequency when the tier includes it, and PharmGKB when present.
You do not get a SNPedia sentence for every GWAS hit. You do not get a Promethease magnitude ranking. You do not get a clinical test.
If you need literature text, add it yourself from papers you are allowed to use. Do not scrape a marketplace. Do not pretend a CLI row is a magnitude score.
If you miss SNPedia prose, quote papers you have the right to quote, or link out. Do not scrape a marketplace you just decided not to upload to. The local tool is the lookup, not a bootleg of someone else's report language.
- Included: identifier lookup against the local snapshot
- Optional: printable report template in the CLI repository
- Not included: SNPedia dump, magnitude scores, clinical interpretation
Chip limits: not called is not wild type
A genotyping chip is not whole-genome sequencing and is not a complete BRCA test. Most pathogenic BRCA1 variants will not be on the array.
If rs1800562 is absent, write not called. If rs429358 is present and rs7412 is not, do not invent an APOE haplotype. If rs334 is missing, you did not test the sickle allele.
The PDF template is a structured report, not a dump of 600,000 rows. Status pills in the template are informational labels, not diagnoses.
genome query rs1800562 --format json genome query rs429358 --format json genome query rs7412 --format json grep -w rs334 23andme.txt || echo not called
Privacy compared with upload reports
An upload report sends the whole genotype table to someone else. Even if they promise deletion, you created a copy you do not control.
Local annotation never needs that copy. Identifier queries can still hit https://api.genome.sh for public rsIDs. That is the split Promethease-style products often blur.
Do not paste the raw file into a chatbot to skip the CLI. The homepage ships a prompt that forbids that. Use it.
A marketplace can still exist as a product you choose not to use. The comparison is the upload. genome.sh is the path that never needs that copy of your table.
How to start without an agent
Pick the rsIDs you care about, then query them and grep the file. Write not called where the row is missing. That is already a Promethease alternative for the questions people actually type.
If you want a PDF, copy the template and fill it by hand or with an agent on the same machine. Do not commit filled HTML. Do not email the export.
genome.sh prints public annotations. It is not a medical device and not affiliated with Promethease.
A first pass of rsIDs before you fill a PDF
Start with rs1800562, rs1799945, rs429358, rs7412, and rs334. Query the public records, grep the export, and write not called where needed. That pass already beats uploading the whole table to a stranger.
Add PharmGKB tags such as rs4244285 if you care about drug-gene annotations. Still not a prescription. Add BRCA1 only as a gene catalog plus a chip-limit sentence, never as a negative test.
If an agent fills the PDF, it must run genome query --format json on the same machine as the file. Copy the homepage prompt. Do not paste genotypes into the chat to save a step.
genome query rs1800562 rs1799945 rs429358 rs7412 rs334 --format json | jq . curl -s https://api.genome.sh/v1/query/rs1800562 | jq . grep -E 'rs1800562|rs429358|rs334' 23andme.txt || true
Questions
What is a good Promethease alternative in 2026?
A local lookup path. genome.sh matches consumer rsIDs to ClinVar on disk, without a marketplace upload. It is not affiliated with SNPedia or Promethease.
Is genome.sh affiliated with SNPedia or Promethease?
No.
Will the PDF list every 23andMe row?
No. The template is a structured report, not a dump of 600,000 rsIDs. Missing chip sites stay not called.
Do I have to use an AI agent?
No. Query by hand or annotate with the CLI. The agent is optional and must keep the file local.
Can I rebuild a Promethease-style report without uploading?
Yes. Keep the export on disk, run genome query or the in-browser importer, and fill a local template. Public rsIDs can still be looked up over HTTPS. Promethease-style reports can be rebuilt locally without a marketplace upload.
Will this find BRCA1 mutations in my 23andMe file?
Only sites that were called. A consumer chip is not a BRCA test. Most pathogenic BRCA1 variants are not on the array. Write not called for missing sites and do not title the PDF as BRCA-negative.
Does genome.sh store my DNA file?
No. The website importer does not upload. The CLI reads from disk. The HTTP API rejects genome files.
Is this medical advice?
No. Public annotations plus a chip file are not a clinical test.