Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript)
PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 · Peer-reviewed
What this source contributed
Records in this release that cite this source. A record can cite several sources.
Results
Values as the source printed them. Compare results only under compatible protocols, datasets and metrics.
Claims
Statements this source supports, each with where in the source it was checked.
- Relevance of vep-uc-20261014-protocol-bergquist2025-point-intervals to use-case-missense-pp3-bp4-calibrated-evidence: Assessed by PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) (vep-uc-20261014-source-bergquist2025: Table 1 and caption; Materials and Methods; Results; vep-uc-20261014-source-tejura2024: Summary)
Models, benchmarks and other records
Configurations (3)
Benchmarks (1)
Protocols (1)
Evaluations (7)
- AlphaMissense: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)
- BayesDel: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)
- ESM1b: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)
- MutPred2: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)
- REVEL: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)
- VARITY_R: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)
- VEST4: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)
Use cases (1)
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
27 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.artifact_sha256 4fe954451167b5a5717a4c37f4054432e1f02fb59862d0fb909edb525e6bb8e2 Source metadata | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) No field-specific location recorded Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
| Doi 10.1016/j.gim.2025.101402 Source metadata | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) No field-specific location recorded Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
| Hash scope artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. Source metadata | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) No field-specific location recorded Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
| Licence NIH author manuscript in PMC; publisher copyright, no open licence stated Source metadata | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) No field-specific location recorded Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
Limitations2 values
| Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) No field-specific location recorded Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
| Media type text/html Source metadata | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) No field-specific location recorded Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
| Publication status peer_reviewed Source metadata | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) No field-specific location recorded Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
| Retrieved at 2026-10-14T14:44:51Z Source metadata | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) No field-specific location recorded Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
| attributes.review.artifact_sha256 4fe954451167b5a5717a4c37f4054432e1f02fb59862d0fb909edb525e6bb8e2 Source metadata | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) No field-specific location recorded Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
| Review: method note Re-downloaded on 2026-10-14 and matched the pinned SHA-256 (PMC pages after blanking the ncbi_phid and csrfmiddlewaretoken values, checked by an independent normaliser). Source metadata | Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) No field-specific location recorded Version: PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402 | catalogued No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4. |
Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
Calibration of AlphaMissense, ESM1b and VARITY_R (EVE attempted) for ACMG/AMP PP3 and BP4 with the Pejaver et al. 2022 data and method, and point-based score intervals for BayesDel, MutPred2, REVEL and VEST4.
Technical metadata and extraction receipts
Stable ID: vep-uc-20261014-source-bergquist2025
- areas
- dna-genomes
- contexts
- clinical_research
- url
- https://pmc.ncbi.nlm.nih.gov/articles/PMC12208618/
- version
- PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402
- retrieved at
- 2026-10-14T14:44:51Z
- artifact sha256
- 4fe954451167b5a5717a4c37f4054432e1f02fb59862d0fb909edb525e6bb8e2
- publication status
- peer_reviewed
- licence
- NIH author manuscript in PMC; publisher copyright, no open licence stated
- source locator
- Abstract; Materials and Methods; Results; Table 1 and caption
- doi
- 10.1016/j.gim.2025.101402
- media type
- text/html
- hash scope
- artifact_sha256 is the SHA-256 of the retrieved page with the two per-request tokens blanked (the content of <meta name="ncbi_phid"> and the csrfmiddlewaretoken value), computed by data/omics/vep-use-cases-20261014/extract/pmc_html.py. The page is a mutable website: this hash describes the retrievals of 2026-10-14 (the collector's, and two by the reviewer, gave the same normalised hash); a later change to the page would change it. The raw bytes of the 2026-10-14 retrieval hashed to 214864e7b556fcd7f8344a328a5b42ab5c334703de96063e130406ebe304c2d4.
- limitations
- Author manuscript, not the publisher's version of record.; EVE thresholds are given in the text, but the authors do not recommend them because EVE scored only about half of the benign variants (Results); they are not extracted.
- review
- reviewer: claude; reviewer note: Claude review agent; no human review claimed. Independent Claude (Opus 5.5) review agent, separate from the extraction agent that built this batch. Automated review only. Transcription, not reproduction.; reviewed at: 2026-10-14T16:00:00Z; artifact sha256: 4fe954451167b5a5717a4c37f4054432e1f02fb59862d0fb909edb525e6bb8e2; retrieval url: https://pmc.ncbi.nlm.nih.gov/articles/PMC12208618/; method: source-hash-verification; method note: Re-downloaded on 2026-10-14 and matched the pinned SHA-256 (PMC pages after blanking the ncbi_phid and csrfmiddlewaretoken values, checked by an independent normaliser).; note: Hash matches.