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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: 3-123494913-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=123494913&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 123494913,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_198402.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HACD2",
"gene_hgnc_id": 9640,
"hgvs_c": "c.740C>A",
"hgvs_p": "p.Thr247Asn",
"transcript": "NM_198402.5",
"protein_id": "NP_940684.1",
"transcript_support_level": null,
"aa_start": 247,
"aa_end": null,
"aa_length": 254,
"cds_start": 740,
"cds_end": null,
"cds_length": 765,
"cdna_start": 766,
"cdna_end": null,
"cdna_length": 4125,
"mane_select": "ENST00000383657.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HACD2",
"gene_hgnc_id": 9640,
"hgvs_c": "c.740C>A",
"hgvs_p": "p.Thr247Asn",
"transcript": "ENST00000383657.10",
"protein_id": "ENSP00000373153.5",
"transcript_support_level": 1,
"aa_start": 247,
"aa_end": null,
"aa_length": 254,
"cds_start": 740,
"cds_end": null,
"cds_length": 765,
"cdna_start": 766,
"cdna_end": null,
"cdna_length": 4125,
"mane_select": "NM_198402.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HACD2",
"gene_hgnc_id": 9640,
"hgvs_c": "c.809C>A",
"hgvs_p": "p.Thr270Asn",
"transcript": "NM_001329783.2",
"protein_id": "NP_001316712.1",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 277,
"cds_start": 809,
"cds_end": null,
"cds_length": 834,
"cdna_start": 835,
"cdna_end": null,
"cdna_length": 4194,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HACD2",
"gene_hgnc_id": 9640,
"hgvs_c": "c.407C>A",
"hgvs_p": "p.Thr136Asn",
"transcript": "NM_001329784.4",
"protein_id": "NP_001316713.2",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 143,
"cds_start": 407,
"cds_end": null,
"cds_length": 432,
"cdna_start": 903,
"cdna_end": null,
"cdna_length": 4262,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HACD2",
"gene_hgnc_id": 9640,
"hgvs_c": "c.407C>A",
"hgvs_p": "p.Thr136Asn",
"transcript": "NM_001329786.2",
"protein_id": "NP_001316715.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 143,
"cds_start": 407,
"cds_end": null,
"cds_length": 432,
"cdna_start": 747,
"cdna_end": null,
"cdna_length": 4106,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HACD2",
"gene_hgnc_id": 9640,
"hgvs_c": "c.407C>A",
"hgvs_p": "p.Thr136Asn",
"transcript": "NM_001329787.2",
"protein_id": "NP_001316716.1",
"transcript_support_level": null,
"aa_start": 136,
"aa_end": null,
"aa_length": 143,
"cds_start": 407,
"cds_end": null,
"cds_length": 432,
"cdna_start": 801,
"cdna_end": null,
"cdna_length": 4160,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HACD2",
"gene_hgnc_id": 9640,
"hgvs_c": "c.461C>A",
"hgvs_p": "p.Thr154Asn",
"transcript": "XM_047447664.1",
"protein_id": "XP_047303620.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 161,
"cds_start": 461,
"cds_end": null,
"cds_length": 486,
"cdna_start": 1706,
"cdna_end": null,
"cdna_length": 5065,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HACD2",
"gene_hgnc_id": 9640,
"hgvs_c": "c.461C>A",
"hgvs_p": "p.Thr154Asn",
"transcript": "XM_047447665.1",
"protein_id": "XP_047303621.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 161,
"cds_start": 461,
"cds_end": null,
"cds_length": 486,
"cdna_start": 938,
"cdna_end": null,
"cdna_length": 4297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HACD2",
"gene_hgnc_id": 9640,
"hgvs_c": "c.*4723C>A",
"hgvs_p": null,
"transcript": "XM_047447663.1",
"protein_id": "XP_047303619.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 228,
"cds_start": -4,
"cds_end": null,
"cds_length": 687,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8795,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HACD2",
"gene_hgnc_id": 9640,
"hgvs_c": "n.-83C>A",
"hgvs_p": null,
"transcript": "ENST00000471236.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 403,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HACD2",
"gene_hgnc_id": 9640,
"dbsnp": "rs748902443",
"frequency_reference_population": 0.0000028426816,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000284268,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11724299192428589,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.127,
"revel_prediction": "Benign",
"alphamissense_score": 0.1044,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.57,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.782,
"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": 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": "NM_198402.5",
"gene_symbol": "HACD2",
"hgnc_id": 9640,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.740C>A",
"hgvs_p": "p.Thr247Asn"
}
],
"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
}