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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: 5-167375258-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=167375258&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 167375258,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_001395460.1",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM2",
"gene_hgnc_id": 29943,
"hgvs_c": "c.287A>G",
"hgvs_p": "p.Tyr96Cys",
"transcript": "NM_001395460.1",
"protein_id": "NP_001382389.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 2774,
"cds_start": 287,
"cds_end": null,
"cds_length": 8325,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000518659.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001395460.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM2",
"gene_hgnc_id": 29943,
"hgvs_c": "c.287A>G",
"hgvs_p": "p.Tyr96Cys",
"transcript": "ENST00000518659.6",
"protein_id": "ENSP00000429430.1",
"transcript_support_level": 5,
"aa_start": 96,
"aa_end": null,
"aa_length": 2774,
"cds_start": 287,
"cds_end": null,
"cds_length": 8325,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001395460.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000518659.6"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM2",
"gene_hgnc_id": 29943,
"hgvs_c": "c.287A>G",
"hgvs_p": "p.Tyr96Cys",
"transcript": "NM_001122679.2",
"protein_id": "NP_001116151.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 2765,
"cds_start": 287,
"cds_end": null,
"cds_length": 8298,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001122679.2"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM2",
"gene_hgnc_id": 29943,
"hgvs_c": "c.287A>G",
"hgvs_p": "p.Tyr96Cys",
"transcript": "XM_017009661.2",
"protein_id": "XP_016865150.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 2767,
"cds_start": 287,
"cds_end": null,
"cds_length": 8304,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009661.2"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM2",
"gene_hgnc_id": 29943,
"hgvs_c": "c.287A>G",
"hgvs_p": "p.Tyr96Cys",
"transcript": "XM_005265950.3",
"protein_id": "XP_005266007.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 2765,
"cds_start": 287,
"cds_end": null,
"cds_length": 8298,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_005265950.3"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM2",
"gene_hgnc_id": 29943,
"hgvs_c": "c.287A>G",
"hgvs_p": "p.Tyr96Cys",
"transcript": "XM_047417418.1",
"protein_id": "XP_047273374.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 2758,
"cds_start": 287,
"cds_end": null,
"cds_length": 8277,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417418.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM2",
"gene_hgnc_id": 29943,
"hgvs_c": "c.287A>G",
"hgvs_p": "p.Tyr96Cys",
"transcript": "XM_017009662.2",
"protein_id": "XP_016865151.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 2704,
"cds_start": 287,
"cds_end": null,
"cds_length": 8115,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009662.2"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM2",
"gene_hgnc_id": 29943,
"hgvs_c": "c.287A>G",
"hgvs_p": "p.Tyr96Cys",
"transcript": "XM_011534604.3",
"protein_id": "XP_011532906.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 2703,
"cds_start": 287,
"cds_end": null,
"cds_length": 8112,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011534604.3"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM2",
"gene_hgnc_id": 29943,
"hgvs_c": "c.287A>G",
"hgvs_p": "p.Tyr96Cys",
"transcript": "XM_047417419.1",
"protein_id": "XP_047273375.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 2697,
"cds_start": 287,
"cds_end": null,
"cds_length": 8094,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417419.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM2",
"gene_hgnc_id": 29943,
"hgvs_c": "c.287A>G",
"hgvs_p": "p.Tyr96Cys",
"transcript": "XM_047417420.1",
"protein_id": "XP_047273376.1",
"transcript_support_level": null,
"aa_start": 96,
"aa_end": null,
"aa_length": 2696,
"cds_start": 287,
"cds_end": null,
"cds_length": 8091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047417420.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TENM2",
"gene_hgnc_id": 29943,
"hgvs_c": "n.939A>G",
"hgvs_p": null,
"transcript": "ENST00000695884.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000695884.1"
}
],
"gene_symbol": "TENM2",
"gene_hgnc_id": 29943,
"dbsnp": "rs747101270",
"frequency_reference_population": 0.0000045114894,
"hom_count_reference_population": 0,
"allele_count_reference_population": 7,
"gnomad_exomes_af": 0.00000428754,
"gnomad_genomes_af": 0.00000657073,
"gnomad_exomes_ac": 6,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.87087082862854,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.51,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1529,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": 0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.79,
"phylop100way_prediction": "Uncertain_significance",
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3_Moderate,BS2",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PP3_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001395460.1",
"gene_symbol": "TENM2",
"hgnc_id": 29943,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.287A>G",
"hgvs_p": "p.Tyr96Cys"
}
],
"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
}