# gnomAD

许可证声明：宽松（CC0-1.0）；含受限部分；本站处理：只链接原出处。主体部分宽松，可分离的受限部分已逐部分记录。

- 能否商用：是 · 能否改编：是 · 能否再分发：是 · Mdexa 提供文件：否
- 许可证状态：宽松 (CC0-1.0)
- Mdexa 处理：只链接 — 许可证状态：宽松，按公开规则判定并经第二遍模型复核。仅链接。
- 最近核实：2026-11-13
- 信息卡：https://mdexa.com/zh/datasets/gnomad/

## 关键事实

- 领域：基因与组学
- 内容类型：结构化数据库
- 规模：—
- 语言：英文
- 模态：表格
- 发布方：The Broad Institute, Inc.
- 年份：—

## gnomAD 是否允许商业使用

- 商业使用：是。
整体结论取各部分中最严的一项；各部分许可不同，见下列。
- 许可状态：宽松，含有限制部分。
- 条件：保留声明、不得重新识别
- 许可部分：primary data from the gnomAD exomes and genomes — 宽松 (CC0-1.0)
- 许可部分：Screenshots of the website — 宽松 (NOASSERTION)
- 许可部分：SpliceAI annotations — 有限制 (CC-BY-NC-4.0)
结论仅记录来源所述，不构成法律意见。

## gnomAD 许可证证据

主体部分宽松，可分离的受限部分已逐部分记录

- **使用条款页**：在快照 s01（terms-page）中找到的声明 — "All data here are released openly and publicly for the benefit of the wider biomedical community." — https://gnomad.broadinstitute.org/terms (2026-11-13; 亲自打开)
- **使用条款页**：在快照 s01（terms-page）中找到的声明 — "There are absolutely no restrictions or embargoes on the publication of results derived from gnomAD data." — https://gnomad.broadinstitute.org/terms (2026-11-13; 亲自打开)
- **使用条款页**：在快照 s01（terms-page）中找到的声明 — "All users of gnomAD data agree to not attempt to reidentify participants." — https://gnomad.broadinstitute.org/terms (2026-11-13; 亲自打开)
- **使用条款页** — CC0-1.0：在快照 s01（terms-page）中找到的声明 — "The primary data from the gnomAD exomes and genomes are available free of restrictions under the Creative Commons Zero Public Domain Dedication." — https://gnomad.broadinstitute.org/terms (2026-11-13; 亲自打开)
- **使用条款页**：在快照 s01（terms-page）中找到的声明 — "Screenshots of the website may also be used without restriction." — https://gnomad.broadinstitute.org/terms (2026-11-13; 亲自打开)
- **使用条款页** — CC-BY-NC-4.0：在快照 s01（terms-page）中找到的声明 — "Some annotations may have restrictions on usage. For instance, SpliceAI annotations have been computed by Illumina and are provided with permission under a CC BY NC 4.0 license for academic and non-commercial use SpliceAI." — https://gnomad.broadinstitute.org/terms (2026-11-13; 亲自打开)
- **使用条款页**：在快照 s01（terms-page）中找到的声明 — "we ask that you refrain from incorporating "gnomAD" or "Genome Aggregation Database'' into the name of your tool and from using the gnomAD logo without permission." — https://gnomad.broadinstitute.org/terms (2026-11-13; 亲自打开)
- **使用条款页**：在快照 s01（terms-page）中找到的声明 — "gnomAD™ is a trademark owned by The Broad Institute, Inc." — https://gnomad.broadinstitute.org/terms (2026-11-13; 亲自打开)
- **使用条款页**：在快照 s01（terms-page）中找到的声明 — "It is the responsibility of users to abide by all relevant licensing requirements." — https://gnomad.broadinstitute.org/terms (2026-11-13; 亲自打开)
- **使用条款页**：在快照 s01（terms-page）中找到的声明 — "Some annotations may have restrictions on usage." — https://gnomad.broadinstitute.org/terms (2026-11-13; 亲自打开)
- **使用条款页**：在快照 s01（terms-page）中找到的声明 — "For instance, SpliceAI annotations have been computed by Illumina and are provided with permission under a CC BY NC 4.0 license for academic and non-commercial use SpliceAI." — https://gnomad.broadinstitute.org/terms (2026-11-13; 亲自打开)

