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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: 6-42721913-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=42721913&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 42721913,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000230381.7",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"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.422A>G",
"hgvs_p": "p.Tyr141Cys",
"transcript": "NM_000322.5",
"protein_id": "NP_000313.2",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 346,
"cds_start": 422,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 685,
"cdna_end": null,
"cdna_length": 3001,
"mane_select": "ENST00000230381.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"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.422A>G",
"hgvs_p": "p.Tyr141Cys",
"transcript": "ENST00000230381.7",
"protein_id": "ENSP00000230381.5",
"transcript_support_level": 1,
"aa_start": 141,
"aa_end": null,
"aa_length": 346,
"cds_start": 422,
"cds_end": null,
"cds_length": 1041,
"cdna_start": 685,
"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.685A>G",
"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": "rs61755781",
"frequency_reference_population": 6.840441e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84044e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9823545217514038,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.881,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9872,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.46,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.984,
"phylop100way_prediction": "Pathogenic",
"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": 19,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PM5,PP2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 19,
"benign_score": 0,
"pathogenic_score": 19,
"criteria": [
"PM1",
"PM2",
"PM5",
"PP2",
"PP3_Strong",
"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.422A>G",
"hgvs_p": "p.Tyr141Cys"
}
],
"clinvar_disease": " central areolar 2,Autosomal recessive bestrophinopathy,Choroidal dystrophy,Cone-rod dystrophy,PRPH2-related disorder,Patterned dystrophy of the retinal pigment epithelium,Patterned macular dystrophy 1,Pigmentary retinal dystrophy,Retinal dystrophy,Retinitis pigmentosa,Retinitis pigmentosa 7,Stargardt disease,Vitelliform macular dystrophy 3,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:10 LP:1 O:1",
"phenotype_combined": "not provided|Stargardt disease|Patterned macular dystrophy 1|PRPH2-related disorder|Retinal dystrophy|Patterned dystrophy of the retinal pigment epithelium|Retinitis pigmentosa|Cone-rod dystrophy|Autosomal recessive bestrophinopathy|Choroidal dystrophy, central areolar 2;Patterned macular dystrophy 1;Pigmentary retinal dystrophy;Retinitis pigmentosa 7;Vitelliform macular dystrophy 3|Vitelliform macular dystrophy 3",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}