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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: 4-98476427-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=98476427&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 98476427,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000305798.8",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.610G>A",
"hgvs_p": "p.Ala204Thr",
"transcript": "NM_005723.4",
"protein_id": "NP_005714.2",
"transcript_support_level": null,
"aa_start": 204,
"aa_end": null,
"aa_length": 268,
"cds_start": 610,
"cds_end": null,
"cds_length": 807,
"cdna_start": 995,
"cdna_end": null,
"cdna_length": 3347,
"mane_select": "ENST00000305798.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.610G>A",
"hgvs_p": "p.Ala204Thr",
"transcript": "ENST00000305798.8",
"protein_id": "ENSP00000307701.3",
"transcript_support_level": 1,
"aa_start": 204,
"aa_end": null,
"aa_length": 268,
"cds_start": 610,
"cds_end": null,
"cds_length": 807,
"cdna_start": 995,
"cdna_end": null,
"cdna_length": 3347,
"mane_select": "NM_005723.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Ala133Thr",
"transcript": "ENST00000505184.5",
"protein_id": "ENSP00000423916.1",
"transcript_support_level": 2,
"aa_start": 133,
"aa_end": null,
"aa_length": 197,
"cds_start": 397,
"cds_end": null,
"cds_length": 594,
"cdna_start": 682,
"cdna_end": null,
"cdna_length": 1191,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.463G>A",
"hgvs_p": "p.Ala155Thr",
"transcript": "XM_005262680.2",
"protein_id": "XP_005262737.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 219,
"cds_start": 463,
"cds_end": null,
"cds_length": 660,
"cdna_start": 848,
"cdna_end": null,
"cdna_length": 3200,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Ala133Thr",
"transcript": "XM_047449472.1",
"protein_id": "XP_047305428.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 197,
"cds_start": 397,
"cds_end": null,
"cds_length": 594,
"cdna_start": 1088,
"cdna_end": null,
"cdna_length": 3440,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Ala133Thr",
"transcript": "XM_047449473.1",
"protein_id": "XP_047305429.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 197,
"cds_start": 397,
"cds_end": null,
"cds_length": 594,
"cdna_start": 927,
"cdna_end": null,
"cdna_length": 3279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Ala133Thr",
"transcript": "XM_047449475.1",
"protein_id": "XP_047305431.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 197,
"cds_start": 397,
"cds_end": null,
"cds_length": 594,
"cdna_start": 639,
"cdna_end": null,
"cdna_length": 2991,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.546G>A",
"hgvs_p": "p.Met182Ile",
"transcript": "XM_047449476.1",
"protein_id": "XP_047305432.1",
"transcript_support_level": null,
"aa_start": 182,
"aa_end": null,
"aa_length": 193,
"cds_start": 546,
"cds_end": null,
"cds_length": 582,
"cdna_start": 931,
"cdna_end": null,
"cdna_length": 1056,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "c.399G>A",
"hgvs_p": "p.Met133Ile",
"transcript": "XM_047449477.1",
"protein_id": "XP_047305433.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 144,
"cds_start": 399,
"cds_end": null,
"cds_length": 435,
"cdna_start": 784,
"cdna_end": null,
"cdna_length": 915,
"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": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "n.546G>A",
"hgvs_p": null,
"transcript": "ENST00000508798.5",
"protein_id": "ENSP00000421808.1",
"transcript_support_level": 5,
"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": 3242,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"hgvs_c": "n.3688G>A",
"hgvs_p": null,
"transcript": "ENST00000511753.5",
"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": 4062,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TSPAN5",
"gene_hgnc_id": 17753,
"dbsnp": "rs771619825",
"frequency_reference_population": 0.0000030977553,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000205216,
"gnomad_genomes_af": 0.0000131409,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.23171856999397278,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.341,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1532,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.19,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.827,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000305798.8",
"gene_symbol": "TSPAN5",
"hgnc_id": 17753,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.610G>A",
"hgvs_p": "p.Ala204Thr"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}