## 来源与血缘

—

## gnomAD 已知问题

- 短读长测序数据的变异检出与过滤是不完美的概率过程，仍可能存在许多错误。

## 预检

未预检（数据未入库）。

## gnomAD 下载、接口与获取方式

Mdexa 站内不提供文件。原始出处：
- https://gnomad.broadinstitute.org/
- https://gnomad.broadinstitute.org/policies

### 取用配方

- 最新版本：4.1.1
- chr1 sites VCF (Google) · https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1.1/vcf/exomes/gnomad.exomes.v4.1.1.sites.chr1.vcf.bgz
- chr1 sites VCF (Amazon) · https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.1.1/vcf/exomes/gnomad.exomes.v4.1.1.sites.chr1.vcf.bgz
- chr1 sites VCF index (Google) · https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1.1/vcf/exomes/gnomad.exomes.v4.1.1.sites.chr1.vcf.bgz.tbi
- 批量下载：`gsutil ls gs://gcp-public-data--gnomad/release/`
- 批量下载：`aws s3 ls s3://gnomad-public-us-east-1/release/`

```sh
curl -L --create-dirs -o "gnomad.exomes.v4.1.1.sites.chr1.vcf.bgz" "https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1.1/vcf/exomes/gnomad.exomes.v4.1.1.sites.chr1.vcf.bgz"
curl -L --create-dirs -o "gnomad.exomes.v4.1.1.sites.chr1.vcf.bgz.tbi" "https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1.1/vcf/exomes/gnomad.exomes.v4.1.1.sites.chr1.vcf.bgz.tbi"
```

## gnomAD 引用格式

原始资料没有给出推荐引用文本。

## 机器可读

- JSON: https://mdexa.com/datasets/gnomad.json
- 2026-11-14 补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。
- 2026-11-14 实用卡字段（内容范围、标识符、取用方式、版本、已知缺陷）由自动流水线根据已存快照添加，每条陈述带逐字引文。
- 2026-11-14 补入来自所引来源（论文、发布说明、官方页面）的已知缺陷、版本说明与取用方式，每条标明出自谁、何时、来源类型。
- 2026-11-13 2026-11-13 上架。按公开规则判定，经二次核对后收录。 以下部分未能取到：gnomAD 条款页的后半部分（隐私政策草案、伦理政策、数据保存、数据生成、低频等位基因计数声明、论文引用）。结论依据已取到的前半部分，其中含 CC0 声明与分部分说明。

## 实用信息

### 内容范围

- v4 发布包含来自 807,162 个个体的数据。
  > Today, we are delighted to announce the release of gnomAD v4, which includes data from 807,162 total individuals.
  https://gnomad.broadinstitute.org/news/2023-11-gnomad-v4-0/ (2026-11-13)
- v4 数据集包含 730,947 个外显子组和 76,215 个全基因组的数据，均比对到 GRCh38 参考序列。
  > The gnomAD v4 data set contains data from 730,947 exomes and 76,215 whole genomes, all mapped to the GRCh38 reference sequence.
  https://gnomad.broadinstitute.org/downloads (2026-11-13)
- 合并过滤等位基因频率整合了 734,947 个外显子组和 76,215 个基因组的变异等位基因频率。
  > For the first time, in gnomAD v4.0, we released a combined filtering allele frequency (FAF), integrating variant allele frequencies across the 734,947 exomes and 76,215 genomes.
  https://gnomad.broadinstitute.org/news/2024-04-gnomad-v4-1/ (2026-11-13)
- v4.1 调用集包括 416,555 个 UK Biobank 外显子组和 314,392 个非 UK Biobank 外显子组。
  > The gnomAD v4.1 callset includes 416,555 UK Biobank and 314,392 non-UK Biobank exomes, requiring the use of two calling interval lists for processing and quality control pipelines.
  https://gnomad.broadinstitute.org/news/2024-04-gnomad-v4-1/ (2026-11-13)

