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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: 16-30086847-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=30086847&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PP5"
],
"effects": [
"stop_gained"
],
"gene_symbol": "TBX6",
"hgnc_id": 11605,
"hgvs_c": "c.844C>T",
"hgvs_p": "p.Arg282*",
"inheritance_mode": "AR,Unknown,AD,SD",
"pathogenic_score": 9,
"score": 9,
"transcript": "NM_004608.4",
"verdict": "Likely_pathogenic"
}
],
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1,PP5",
"acmg_score": 9,
"allele_count_reference_population": 22,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.48,
"chr": "16",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "Spondylocostal dysostosis 5,not provided",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.47999998927116394,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 436,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1843,
"cdna_start": 944,
"cds_end": null,
"cds_length": 1311,
"cds_start": 844,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_004608.4",
"gene_hgnc_id": 11605,
"gene_symbol": "TBX6",
"hgvs_c": "c.844C>T",
"hgvs_p": "p.Arg282*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000395224.7",
"protein_coding": true,
"protein_id": "NP_004599.2",
"strand": false,
"transcript": "NM_004608.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 436,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 1843,
"cdna_start": 944,
"cds_end": null,
"cds_length": 1311,
"cds_start": 844,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000395224.7",
"gene_hgnc_id": 11605,
"gene_symbol": "TBX6",
"hgvs_c": "c.844C>T",
"hgvs_p": "p.Arg282*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004608.4",
"protein_coding": true,
"protein_id": "ENSP00000378650.2",
"strand": false,
"transcript": "ENST00000395224.7",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 436,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1796,
"cdna_start": 900,
"cds_end": null,
"cds_length": 1311,
"cds_start": 844,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000279386.6",
"gene_hgnc_id": 11605,
"gene_symbol": "TBX6",
"hgvs_c": "c.844C>T",
"hgvs_p": "p.Arg282*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000279386.2",
"strand": false,
"transcript": "ENST00000279386.6",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 468,
"aa_ref": "R",
"aa_start": 314,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2517,
"cdna_start": 1634,
"cds_end": null,
"cds_length": 1407,
"cds_start": 940,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000931584.1",
"gene_hgnc_id": 11605,
"gene_symbol": "TBX6",
"hgvs_c": "c.940C>T",
"hgvs_p": "p.Arg314*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601643.1",
"strand": false,
"transcript": "ENST00000931584.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 436,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1893,
"cdna_start": 994,
"cds_end": null,
"cds_length": 1311,
"cds_start": 844,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000900317.1",
"gene_hgnc_id": 11605,
"gene_symbol": "TBX6",
"hgvs_c": "c.844C>T",
"hgvs_p": "p.Arg282*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000570376.1",
"strand": false,
"transcript": "ENST00000900317.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 436,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2102,
"cdna_start": 1203,
"cds_end": null,
"cds_length": 1311,
"cds_start": 844,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000900318.1",
"gene_hgnc_id": 11605,
"gene_symbol": "TBX6",
"hgvs_c": "c.844C>T",
"hgvs_p": "p.Arg282*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000570377.1",
"strand": false,
"transcript": "ENST00000900318.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 436,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1952,
"cdna_start": 1053,
"cds_end": null,
"cds_length": 1311,
"cds_start": 844,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000931585.1",
"gene_hgnc_id": 11605,
"gene_symbol": "TBX6",
"hgvs_c": "c.844C>T",
"hgvs_p": "p.Arg282*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601644.1",
"strand": false,
"transcript": "ENST00000931585.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 436,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1866,
"cdna_start": 967,
"cds_end": null,
"cds_length": 1311,
"cds_start": 844,
"consequences": [
"stop_gained"
],
"exon_count": 9,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_011545926.4",
"gene_hgnc_id": 11605,
"gene_symbol": "TBX6",
"hgvs_c": "c.844C>T",
"hgvs_p": "p.Arg282*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011544228.1",
"strand": false,
"transcript": "XM_011545926.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 436,
"aa_ref": "R",
"aa_start": 282,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2084,
"cdna_start": 1185,
"cds_end": null,
"cds_length": 1311,
"cds_start": 844,
"consequences": [
"stop_gained"
],
"exon_count": 8,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_047434551.1",
"gene_hgnc_id": 11605,
"gene_symbol": "TBX6",
"hgvs_c": "c.844C>T",
"hgvs_p": "p.Arg282*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047290507.1",
"strand": false,
"transcript": "XM_047434551.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1227,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XR_007064904.1",
"gene_hgnc_id": 11605,
"gene_symbol": "TBX6",
"hgvs_c": "n.1065C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_007064904.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1543,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000567664.5",
"gene_hgnc_id": 11605,
"gene_symbol": "TBX6",
"hgvs_c": "n.*48-152C>T",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000460425.1",
"strand": false,
"transcript": "ENST00000567664.5",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs201620629",
"effect": "stop_gained",
"frequency_reference_population": 0.00001367212,
"gene_hgnc_id": 11605,
"gene_symbol": "TBX6",
"gnomad_exomes_ac": 20,
"gnomad_exomes_af": 0.0000136986,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000134124,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "Spondylocostal dysostosis 5|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.119,
"pos": 30086847,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004608.4"
}
]
}