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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 6-42721821-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=42721821&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 42721821,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000230381.7",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPH2",
"gene_hgnc_id": 9942,
"hgvs_c": "c.514C>T",
"hgvs_p": "p.Arg172Trp",
"transcript": "NM_000322.5",
"protein_id": "NP_000313.2",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 346,
"cds_start": 514,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 777,
"cdna_end": null,
"cdna_length": 3001,
"mane_select": "ENST00000230381.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPH2",
"gene_hgnc_id": 9942,
"hgvs_c": "c.514C>T",
"hgvs_p": "p.Arg172Trp",
"transcript": "ENST00000230381.7",
"protein_id": "ENSP00000230381.5",
"transcript_support_level": 1,
"aa_start": 172,
"aa_end": null,
"aa_length": 346,
"cds_start": 514,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 777,
"cdna_end": null,
"cdna_length": 3001,
"mane_select": "NM_000322.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PRPH2",
"gene_hgnc_id": 9942,
"hgvs_c": "n.777C>T",
"hgvs_p": null,
"transcript": "XR_007059288.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1112,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PRPH2",
"gene_hgnc_id": 9942,
"dbsnp": "rs61755792",
"frequency_reference_population": 0.0000020521325,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205213,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.840487003326416,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.67,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.3182,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 2.532,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 17,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 17,
"benign_score": 0,
"pathogenic_score": 17,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000230381.7",
"gene_symbol": "PRPH2",
"hgnc_id": 9942,
"effects": [
"missense_variant"
],
"inheritance_mode": "SD,AD,AR",
"hgvs_c": "c.514C>T",
"hgvs_p": "p.Arg172Trp"
}
],
"clinvar_disease": " central areolar 2,Choroidal dystrophy,Cone-rod dystrophy,PRPH2-related disorder,Patterned dystrophy of the retinal pigment epithelium,Patterned macular dystrophy 1,Retinal dystrophy,Retinitis pigmentosa,Retinitis pigmentosa 7,Stargardt disease,Vitelliform macular dystrophy 2,maculopathy,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:13 LP:2 O:1",
"phenotype_combined": "Choroidal dystrophy, central areolar 2|not provided|PRPH2-related disorder|maculopathy|Retinitis pigmentosa|Patterned dystrophy of the retinal pigment epithelium|Vitelliform macular dystrophy 2|Cone-rod dystrophy|Stargardt disease|Patterned macular dystrophy 1|Retinitis pigmentosa 7|Retinal dystrophy",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}