### 标识符

- 页面给出 gnomAD v4.1 中写作 1-55039909-TC-T 的变异标识符。
  > This variant maps to 1-55039909-TC-T in gnomAD v4.1, where it still has an allele count of 1 (still present in only a single exome sample).
  https://gnomad.broadinstitute.org/news/2024-04-gnomad-v4-1/ (2026-11-13)
- 页面举例说明变异 1-55505582-TC-T 在 gnomAD v2.1.1 中仅存在于 v2.1.1 外显子组。
  > For example, 1-55505582-TC-T in gnomAD v2.1.1 is present only in the v2.1.1 exomes, and therefore the total AN at this site only contains information from the exomes.
  https://gnomad.broadinstitute.org/news/2024-04-gnomad-v4-1/ (2026-11-13)

### 取用方式

- 批量下载：https://gnomad.broadinstitute.org/downloads
- 数据库转储：https://gnomad.broadinstitute.org/downloads
- 仅网页界面：https://raw.githubusercontent.com/broadinstitute/gnomad-browser/main/browser/about/policies/terms.md

### 版本

- v4.1（2024-04-19）修正了 v4.0 的等位基因数问题，新增全部可检出位点的联合等位基因数及外显子组/基因组频率不一致标记。
  > This update fixes the allele number issue in gnomAD v4.0 previously described here and critically adds two new functionalities: joint allele number across all called sites in the exomes and genomes and a new flag indicating when the frequencies in the exomes and genomes are highly discordant.
  https://gnomad.broadinstitute.org/news/2024-04-gnomad-v4-1/ (2026-11-14)
- v4 发布采用增量发布模式，v4.0 为仅包含数据库最关键组件的最小可行产品（MVP）发布。
  > In the v4 release, we have moved towards the model of incremental releases. This means that the v4.0 release is a minimum viable product (MVP) release, or a release that contains only the most critical components of the gnomAD database.
  https://gnomad.broadinstitute.org/news/2023-11-gnomad-v4-0/ (2026-11-13)
- v4.0 发布不包含 v2 或 v3 发布的全部功能；这些功能将在后续次要版本中发布。
  > This means that the v4.0 release will not have all of the features of the v2 or v3 releases, and these features will be released in subsequent minor releases.
  https://gnomad.broadinstitute.org/news/2023-11-gnomad-v4-0/ (2026-11-13)
- gnomAD v3 发布有五个子集，而 gnomAD v4 只有一个子集（non-UKBB）。
  > The gnomAD v3 release had five subsets, whereas gnomAD v4 has a single subset (non-UKBB; see Dataset selection ).
  https://gnomad.broadinstitute.org/news/2023-11-gnomad-v4-0/ (2026-11-13)
- v4.1 更新修复了页面此前描述的 gnomAD v4.0 等位基因数问题。
  > This update fixes the allele number issue in gnomAD v4.0 previously described here
  https://gnomad.broadinstitute.org/news/2024-04-gnomad-v4-1/ (2026-11-13)
- v4 外显子组取消了队列子集（如非疾病子集），部分原因是生物银行样本缺乏表型元数据。
  > We have removed support for subsets from the gnomAD v4 exomes for two major reasons: given the large size of gnomAD v4 and the small size of any single cohort, we do not feel that the prevalence of any disease is high enough to warrant subsets.
  https://gnomad.broadinstitute.org/news/2023-11-gnomad-v4-0/ (2026-11-14)
- v3.1 基因组的变异被直接并入 v4，改称 v4 基因组。
  > Variants from the genomes in v3.1 were brought directly into v4 and are now labeled v4 genomes.
  https://raw.githubusercontent.com/broadinstitute/gnomad-browser/main/browser/help/topics/variant-qc.md (2026-11-14)

