Rare SNVs in GTEx WGS that create a GT or AG dinucleotide, labelled cryptic gains when matched RNA-seq shows a novel junction at the site only in carriers (and in more than one sample), or null when the gene is highly expressed, the variant is carried by at least ten individuals and no junction is seen.
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10 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Assay Short-read RNA-seq junctions from STAR alignments to a personalised diploid genome, reads from the variant-carrying haplotype Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Main 'Hierarchical model of RNA splicing' paragraph 3; Methods 'Variant effect benchmarks' (GTEx and GEL GT/AG); Fig. 1d; Acknowledgements Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Negatives 573967 Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Main 'Hierarchical model of RNA splicing' paragraph 3; Methods 'Variant effect benchmarks' (GTEx and GEL GT/AG); Fig. 1d; Acknowledgements Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Population 4,545 cryptic splice variants and 573,967 null variants; essential splice variants excluded Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Main 'Hierarchical model of RNA splicing' paragraph 3; Methods 'Variant effect benchmarks' (GTEx and GEL GT/AG); Fig. 1d; Acknowledgements Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Positives 4545 Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Main 'Hierarchical model of RNA splicing' paragraph 3; Methods 'Variant effect benchmarks' (GTEx and GEL GT/AG); Fig. 1d; Acknowledgements Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Reuse restrictions Controlled access: GTEx individual-level WGS and RNA-seq through dbGaP phs000424.v9.p2. The derived benchmark variant lists are not released with the paper (Data and code availability names only code, weights and precomputed scores). Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Main 'Hierarchical model of RNA splicing' paragraph 3; Methods 'Variant effect benchmarks' (GTEx and GEL GT/AG); Fig. 1d; Acknowledgements Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Source location Main 'Hierarchical model of RNA splicing' paragraph 3; Methods 'Variant effect benchmarks' (GTEx and GEL GT/AG); Fig. 1d; Acknowledgements Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Main 'Hierarchical model of RNA splicing' paragraph 3; Methods 'Variant effect benchmarks' (GTEx and GEL GT/AG); Fig. 1d; Acknowledgements Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Split No split; scored with pretrained models Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Main 'Hierarchical model of RNA splicing' paragraph 3; Methods 'Variant effect benchmarks' (GTEx and GEL GT/AG); Fig. 1d; Acknowledgements Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Version GTEx WGS and matched RNA-seq (dbGaP phs000424.v9.p2), as processed by the authors Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Main 'Hierarchical model of RNA splicing' paragraph 3; Methods 'Variant effect benchmarks' (GTEx and GEL GT/AG); Fig. 1d; Acknowledgements Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Description Rare SNVs in GTEx WGS that create a GT or AG dinucleotide, labelled cryptic gains when matched RNA-seq shows a novel junction at the site only in carriers (and in more than one sample), or null when the gene is highly expressed, the variant is carried by at least ten individuals and no junction is seen. Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Main 'Hierarchical model of RNA splicing' paragraph 3; Methods 'Variant effect benchmarks' (GTEx and GEL GT/AG); Fig. 1d; Acknowledgements Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
| Name GTEx rare GT/AG-creating SNVs with RNA-seq cryptic splicing labels (Jaganathan et al. 2026) Context-only references | A unified framework for quantitative splicing and transcript prediction (Jaganathan et al., bioRxiv 2026) Main 'Hierarchical model of RNA splicing' paragraph 3; Methods 'Variant effect benchmarks' (GTEx and GEL GT/AG); Fig. 1d; Acknowledgements Version: bioRxiv preprint version 1, posted 2026-10-11; full-text PDF (57 pages) | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of one retrieval of the bioRxiv PDF. bioRxiv stamps the PDF when serving it (XMP ModifyDate, MetadataDate, DocumentID, InstanceID, Info ModDate and the second trailer ID), so later retrievals differ. A reviewer retrieval on 2026-10-13 of the same length (2,679,664 bytes) had SHA-256 407f5884427dda0226e0ce1f022e4479d3ff2b243da18bcc691eb345b0e04a6a and ModDate D:20261013063115-07'00'; its bytes differ only in those fields and its pdftotext text layer is identical to the pinned copy. |
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Stable ID: rna-splicing-20261013-spliceai2-data-gtex-gtag