Baseshift for Academic Medical Centers & NIH-Funded Genomics Programs

What Baseshift Does

Baseshift is a cloud-based genomic variant analysis pipeline that turns raw sequencing output into an annotated, classification-ready clinical report — without staffing a bioinformatics team.

• VCF → clinical report in ~2 minutes. Upload a VCF or VCF.GZ; Baseshift parses, normalizes, and annotates every variant against ClinVar, gnomAD v4, and OMIM in real time.
• Automated ACMG/AMP classification. Every variant is scored under ACMG/AMP rules (PVS1, PS1–PS4, PM1–PM6, PP1–PP5, BA1/BS1–BS4) — verdicts stored per-variant and surfaced in the report.
• Clinical-grade PDF output. Downloadable report includes HGVS notation, zygosity, gnomAD allele frequency (color-coded), pathogenicity verdict, and interpretation narrative.

For per-variant-call pricing and SLA tiers, see the Baseshift pricing overview. For a technical walkthrough of annotation sources and ACMG classification, see the annotation pipeline overview.

NIH & HECVAT Compliance Posture

Designed to clear NIH and university procurement review on first pass. Detailed mappings are linked below.

Need deeper answers on data residency, PHI handling, NIH GDS, BAA terms, IRBs/DUAs, exit clauses, or the pilot → paid path? See the Baseshift FAQ.

HIPAA-Covered PHI Handling

Baseshift is engineered for covered-entity and hybrid-entity workflows. The Institution is responsible for de-identifying uploads per HIPAA §164.514 prior to submission (no names, DOBs, MRNs, SSNs, or geographic data smaller than state in VCF headers, BAM RG tags, or filenames). Once de-identified on the Institution side, Baseshift maintains additional technical controls: the AI annotation pipeline transmits only variant coordinates, alleles, gene symbols, and computed annotation fields — no patient identifiers of any kind leave the de-identified dataset. A Business Associate Agreement is available on request; the Genomic Data Use Agreement Addendum (template) commits to 72-hour breach notification, written subprocessor disclosure, and 90-day post-delivery retention with secure deletion on request. Email sales@baseshift.io for a BAA.

Sequencer & Pipeline Integrations

Works with the platforms your genomics core is already running. Standard VCF/VCF.GZ ingest — no platform-specific configuration required.