### 已知缺陷与常见误用

- 页面称短读长测序数据的变异调用和过滤是不完美且概率性的过程，因此无疑仍存在许多错误。
  > This data set has been subjected to extensive quality control, but variant calling and filtering from short-read sequencing data is an imperfect and probabilistic process, so many errors no doubt remain.
  https://gnomad.broadinstitute.org/policies (2026-11-13)
- 纳入 v4 的 76,156 个来自 v3.1.2 的基因组未更新质量控制，但已更新 HGDP/1KG 子集的部分频率。
  > The 76,156 genomes from gnomAD v3.1.2 have been included in gnomAD v4. We have not updated the quality control (QC) of these samples, but we have updated some of the frequencies within the HGDP and 1000 Genomes (HGDP/1KG) subset .
  https://gnomad.broadinstitute.org/news/2023-11-gnomad-v4-0/ (2026-11-13)
- 页面称合并数据集带来挑战，涉及测序和处理方法不同以及样本构成因抽样偏倚而变化的数据集。
  > However, it also introduces challenges related to integrating datasets that not only differ in their sequencing and processing methods, but also exhibit variations in sample composition due to ascertainment biases.
  https://gnomad.broadinstitute.org/news/2024-04-gnomad-v4-1/ (2026-11-13)
- 页面称插入缺失的频率估计通常较不稳定，可能因为 gnomAD 中的大多数插入缺失位于低复杂度区域或与片段重复重叠的区域。
  > In addition, indels generally tend to have less stable frequency estimates 1 , likely because most of the indels in gnomAD tend to occur in low-complexity regions or in regions overlapping a segmental duplication (see flags ).
  https://gnomad.broadinstitute.org/news/2024-04-gnomad-v4-1/ (2026-11-13)
- Gudmundsson 等：有近缘旁系同源基因、假基因或片段重复的基因可能存在短读长比对问题，会抬高观察到的变异数。
  > However, genes with highly similar paralogs, pseudogenes, or segmental duplications may have mapping challenges with short read data that can inflate observed variant counts.
  https://pmc.ncbi.nlm.nih.gov/articles/PMC9160216/ (2026-11-14)
- 等位基因计数为 0 或缺失可能表示无数据（如位于外显子捕获区外）、无替代等位基因检出或无高质量检出。
  > There are three reasons why a variant will have an allele count of 0 or an undefined (missing) allele count (indicated by `-`):
  https://raw.githubusercontent.com/broadinstitute/gnomad-browser/main/browser/help/topics/allele-count-zero.md (2026-11-14)

### 适合的任务

- 页面称用户可以自由下载和搜索数据，并鼓励使用和发表由这些数据产生的结果。
  > You can freely download and search the data, and we encourage the use and publication of results generated from these data.
  https://gnomad.broadinstitute.org/policies (2026-11-13)
- 页面称，在需要低延迟查询相对少量记录的场景中，按需使用 API 请求记录可能比使用下载的 gnomAD 数据更合适。
  > In use cases involving querying a relatively small number of records with low latency, using the API to request records as needed may be more suitable than working with downloaded gnomAD data.
  https://gnomad.broadinstitute.org/downloads (2026-11-13)
- 过滤等位基因频率（FAF）用于按疾病特定频率阈值过滤变异（如 ACMG/AMP BA1）；瓶颈人群（ami、asj、fin、rmi）不计算该指标。
  > This annotation can be used for filtering variants by allele frequency against a disease-specific threshold that can be set for each disease (e.g. BA1 in the 2015 ACMG/AMP guidelines).
  https://raw.githubusercontent.com/broadinstitute/gnomad-browser/main/browser/help/topics/faf.md (2026-11-14)

### 不适合的任务

- 页面称，鉴于 gnomAD v4 规模很大而任何单个队列规模很小，其认为任何疾病的患病率都不足以支持划分子集。
  > given the large size of gnomAD v4 and the small size of any single cohort, we do not feel that the prevalence of any disease is high enough to warrant subsets.
  https://gnomad.broadinstitute.org/news/2023-11-gnomad-v4-0/ (2026-11-13)
- 页面称，对于低延迟查询相对少量记录，使用下载的 gnomAD 数据可能不如使用 API 合适。
  > In use cases involving querying a relatively small number of records with low latency, using the API to request records as needed may be more suitable than working with downloaded gnomAD data.
  https://gnomad.broadinstitute.org/downloads (2026-11-13)

### 尚无有出处的说明

商业授权入口

## 在本库继续查找

本条目是 109 条已处理并核实的记录之一（数据集、数据资源与开源模型）。查找其他条目：调用 `https://mcp.mdexa.com/v1/datasets?q=<关键词>`，或连接 MCP 服务 `https://mcp.mdexa.com/mcp`；每分钟 20 次以内无需密钥。每行返回不到 1 KB；空结果即"数据库未收录"。核对一份清单：一次批量核对（免费账号）即返回报告。说明：/agents.md。相似条目：AlphaFold Protein Structure Database (https://mdexa.com/zh/datasets/alphafold-db/)；GEO (https://mdexa.com/zh/datasets/geo/)；ClinPGx/PharmGKB (https://mdexa.com/zh/datasets/pharmgkb/)。