# ClinVar Genetic Variants Scraper — Variant Pathogenicity Data (`compute-edge/clinvar-genetic-variants-scraper`) Actor Extract genetic variants from NCBI ClinVar. Filter by gene and pathogenicity. Get clinical significance, associated conditions, protein change, molecular consequence, and GRCh38 coordinates as JSON or CSV. - **URL**: https://apify.com/compute-edge/clinvar-genetic-variants-scraper.md - **Developed by:** [Compute Edge](https://apify.com/compute-edge) (community) - **Categories:** Lead generation - **Stats:** 2 total users, 1 monthly users, 100.0% runs succeeded, 0 bookmarks - **User rating**: No ratings yet ## Pricing from $3.00 / 1,000 results This Actor is paid per event. You are not charged for the Apify platform usage, but only a fixed price for specific events. Learn more: https://docs.apify.com/platform/actors/running/actors-in-store#pay-per-event ## What's an Apify Actor? Actors are a software tools running on the Apify platform, for all kinds of web data extraction and automation use cases. In Batch mode, an Actor accepts a well-defined JSON input, performs an action which can take anything from a few seconds to a few hours, and optionally produces a well-defined JSON output, datasets with results, or files in key-value store. In Standby mode, an Actor provides a web server which can be used as a website, API, or an MCP server. Actors are written with capital "A". ## How to integrate an Actor? If asked about integration, you help developers integrate Actors into their projects. You adapt to their stack and deliver integrations that are safe, well-documented, and production-ready. The best way to integrate Actors is as follows. In JavaScript/TypeScript projects, use official [JavaScript/TypeScript client](https://docs.apify.com/api/client/js.md): ```bash npm install apify-client ``` In Python projects, use official [Python client library](https://docs.apify.com/api/client/python.md): ```bash pip install apify-client ``` In shell scripts, use [Apify CLI](https://docs.apify.com/cli/docs.md): ````bash # MacOS / Linux curl -fsSL https://apify.com/install-cli.sh | bash # Windows irm https://apify.com/install-cli.ps1 | iex ```bash In AI frameworks, you might use the [Apify MCP server](https://docs.apify.com/platform/integrations/mcp.md). If your project is in a different language, use the [REST API](https://docs.apify.com/api/v2.md). For usage examples, see the [API](#api) section below. For more details, see Apify documentation as [Markdown index](https://docs.apify.com/llms.txt) and [Markdown full-text](https://docs.apify.com/llms-full.txt). # README ## ClinVar Genetic Variants Scraper — Variant Pathogenicity API Extract **genetic variants** and their **clinical significance** from **NCBI ClinVar**, the NIH public archive of relationships between human genetic variation and health. ClinVar is the reference database used by clinical geneticists, diagnostic labs, and pharmacogenomics teams worldwide — this Actor turns it into clean **JSON, CSV, or Excel** without writing a single Entrez query. ### What you get Each record is one ClinVar variant with the fields that matter for interpretation: | Field | Description | |-------|-------------| | `accession` | ClinVar variation accession (e.g. `VCV004856269`) | | `gene` | Associated gene symbol (e.g. `BRCA1`, `TP53`) | | `variantTitle` | HGVS variant name (e.g. `NM_004656.4(BAP1):c.687C>G (p.Asn229Lys)`) | | `clinicalSignificance` | Germline classification — Pathogenic, Likely pathogenic, VUS, Benign, etc. | | `associatedConditions` | Disease / phenotype trait names linked to the variant | | `proteinChange` | Amino-acid change (e.g. `N229K`) | | `molecularConsequence` | Missense, nonsense, splice, intron variant, etc. | | `reviewStatus` | ClinVar review status / star rating context | | `lastEvaluated` | Date the classification was last evaluated | | `variantType` | SNV, deletion, duplication, etc. | | `chromosome`, `start`, `stop`, `assembly` | GRCh38 