Configuration

AlphaMissense (Bergquist et al. 2025 calibration)

AlphaMissense precomputed scores as calibrated for PP3/BP4 in Bergquist et al. 2025.

Overview

An explanatory profile has not yet been reviewed for this record.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

Evaluations and results

1 evaluation · 9 results. Different protocols are not a single leaderboard.

Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) · Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022)

In source order. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Evidence strength score interval (BP4 3 points, ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (BP4 Moderate, ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (BP4 Strong, ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (BP4 Supporting, ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (Indeterminate (0 points), ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (PP3 3 points, ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (PP3 Moderate, ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (PP3 Strong, ClinGen SVI calibration, points scale (Bergquist et al. 2025))	Evidence strength score interval (PP3 Supporting, ClinGen SVI calibration, points scale (Bergquist et al. 2025))
AlphaMissense (Bergquist et al. 2025 calibration)Evaluation	≤ 0.07	[0.071, 0.099]	-	[0.100, 0.169]	[0.170, 0.791]	[0.972, 0.989]	[0.906, 0.971]	≥ 0.99	[0.792, 0.905]

All 9 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: AlphaMissense (Bergquist et al. 2025 calibration)	Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022)	[0.170, 0.791] Evidence strength score interval (Indeterminate (0 points), ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'AlphaMissense', column 'Indeterminate (0)'
Configuration: AlphaMissense (Bergquist et al. 2025 calibration)	Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022)	[0.100, 0.169] Evidence strength score interval (BP4 Supporting, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'AlphaMissense', column 'Supporting (−1)'
Configuration: AlphaMissense (Bergquist et al. 2025 calibration)	Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022)	[0.071, 0.099] Evidence strength score interval (BP4 Moderate, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'AlphaMissense', column 'Moderate (−2)'
Configuration: AlphaMissense (Bergquist et al. 2025 calibration)	Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022)	≤ 0.07 Evidence strength score interval (BP4 3 points, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'AlphaMissense', column '(−3)'
Configuration: AlphaMissense (Bergquist et al. 2025 calibration)	Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022)	- Evidence strength score interval (BP4 Strong, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not applicable: Strength not reached Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'AlphaMissense', column 'Strong (−4)'
Configuration: AlphaMissense (Bergquist et al. 2025 calibration)	Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022)	[0.792, 0.905] Evidence strength score interval (PP3 Supporting, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'AlphaMissense', column 'Supporting (+1)'
Configuration: AlphaMissense (Bergquist et al. 2025 calibration)	Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022)	[0.906, 0.971] Evidence strength score interval (PP3 Moderate, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'AlphaMissense', column 'Moderate (+2)'
Configuration: AlphaMissense (Bergquist et al. 2025 calibration)	Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022)	[0.972, 0.989] Evidence strength score interval (PP3 3 points, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'AlphaMissense', column '(+3)'
Configuration: AlphaMissense (Bergquist et al. 2025 calibration)	Protocol: PP3/BP4 score intervals on the points scale (Bergquist et al. 2025 Table 1) Dataset: ClinVar 2019 calibration set (Pejaver et al. 2022)	≥ 0.99 Evidence strength score interval (PP3 Strong, ClinGen SVI calibration, points scale (Bergquist et al. 2025)) unitless · unknown Uncertainty: Not yet extracted: The main text prints no bounds for the thresholds; Figure 1 shows one-sided 95% bootstrap bounds as curves. The Supplementary Material PDF was not retrieved (PMC returned an HTML page on 2026-10-14). Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source AlphaMissense: points-scale PP3/BP4 score intervals (Bergquist et al. 2025) vep-uc-20261014-protocol-bergquist2025-point-intervals Aggregation: Not reported Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Table 1, row 'AlphaMissense', column 'Strong (+4)'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Use this configuration

How it works, versions and access

Strengths, limitations and unresolved questions

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.

0 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance

No evidence rows match these filters. Choose another scope or clear the search.

How to read the evidence

Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

Bergquist et al. 2025, Genet Med 27:101402 (PMC author manuscript) · Original source · PMC12208618, NIH author manuscript of Genet Med 2025;27(6):101402

Download this release (gzip)

Technical metadata and extraction receipts

Stable ID: vep-uc-20261014-config-bergquist2025-alphamissense

areas: dna-genomes
contexts: clinical_research
method types: supervised_machine_learning
reported name: AlphaMissense
configuration type: paper_evaluation
foundation model eligible: false
version: Precomputed AlphaMissense scores, mapped to the calibration variants by the authors' protocol (Supplementary Materials and Methods, not retrieved); release not stated in the main text
access reuse: Precomputed scores are freely and publicly available for all possible variants (Materials and Methods)
score training overlap: Only VARITY was explicitly trained on ClinVar; no extra filtering against training data was done (Materials and Methods)
source locator: Materials and Methods 'Selection of computational tools and data preparation'; Table 1
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; ai-assisted-source-review; method note: Checked against the Methods, table captions and author lists of the pinned sources.; note: Checked; see the dated review for rulings on origin and carried-over rows.

Related records

configuration of: AlphaMissense
system: AlphaMissense: points-scale PP3/BP4 score intervals (Bergquist et al. 2025)

Suggest a correction