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Skill v1.0.1
currentAutomated scan100/100internscience/scp/variant-functional-prediction
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PublishedJune 16, 2026 at 01:28 AM
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version: "1.0.1" name: variant-functional-prediction description: "Query FAVOR API for variant functional prediction scores (CADD, SIFT, PolyPhen, REVEL, etc.) and gene annotation." license: MIT license metadata: skill-author: PJLab
FAVOR Functional Prediction
Usage
Tool Description
tex
Query FAVOR (GenoHub) API to get variant functional prediction scores.API: GET https://api.genohub.org/v1/rsids/{rs_id}Note: Returns a JSON list; use first element.Args:rs_id (str): dbSNP rsID (e.g. "rs7412")Return:Gene name, exonic category, functional prediction scores(CADD, SIFT, PolyPhen2, MutationTaster, GERP, etc.)
Query Example
python
import requestsrs_id = "rs7412"url = f"https://api.genohub.org/v1/rsids/{rs_id}"resp = requests.get(url, timeout=30).json()d = resp[0] if isinstance(resp, list) else respprint(f"[FAVOR] variant: {d.get('variant_vcf')}")print(f"[FAVOR] 基因: {d.get('genecode_comprehensive_info')}")print(f"[FAVOR] 区域: {d.get('genecode_comprehensive_category')}")print(f"[FAVOR] 外显子变异类别: {d.get('genecode_comprehensive_exonic_category')}")print(f"[FAVOR] CADD phred: {d.get('cadd_phred')} (>20=有害)")print(f"[FAVOR] SIFT: {d.get('sift_cat')} (val={d.get('sift_val')})")print(f"[FAVOR] PolyPhen2 HDIV: {d.get('polyphen2_hdiv_score')}")print(f"[FAVOR] PolyPhen2 HVAR: {d.get('polyphen2_hvar_score')}")print(f"[FAVOR] MutationTaster: {d.get('mutation_taster_score')}")print(f"[FAVOR] MutationAssessor: {d.get('mutation_assessor_score')}")print(f"[FAVOR] MetaSVM pred: {d.get('metasvm_pred')}")print(f"[FAVOR] GERP_N: {d.get('gerp_n')}, GERP_S: {d.get('gerp_s')}")print(f"[FAVOR] BRAVO AF: {d.get('bravo_af')}")