genomic coordinates | | `canonicalSPDI` | Canonical SPDI allele expression | | `clinvarUrl` | Direct link to the ClinVar variation page | ### Why this matters Variant interpretation is high-stakes and high-value: a single misclassified pathogenic variant can change a clinical decision. Use this Actor to: - **Build or refresh a variant knowledge base** for a clinical/diagnostic pipeline - **Audit a gene panel** (e.g. all pathogenic `BRCA1`/`BRCA2` variants) - **Power pharmacogenomics and research dashboards** with structured variant data - **Feed RAG / LLM agents** clean variant-condition relationships instead of raw XML ### How to scrape ClinVar genetic variants 1. Click **Try for free**. 2. Set your filters: - **Gene Symbol** — the gene to pull variants for (default `BRCA1`). - **Search Term** — optional advanced Entrez query, combined with the gene using `AND`. - **Pathogenic / Likely Pathogenic Only** — toggle to keep only actionable variants. - **Max Results** — cap the run, or `0` for every matching variant. 3. Click **Start**, then download as JSON, CSV, or Excel. #### Example input ```json { "geneSymbol": "TP53", "pathogenicOnly": true, "maxResults": 1000 } ```` #### Example output ```json { "accession": "VCV004856269", "gene": "BAP1", "variantTitle": "NM_004656.4(BAP1):c.687C>G (p.Asn229Lys)", "clinicalSignificance": "Likely pathogenic", "associatedConditions": "Tumor predisposition syndrome", "proteinChange": "N229K", "molecularConsequence": "missense variant; intron variant", "reviewStatus": "criteria provided, single submitter", "chromosome": "3", "start": "52406349", "assembly": "GRCh38", "clinvarUrl": "https://www.ncbi.nlm.nih.gov/clinvar/variation/4967194/" } ``` ### Pricing This Actor uses **pay-per-result** pricing — a few cents for hundreds of fully-structured variant records, plus standard Apify compute. The Actor paces its requests to respect NCBI's public E-utilities rate limits. ### FAQ **Where does the data come from?** The official NCBI E-utilities API over the `clinvar` database. Only public ClinVar records are returned. **How fresh is the data?** Live — each run queries NCBI directly, so newly submitted classifications appear immediately. **Can I query by disease instead of gene?** Yes — use the Search Term field with an Entrez clause like `breast cancer[disease]`. **Do I need an API key?** No. The Actor uses the public, key-free E-utilities endpoints and self-throttles to stay within NCBI's fair-use limits. ### Other Actors Building a genomics or clinical data pipeline? Pair this with our other FDA, drug-label, and clinical-trial scrapers on the Apify Store. ### Legal This Actor retrieves only **publicly available** variant data from NCBI ClinVar. It does not access personal or patient data and respects NCBI's rate limits. You are responsible for using the output in compliance with NCBI's usage policies and applicable law. # Actor input Schema ## `geneSymbol` (type: `string`): HGNC gene symbol to fetch variants for. Examples: 'BRCA1', 'TP53', 'CFTR', 'MLH1'. Leave blank to rely on Search Term instead. ## `searchTerm` (type: `string`): Advanced NCBI Entrez query for ClinVar (combined with the gene filter using AND). Example: 'breast cancer\[disease]'. Leave blank for none. ## `pathogenicOnly` (type: `boolean`): If enabled, only return variants classified as pathogenic or likely pathogenic. ## `maxResults` (type: `integer`): Maximum number of variant records to return. Set to 0 for unlimited (all matching variants). ## Actor input object example ```json { "geneSymbol": "BRCA1", "searchTerm": "", "pathogenicOnly": false, "maxResults": 500 } ``` # Actor output Schema ## `dataset` (type: `string`): No description # API You can run this Actor programmatically using our API. Below are code examples in JavaScript, Python, and CLI, as well as the OpenAPI specification and MCP server setup. ## JavaScript example ```javascript import { ApifyClient } from 