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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: 3-112471290-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=112471290&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 112471290,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000334529.10",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BTLA",
"gene_hgnc_id": 21087,
"hgvs_c": "c.469C>A",
"hgvs_p": "p.Arg157Ser",
"transcript": "NM_181780.4",
"protein_id": "NP_861445.4",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 289,
"cds_start": 469,
"cds_end": null,
"cds_length": 870,
"cdna_start": 583,
"cdna_end": null,
"cdna_length": 3126,
"mane_select": "ENST00000334529.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BTLA",
"gene_hgnc_id": 21087,
"hgvs_c": "c.469C>A",
"hgvs_p": "p.Arg157Ser",
"transcript": "ENST00000334529.10",
"protein_id": "ENSP00000333919.5",
"transcript_support_level": 1,
"aa_start": 157,
"aa_end": null,
"aa_length": 289,
"cds_start": 469,
"cds_end": null,
"cds_length": 870,
"cdna_start": 583,
"cdna_end": null,
"cdna_length": 3126,
"mane_select": "NM_181780.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "BTLA",
"gene_hgnc_id": 21087,
"hgvs_c": "c.404-1486C>A",
"hgvs_p": null,
"transcript": "ENST00000383680.5",
"protein_id": "ENSP00000373178.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 241,
"cds_start": -4,
"cds_end": null,
"cds_length": 726,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5767,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BTLA",
"gene_hgnc_id": 21087,
"hgvs_c": "c.487C>A",
"hgvs_p": "p.Arg163Ser",
"transcript": "XM_011512447.4",
"protein_id": "XP_011510749.1",
"transcript_support_level": null,
"aa_start": 163,
"aa_end": null,
"aa_length": 295,
"cds_start": 487,
"cds_end": null,
"cds_length": 888,
"cdna_start": 652,
"cdna_end": null,
"cdna_length": 3195,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BTLA",
"gene_hgnc_id": 21087,
"hgvs_c": "c.469C>A",
"hgvs_p": "p.Arg157Ser",
"transcript": "XM_017005748.3",
"protein_id": "XP_016861237.1",
"transcript_support_level": null,
"aa_start": 157,
"aa_end": null,
"aa_length": 289,
"cds_start": 469,
"cds_end": null,
"cds_length": 870,
"cdna_start": 634,
"cdna_end": null,
"cdna_length": 3177,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "BTLA",
"gene_hgnc_id": 21087,
"hgvs_c": "c.404-1486C>A",
"hgvs_p": null,
"transcript": "NM_001085357.2",
"protein_id": "NP_001078826.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 241,
"cds_start": -4,
"cds_end": null,
"cds_length": 726,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2982,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000303317",
"gene_hgnc_id": null,
"hgvs_c": "n.393-46718G>T",
"hgvs_p": null,
"transcript": "ENST00000793585.1",
"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": 538,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "BTLA",
"gene_hgnc_id": 21087,
"hgvs_c": "c.404-1486C>A",
"hgvs_p": null,
"transcript": "XM_047447496.1",
"protein_id": "XP_047303452.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 241,
"cds_start": -4,
"cds_end": null,
"cds_length": 726,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BTLA",
"gene_hgnc_id": 21087,
"dbsnp": "rs2931761",
"frequency_reference_population": 0.99818045,
"hom_count_reference_population": 804165,
"allele_count_reference_population": 1611177,
"gnomad_exomes_af": 0.99891,
"gnomad_genomes_af": 0.991174,
"gnomad_exomes_ac": 1460239,
"gnomad_genomes_ac": 150938,
"gnomad_exomes_homalt": 729352,
"gnomad_genomes_homalt": 74813,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 7.149832299546688e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.033,
"revel_prediction": "Benign",
"alphamissense_score": 0.0559,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.49,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000334529.10",
"gene_symbol": "BTLA",
"hgnc_id": 21087,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.469C>A",
"hgvs_p": "p.Arg157Ser"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000793585.1",
"gene_symbol": "ENSG00000303317",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.393-46718G>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}