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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: 16-1461460-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=1461460&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 1461460,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000382745.9",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN7",
"gene_hgnc_id": 2025,
"hgvs_c": "c.296A>G",
"hgvs_p": "p.Tyr99Cys",
"transcript": "NM_001287.6",
"protein_id": "NP_001278.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 805,
"cds_start": 296,
"cds_end": null,
"cds_length": 2418,
"cdna_start": 350,
"cdna_end": null,
"cdna_length": 4168,
"mane_select": "ENST00000382745.9",
"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": 4,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN7",
"gene_hgnc_id": 2025,
"hgvs_c": "c.296A>G",
"hgvs_p": "p.Tyr99Cys",
"transcript": "ENST00000382745.9",
"protein_id": "ENSP00000372193.4",
"transcript_support_level": 1,
"aa_start": 99,
"aa_end": null,
"aa_length": 805,
"cds_start": 296,
"cds_end": null,
"cds_length": 2418,
"cdna_start": 350,
"cdna_end": null,
"cdna_length": 4168,
"mane_select": "NM_001287.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN7",
"gene_hgnc_id": 2025,
"hgvs_c": "c.224A>G",
"hgvs_p": "p.Tyr75Cys",
"transcript": "ENST00000262318.12",
"protein_id": "ENSP00000262318.8",
"transcript_support_level": 5,
"aa_start": 75,
"aa_end": null,
"aa_length": 901,
"cds_start": 224,
"cds_end": null,
"cds_length": 2706,
"cdna_start": 307,
"cdna_end": null,
"cdna_length": 3717,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN7",
"gene_hgnc_id": 2025,
"hgvs_c": "c.296A>G",
"hgvs_p": "p.Tyr99Cys",
"transcript": "ENST00000699947.1",
"protein_id": "ENSP00000514703.1",
"transcript_support_level": null,
"aa_start": 99,
"aa_end": null,
"aa_length": 808,
"cds_start": 296,
"cds_end": null,
"cds_length": 2427,
"cdna_start": 360,
"cdna_end": null,
"cdna_length": 2628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN7",
"gene_hgnc_id": 2025,
"hgvs_c": "c.224A>G",
"hgvs_p": "p.Tyr75Cys",
"transcript": "NM_001114331.3",
"protein_id": "NP_001107803.1",
"transcript_support_level": null,
"aa_start": 75,
"aa_end": null,
"aa_length": 781,
"cds_start": 224,
"cds_end": null,
"cds_length": 2346,
"cdna_start": 278,
"cdna_end": null,
"cdna_length": 4096,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN7",
"gene_hgnc_id": 2025,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Tyr41Cys",
"transcript": "ENST00000569851.6",
"protein_id": "ENSP00000461009.1",
"transcript_support_level": 5,
"aa_start": 41,
"aa_end": null,
"aa_length": 215,
"cds_start": 122,
"cds_end": null,
"cds_length": 648,
"cdna_start": 488,
"cdna_end": null,
"cdna_length": 1014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN7",
"gene_hgnc_id": 2025,
"hgvs_c": "c.191A>G",
"hgvs_p": "p.Tyr64Cys",
"transcript": "ENST00000564568.1",
"protein_id": "ENSP00000454845.1",
"transcript_support_level": 4,
"aa_start": 64,
"aa_end": null,
"aa_length": 117,
"cds_start": 191,
"cds_end": null,
"cds_length": 356,
"cdna_start": 368,
"cdna_end": null,
"cdna_length": 533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN7",
"gene_hgnc_id": 2025,
"hgvs_c": "c.122A>G",
"hgvs_p": "p.Tyr41Cys",
"transcript": "XM_011522354.2",
"protein_id": "XP_011520656.1",
"transcript_support_level": null,
"aa_start": 41,
"aa_end": null,
"aa_length": 747,
"cds_start": 122,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 295,
"cdna_end": null,
"cdna_length": 4113,
"mane_select": null,
"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": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN7",
"gene_hgnc_id": 2025,
"hgvs_c": "n.326A>G",
"hgvs_p": null,
"transcript": "ENST00000561665.5",
"protein_id": null,
"transcript_support_level": 4,
"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": 561,
"mane_select": null,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN7",
"gene_hgnc_id": 2025,
"hgvs_c": "n.347A>G",
"hgvs_p": null,
"transcript": "ENST00000567139.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 581,
"mane_select": null,
"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": 4,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN7",
"gene_hgnc_id": 2025,
"hgvs_c": "n.296A>G",
"hgvs_p": null,
"transcript": "ENST00000699948.1",
"protein_id": "ENSP00000514704.1",
"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": 3676,
"mane_select": null,
"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": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CLCN7",
"gene_hgnc_id": 2025,
"hgvs_c": "n.248A>G",
"hgvs_p": null,
"transcript": "ENST00000699950.1",
"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": 1881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CLCN7",
"gene_hgnc_id": 2025,
"dbsnp": "rs387907576",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9116610288619995,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.887,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9891,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.45,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.866,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PM5,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PM5",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000382745.9",
"gene_symbol": "CLCN7",
"hgnc_id": 2025,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.296A>G",
"hgvs_p": "p.Tyr99Cys"
}
],
"clinvar_disease": "Autosomal dominant osteopetrosis 2,Autosomal recessive osteopetrosis 4,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:1 O:1",
"phenotype_combined": "Autosomal dominant osteopetrosis 2|Autosomal recessive osteopetrosis 4|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}