'apify-client'; // Initialize the ApifyClient with your Apify API token // Replace the '' with your token const client = new ApifyClient({ token: '', }); // Prepare Actor input const input = { "geneSymbol": "BRCA1", "searchTerm": "", "maxResults": 500 }; // Run the Actor and wait for it to finish const run = await client.actor("compute-edge/clinvar-genetic-variants-scraper").call(input); // Fetch and print Actor results from the run's dataset (if any) console.log('Results from dataset'); console.log(`💾 Check your data here: https://console.apify.com/storage/datasets/${run.defaultDatasetId}`); const { items } = await client.dataset(run.defaultDatasetId).listItems(); items.forEach((item) => { console.dir(item); }); // 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/js/docs ``` ## Python example ```python from apify_client import ApifyClient # Initialize the ApifyClient with your Apify API token # Replace '' with your token. client = ApifyClient("") # Prepare the Actor input run_input = { "geneSymbol": "BRCA1", "searchTerm": "", "maxResults": 500, } # Run the Actor and wait for it to finish run = client.actor("compute-edge/clinvar-genetic-variants-scraper").call(run_input=run_input) # Fetch and print Actor results from the run's dataset (if there are any) print("💾 Check your data here: https://console.apify.com/storage/datasets/" + run["defaultDatasetId"]) for item in client.dataset(run["defaultDatasetId"]).iterate_items(): print(item) # 📚 Want to learn more 📖? Go to → https://docs.apify.com/api/client/python/docs/quick-start ``` ## CLI example ```bash echo '{ "geneSymbol": "BRCA1", "searchTerm": "", "maxResults": 500 }' | apify call compute-edge/clinvar-genetic-variants-scraper --silent --output-dataset ``` ## MCP server setup ```json { "mcpServers": { "apify": { "command": "npx", "args": [ "mcp-remote", "https://mcp.apify.com/?tools=compute-edge/clinvar-genetic-variants-scraper", "--header", "Authorization: Bearer " ] } } } ``` ## OpenAPI specification ```json { "openapi": "3.0.1", "info": { "title": "ClinVar Genetic Variants Scraper — Variant Pathogenicity Data", "description": "Extract genetic variants from NCBI ClinVar. Filter by gene and pathogenicity. Get clinical significance, associated conditions, protein change, molecular consequence, and GRCh38 coordinates as JSON or CSV.", "version": "0.1", "x-build-id": "ofvYsQHmzfULgIado" }, "servers": [ { "url": "https://api.apify.com/v2" } ], "paths": { "/acts/compute-edge~clinvar-genetic-variants-scraper/run-sync-get-dataset-items": { "post": { "operationId": "run-sync-get-dataset-items-compute-edge-clinvar-genetic-variants-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor, waits for its completion, and returns Actor's dataset items in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK" } } } }, "/acts/compute-edge~clinvar-genetic-variants-scraper/runs": { "post": { "operationId": "runs-sync-compute-edge-clinvar-genetic-variants-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor and returns information about the initiated run in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK", "content": { "application/json": { "schema": { "$ref": "#/components/schemas/runsResponseSchema" } } } } } } }, "/acts/compute-edge~clinvar-genetic-variants-scraper/run-sync": { "post": { "operationId": "run-sync-compute-edge-clinvar-genetic-variants-scraper", "x-openai-isConsequential": false, "summary": "Executes an Actor, waits for completion, and returns the OUTPUT from Key-value store in response.", "tags": [ "Run Actor" ], "requestBody": { "required": true, "content": { "application/json": { "schema": { "$ref": "#/components/schemas/inputSchema" } } } }, "parameters": [ { "name": "token", "in": "query", "required": true, "schema": { "type": "string" }, "description": "Enter your Apify token here" } ], "responses": { "200": { "description": "OK" } } } } }, "components": { "schemas": { "inputSchema": { "type": "object", "properties": { "geneSymbol": { "title": "Gene