ClinGen Allele Registry — Cross-Database ID Mapping
Usage
Tool Description
Query ClinGen Allele Registry by rsID to get cross-database identifiers.
Maps variant to IDs in ClinVar, gnomAD, COSMIC, UniProtKB, OMIM, etc.
API: GET https://reg.genome.network/alleles?dbSNP.rs={rs_id}
Headers: Accept: application/json
Note: May return multiple alleles (multi-allelic sites); filter out synonymous (reference) alleles.
Args:
rs_id (str): dbSNP rsID (e.g. "rs7412")
Return:
CA ID (canonical allele), and cross-references to ClinVar (alleleId, variationId, RCVs),
gnomAD, COSMIC, UniProtKB, OMIM and other databases.
Return Fields Explanation:
- CA ID: ClinGen 统一分配的等位基因标准标识符 (e.g. CA127498)
- communityStandardTitle: HGVS 标准命名 (e.g. NM_000041.2(APOE):c.526C>T (p.Arg176Cys))
- ClinVarAlleles.alleleId: ClinVar 等位基因内部编号
- ClinVarAlleles.preferredName: ClinVar 的 HGVS 标准命名（转录本:cDNA变化 + 蛋白变化）
- ClinVarVariations.variationId: ClinVar 变异条目编号 (= VCV 编号，如 17848 对应 VCV000017848)
- ClinVarVariations.RCV: 临床评估记录列表，每个 RCV 代表一个独立机构对该变异的临床解读提交
- COSMIC: COSMIC 肿瘤体细胞变异数据库 ID
- gnomAD_2/3/4: 各版本 gnomAD 中的 chr-pos-ref-alt 格式 ID
- ExAC: ExAC（旧版人群频率数据库）中的变异 ID
- MyVariantInfo_hg19/hg38: MyVariant.info API 使用的 HGVS genomic 格式
- dbSNP.rs: 对应的 dbSNP rsID 编号
Query Example
import requests, json
rs_id = "rs7412"
url = f"https://reg.genome.network/alleles?dbSNP.rs={rs_id}"
resp = requests.get(url, headers={"Accept": "application/json"}, timeout=30).json()
if not isinstance(resp, list):
resp = [resp]
print(f"[ClinGen] {rs_id} 对应 {len(resp)} 个等位基因")
for i, allele in enumerate(resp):
ca_id = allele.get("@id", "").split("/")[-1] # e.g. CA127498
titles = allele.get("communityStandardTitle", [])
# 跳过同义变异（参考等位基因，标题含 "=" 表示无变化）
if titles and any("=" in t for t in titles):
print(f"\n── [{i}] CA ID: {ca_id} (同义/参考等位基因，跳过)")
continue
print(f"\n── [{i}] CA ID: {ca_id} ──")
if titles:
print(f" 标准命名(HGVS): {titles}")
# 外部数据库交叉引用
ext = allele.get("externalRecords", {})
# ClinVar: alleleId = 等位基因编号, preferredName = HGVS命名
for cv in ext.get("ClinVarAlleles", []):
print(f" ClinVar Allele ID: {cv.get('alleleId')}, name: {cv.get('preferredName')}")
# ClinVar: variationId = VCV编号, RCV = 各机构临床评估记录列表
for cv in ext.get("ClinVarVariations", []):
print(f" ClinVar Variation ID: {cv.get('variationId')}, RCVs: {cv.get('RCV', [])}")
# COSMIC (肿瘤体细胞变异)
for c in ext.get("COSMIC", []):
print(f" COSMIC: {c.get('id', c)}")
# gnomAD (人群频率, chr-pos-ref-alt 格式)
for ver in ["gnomAD_2", "gnomAD_3", "gnomAD_4"]:
for g in ext.get(ver, []):
gid = g.get("id", g) if isinstance(g, dict) else g
print(f" {ver}: {gid}")
# dbSNP
for d in ext.get("dbSNP", []):
rs = d.get("rs", d) if isinstance(d, dict) else d
print(f" dbSNP: rs{rs}")
# MyVariantInfo (HGVS genomic 格式)
for ver in ["MyVariantInfo_hg19", "MyVariantInfo_hg38"]:
for m in ext.get(ver, []):
mid = m.get("id", m) if isinstance(m, dict) else m
print(f" {ver}: {mid}")
# ExAC (旧版人群频率)
for e in ext.get("ExAC", []):
eid = e.get("id", e) if isinstance(e, dict) else e
print(f" ExAC: {eid}")
gabrielmoreira