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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: 11-78702289-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=78702289&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 78702289,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001098816.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM4",
"gene_hgnc_id": 29945,
"hgvs_c": "c.4324G>A",
"hgvs_p": "p.Ala1442Thr",
"transcript": "NM_001098816.3",
"protein_id": "NP_001092286.2",
"transcript_support_level": null,
"aa_start": 1442,
"aa_end": null,
"aa_length": 2769,
"cds_start": 4324,
"cds_end": null,
"cds_length": 8310,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000278550.12",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001098816.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 34,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM4",
"gene_hgnc_id": 29945,
"hgvs_c": "c.4324G>A",
"hgvs_p": "p.Ala1442Thr",
"transcript": "ENST00000278550.12",
"protein_id": "ENSP00000278550.7",
"transcript_support_level": 5,
"aa_start": 1442,
"aa_end": null,
"aa_length": 2769,
"cds_start": 4324,
"cds_end": null,
"cds_length": 8310,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001098816.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000278550.12"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM4",
"gene_hgnc_id": 29945,
"hgvs_c": "c.4399G>A",
"hgvs_p": "p.Ala1467Thr",
"transcript": "XM_017017525.2",
"protein_id": "XP_016873014.1",
"transcript_support_level": null,
"aa_start": 1467,
"aa_end": null,
"aa_length": 2794,
"cds_start": 4399,
"cds_end": null,
"cds_length": 8385,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017017525.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM4",
"gene_hgnc_id": 29945,
"hgvs_c": "c.4372G>A",
"hgvs_p": "p.Ala1458Thr",
"transcript": "XM_047426736.1",
"protein_id": "XP_047282692.1",
"transcript_support_level": null,
"aa_start": 1458,
"aa_end": null,
"aa_length": 2785,
"cds_start": 4372,
"cds_end": null,
"cds_length": 8358,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426736.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM4",
"gene_hgnc_id": 29945,
"hgvs_c": "c.4351G>A",
"hgvs_p": "p.Ala1451Thr",
"transcript": "XM_047426737.1",
"protein_id": "XP_047282693.1",
"transcript_support_level": null,
"aa_start": 1451,
"aa_end": null,
"aa_length": 2778,
"cds_start": 4351,
"cds_end": null,
"cds_length": 8337,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426737.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM4",
"gene_hgnc_id": 29945,
"hgvs_c": "c.4195G>A",
"hgvs_p": "p.Ala1399Thr",
"transcript": "XM_047426738.1",
"protein_id": "XP_047282694.1",
"transcript_support_level": null,
"aa_start": 1399,
"aa_end": null,
"aa_length": 2726,
"cds_start": 4195,
"cds_end": null,
"cds_length": 8181,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426738.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM4",
"gene_hgnc_id": 29945,
"hgvs_c": "c.4180G>A",
"hgvs_p": "p.Ala1394Thr",
"transcript": "XM_047426739.1",
"protein_id": "XP_047282695.1",
"transcript_support_level": null,
"aa_start": 1394,
"aa_end": null,
"aa_length": 2721,
"cds_start": 4180,
"cds_end": null,
"cds_length": 8166,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426739.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM4",
"gene_hgnc_id": 29945,
"hgvs_c": "c.4168G>A",
"hgvs_p": "p.Ala1390Thr",
"transcript": "XM_047426740.1",
"protein_id": "XP_047282696.1",
"transcript_support_level": null,
"aa_start": 1390,
"aa_end": null,
"aa_length": 2717,
"cds_start": 4168,
"cds_end": null,
"cds_length": 8154,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426740.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM4",
"gene_hgnc_id": 29945,
"hgvs_c": "c.4147G>A",
"hgvs_p": "p.Ala1383Thr",
"transcript": "XM_047426741.1",
"protein_id": "XP_047282697.1",
"transcript_support_level": null,
"aa_start": 1383,
"aa_end": null,
"aa_length": 2710,
"cds_start": 4147,
"cds_end": null,
"cds_length": 8133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426741.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM4",
"gene_hgnc_id": 29945,
"hgvs_c": "c.3997G>A",
"hgvs_p": "p.Ala1333Thr",
"transcript": "XM_047426742.1",
"protein_id": "XP_047282698.1",
"transcript_support_level": null,
"aa_start": 1333,
"aa_end": null,
"aa_length": 2660,
"cds_start": 3997,
"cds_end": null,
"cds_length": 7983,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426742.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM4",
"gene_hgnc_id": 29945,
"hgvs_c": "c.1768G>A",
"hgvs_p": "p.Ala590Thr",
"transcript": "XM_011544933.4",
"protein_id": "XP_011543235.1",
"transcript_support_level": null,
"aa_start": 590,
"aa_end": null,
"aa_length": 1917,
"cds_start": 1768,
"cds_end": null,
"cds_length": 5754,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011544933.4"
}
],
"gene_symbol": "TENM4",
"gene_hgnc_id": 29945,
"dbsnp": "rs375681722",
"frequency_reference_population": 0.00005514141,
"hom_count_reference_population": 0,
"allele_count_reference_population": 89,
"gnomad_exomes_af": 0.0000376273,
"gnomad_genomes_af": 0.000223205,
"gnomad_exomes_ac": 55,
"gnomad_genomes_ac": 34,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8000595569610596,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.768,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.4898,
"alphamissense_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.844,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001098816.3",
"gene_symbol": "TENM4",
"hgnc_id": 29945,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.4324G>A",
"hgvs_p": "p.Ala1442Thr"
}
],
"clinvar_disease": " 5, hereditary essential,Tremor,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Tremor, hereditary essential, 5|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}