ClinVar Annotations

Note

Important Update May 2025: Dear Community, We’d like to inform you of an upcoming change regarding the Genomics open datasets currently available through Azure. After careful consideration, we decided to shift our focus to new initiatives that will better serve our community and align with our long-term goals. As such, access to the Genomics open datasets on Azure will be deprecated in the coming months. We understand these datasets were valuable for research, development, and learning, and we deeply appreciate the contributions and engagement from our community over time. Thank you for your understanding and support.

The ClinVar resource is a freely accessible, public archive of reports - with supporting evidence - about the relationships among human variations and phenotypes. It facilitates access to and communication about the claimed relationships between human variation and observed health status, and about the history of that interpretation. It provides access to a broader set of clinical interpretations that researchers can incorporate into genomics workflows and applications.

Visit the Data Dictionary and the FAQ resource for more information about the data.

Note

Microsoft provides Azure Open Datasets on an “as is” basis. Microsoft makes no warranties, express or implied, guarantees or conditions with respect to your use of the datasets. To the extent permitted under your local law, Microsoft disclaims all liability for any damages or losses, including direct, consequential, special, indirect, incidental or punitive, resulting from your use of the datasets.

This dataset is provided under the original terms that Microsoft received source data. The dataset may include data sourced from Microsoft.

Data source

This dataset is a mirror of the National Library of Medicine ClinVar FTP resource. FTP resource

FTP Overview

Data update frequency

This dataset receives daily updates.

Storage location

This dataset is stored in the West US 2 and West Central US Azure regions. We recommend locating compute resources in West US 2 or West Central US for affinity.

Data Access

West US 2:"https://datasetclinvar.blob.core.windows.net/dataset'"

West Central US: "https://datasetclinvar-secondary.blob.core.windows.net/dataset"

Use Terms

Data is available without restrictions. More information and citation details, see Accessing and using data in ClinVar.

Contact

For any questions or feedback about this dataset, contact clinvar@ncbi.nlm.nih.gov.

Azure Notebooks

azure-storage

Getting the ClinVar data from Azure Open Dataset

Several public genomics data resources were uploaded as Azure Open Dataset at this resource.

Calling the data from 'ClinVar Data Set'

import azureml.core
print("Azure ML SDK Version: ", azureml.core.VERSION)

from azureml.core import  Dataset
reference_dataset = Dataset.File.from_files('https://datasetclinvar.blob.core.windows.net/dataset')
mount = reference_dataset.mount()

import os

REF_DIR = '/dataset'
path = mount.mount_point + REF_DIR

with mount:
    print(os.listdir(path))

import pandas as pd

# create mount context
mount.start()

# specify path to README file
REF_DIR = '/dataset'
metadata_filename = '{}/{}/{}'.format(mount.mount_point, REF_DIR, '_README')

# read README file
metadata = pd.read_table(metadata_filename)
metadata

Download the specific file

import os
import uuid
import sys
from azure.storage.blob import BlockBlobService, PublicAccess

blob_service_client = BlockBlobService(account_name='datasetclinvar', sas_token='sv=2019-02-02&se=2050-01-01T08%3A00%3A00Z&si=prod&sr=c&sig=qFPPwPba1RmBvaffkzkLuzabYU5dZstSTgMwxuLNME8%3D')     
blob_service_client.get_blob_to_path('dataset', 'ClinVarFullRelease_00-latest.xml.gz.md5', './ClinVarFullRelease_00-latest.xml.gz.md5')

Next steps

View the rest of the datasets in the Open Datasets catalog.