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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: 7-120815787-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=120815787&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 120815787,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000222747.8",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN12",
"gene_hgnc_id": 21641,
"hgvs_c": "c.302T>A",
"hgvs_p": "p.Leu101His",
"transcript": "NM_012338.4",
"protein_id": "NP_036470.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 305,
"cds_start": 302,
"cds_end": null,
"cds_length": 918,
"cdna_start": 697,
"cdna_end": null,
"cdna_length": 2585,
"mane_select": "ENST00000222747.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN12",
"gene_hgnc_id": 21641,
"hgvs_c": "c.302T>A",
"hgvs_p": "p.Leu101His",
"transcript": "ENST00000222747.8",
"protein_id": "ENSP00000222747.3",
"transcript_support_level": 1,
"aa_start": 101,
"aa_end": null,
"aa_length": 305,
"cds_start": 302,
"cds_end": null,
"cds_length": 918,
"cdna_start": 697,
"cdna_end": null,
"cdna_length": 2585,
"mane_select": "NM_012338.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN12",
"gene_hgnc_id": 21641,
"hgvs_c": "c.302T>A",
"hgvs_p": "p.Leu101His",
"transcript": "ENST00000415871.5",
"protein_id": "ENSP00000397699.1",
"transcript_support_level": 5,
"aa_start": 101,
"aa_end": null,
"aa_length": 305,
"cds_start": 302,
"cds_end": null,
"cds_length": 918,
"cdna_start": 661,
"cdna_end": null,
"cdna_length": 1495,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"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": "TSPAN12",
"gene_hgnc_id": 21641,
"hgvs_c": "c.302T>A",
"hgvs_p": "p.Leu101His",
"transcript": "ENST00000441017.5",
"protein_id": "ENSP00000411158.1",
"transcript_support_level": 4,
"aa_start": 101,
"aa_end": null,
"aa_length": 146,
"cds_start": 302,
"cds_end": null,
"cds_length": 442,
"cdna_start": 411,
"cdna_end": null,
"cdna_length": 551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN12",
"gene_hgnc_id": 21641,
"hgvs_c": "c.302T>A",
"hgvs_p": "p.Leu101His",
"transcript": "ENST00000433758.5",
"protein_id": "ENSP00000399059.1",
"transcript_support_level": 4,
"aa_start": 101,
"aa_end": null,
"aa_length": 119,
"cds_start": 302,
"cds_end": null,
"cds_length": 360,
"cdna_start": 493,
"cdna_end": null,
"cdna_length": 551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN12",
"gene_hgnc_id": 21641,
"hgvs_c": "c.302T>A",
"hgvs_p": "p.Leu101His",
"transcript": "ENST00000424710.5",
"protein_id": "ENSP00000404942.1",
"transcript_support_level": 3,
"aa_start": 101,
"aa_end": null,
"aa_length": 111,
"cds_start": 302,
"cds_end": null,
"cds_length": 338,
"cdna_start": 533,
"cdna_end": null,
"cdna_length": 569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN12",
"gene_hgnc_id": 21641,
"hgvs_c": "c.302T>A",
"hgvs_p": "p.Leu101His",
"transcript": "XM_005250239.4",
"protein_id": "XP_005250296.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 305,
"cds_start": 302,
"cds_end": null,
"cds_length": 918,
"cdna_start": 643,
"cdna_end": null,
"cdna_length": 2531,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN12",
"gene_hgnc_id": 21641,
"hgvs_c": "c.302T>A",
"hgvs_p": "p.Leu101His",
"transcript": "XM_047420095.1",
"protein_id": "XP_047276051.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 305,
"cds_start": 302,
"cds_end": null,
"cds_length": 918,
"cdna_start": 673,
"cdna_end": null,
"cdna_length": 2561,
"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": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TSPAN12",
"gene_hgnc_id": 21641,
"hgvs_c": "n.38T>A",
"hgvs_p": null,
"transcript": "ENST00000450414.5",
"protein_id": "ENSP00000397411.1",
"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": 1167,
"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": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "TSPAN12",
"gene_hgnc_id": 21641,
"hgvs_c": "c.286-5217T>A",
"hgvs_p": null,
"transcript": "XM_047420096.1",
"protein_id": "XP_047276052.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 280,
"cds_start": -4,
"cds_end": null,
"cds_length": 843,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2456,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TSPAN12",
"gene_hgnc_id": 21641,
"dbsnp": "rs267607152",
"frequency_reference_population": 0.000008900221,
"hom_count_reference_population": 0,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.00000890022,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 13,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9651068449020386,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.959,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9829,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.38,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.39,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP3_Strong,BS2",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 4,
"pathogenic_score": 4,
"criteria": [
"PP3_Strong",
"BS2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000222747.8",
"gene_symbol": "TSPAN12",
"hgnc_id": 21641,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,SD",
"hgvs_c": "c.302T>A",
"hgvs_p": "p.Leu101His"
}
],
"clinvar_disease": "Exudative vitreoretinopathy 5,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Exudative vitreoretinopathy 5|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}