Symbol", "type": "string", "description": "HGNC gene symbol to fetch variants for. Examples: 'BRCA1', 'TP53', 'CFTR', 'MLH1'. Leave blank to rely on Search Term instead.", "default": "BRCA1" }, "searchTerm": { "title": "Search Term", "type": "string", "description": "Advanced NCBI Entrez query for ClinVar (combined with the gene filter using AND). Example: 'breast cancer[disease]'. Leave blank for none.", "default": "" }, "pathogenicOnly": { "title": "Pathogenic / Likely Pathogenic Only", "type": "boolean", "description": "If enabled, only return variants classified as pathogenic or likely pathogenic.", "default": false }, "maxResults": { "title": "Max Results", "minimum": 0, "maximum": 50000, "type": "integer", "description": "Maximum number of variant records to return. Set to 0 for unlimited (all matching variants).", "default": 500 } } }, "runsResponseSchema": { "type": "object", "properties": { "data": { "type": "object", "properties": { "id": { "type": "string" }, "actId": { "type": "string" }, "userId": { "type": "string" }, "startedAt": { "type": "string", "format": "date-time", "example": "2025-01-08T00:00:00.000Z" }, "finishedAt": { "type": "string", "format": "date-time", "example": "2025-01-08T00:00:00.000Z" }, "status": { "type": "string", "example": "READY" }, "meta": { "type": "object", "properties": { "origin": { "type": "string", "example": "API" }, "userAgent": { "type": "string" } } }, "stats": { "type": "object", "properties": { "inputBodyLen": { "type": "integer", "example": 2000 }, "rebootCount": { "type": "integer", "example": 0 }, "restartCount": { "type": "integer", "example": 0 }, "resurrectCount": { "type": "integer", "example": 0 }, "computeUnits": { "type": "integer", "example": 0 } } }, "options": { "type": "object", "properties": { "build": { "type": "string", "example": "latest" }, "timeoutSecs": { "type": "integer", "example": 300 }, "memoryMbytes": { "type": "integer", "example": 1024 }, "diskMbytes": { "type": "integer", "example": 2048 } } }, "buildId": { "type": "string" }, "defaultKeyValueStoreId": { "type": "string" }, "defaultDatasetId": { "type": "string" }, "defaultRequestQueueId": { "type": "string" }, "buildNumber": { "type": "string", "example": "1.0.0" }, "containerUrl": { "type": "string" }, "usage": { "type": "object", "properties": { "ACTOR_COMPUTE_UNITS": { "type": "integer", "example": 0 }, "DATASET_READS": { "type": "integer", "example": 0 }, "DATASET_WRITES": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_READS": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_WRITES": { "type": "integer", "example": 1 }, "KEY_VALUE_STORE_LISTS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_READS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_WRITES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_INTERNAL_GBYTES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_EXTERNAL_GBYTES": { "type": "integer", "example": 0 }, "PROXY_RESIDENTIAL_TRANSFER_GBYTES": { "type": "integer", "example": 0 }, "PROXY_SERPS": { "type": "integer", "example": 0 } } }, "usageTotalUsd": { "type": "number", "example": 0.00005 }, "usageUsd": { "type": "object", "properties": { "ACTOR_COMPUTE_UNITS": { "type": "integer", "example": 0 }, "DATASET_READS": { "type": "integer", "example": 0 }, "DATASET_WRITES": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_READS": { "type": "integer", "example": 0 }, "KEY_VALUE_STORE_WRITES": { "type": "number", "example": 0.00005 }, "KEY_VALUE_STORE_LISTS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_READS": { "type": "integer", "example": 0 }, "REQUEST_QUEUE_WRITES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_INTERNAL_GBYTES": { "type": "integer", "example": 0 }, "DATA_TRANSFER_EXTERNAL_GBYTES": { "type": "integer", "example": 0 }, "PROXY_RESIDENTIAL_TRANSFER_GBYTES": { "type": "integer", "example": 0 }, "PROXY_SERPS": { "type": "integer", "example": 0 } } } } } } } } } } ```