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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: 3-149040123-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=149040123&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 149040123,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_003071.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2410A>G",
"hgvs_p": "p.Ile804Val",
"transcript": "NM_003071.4",
"protein_id": "NP_003062.2",
"transcript_support_level": null,
"aa_start": 804,
"aa_end": null,
"aa_length": 1009,
"cds_start": 2410,
"cds_end": null,
"cds_length": 3030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000310053.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003071.4"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2410A>G",
"hgvs_p": "p.Ile804Val",
"transcript": "ENST00000310053.10",
"protein_id": "ENSP00000308944.5",
"transcript_support_level": 1,
"aa_start": 804,
"aa_end": null,
"aa_length": 1009,
"cds_start": 2410,
"cds_end": null,
"cds_length": 3030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003071.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000310053.10"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2410A>G",
"hgvs_p": "p.Ile804Val",
"transcript": "ENST00000392912.6",
"protein_id": "ENSP00000376644.2",
"transcript_support_level": 1,
"aa_start": 804,
"aa_end": null,
"aa_length": 1009,
"cds_start": 2410,
"cds_end": null,
"cds_length": 3030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392912.6"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2407A>G",
"hgvs_p": "p.Ile803Val",
"transcript": "ENST00000465259.5",
"protein_id": "ENSP00000420745.1",
"transcript_support_level": 1,
"aa_start": 803,
"aa_end": null,
"aa_length": 1008,
"cds_start": 2407,
"cds_end": null,
"cds_length": 3027,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000465259.5"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2527A>G",
"hgvs_p": "p.Ile843Val",
"transcript": "ENST00000911718.1",
"protein_id": "ENSP00000581777.1",
"transcript_support_level": null,
"aa_start": 843,
"aa_end": null,
"aa_length": 1048,
"cds_start": 2527,
"cds_end": null,
"cds_length": 3147,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911718.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2410A>G",
"hgvs_p": "p.Ile804Val",
"transcript": "NM_001318935.2",
"protein_id": "NP_001305864.1",
"transcript_support_level": null,
"aa_start": 804,
"aa_end": null,
"aa_length": 1009,
"cds_start": 2410,
"cds_end": null,
"cds_length": 3030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318935.2"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2410A>G",
"hgvs_p": "p.Ile804Val",
"transcript": "NM_139048.3",
"protein_id": "NP_620636.1",
"transcript_support_level": null,
"aa_start": 804,
"aa_end": null,
"aa_length": 1009,
"cds_start": 2410,
"cds_end": null,
"cds_length": 3030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_139048.3"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2410A>G",
"hgvs_p": "p.Ile804Val",
"transcript": "ENST00000494055.5",
"protein_id": "ENSP00000420429.1",
"transcript_support_level": 2,
"aa_start": 804,
"aa_end": null,
"aa_length": 1009,
"cds_start": 2410,
"cds_end": null,
"cds_length": 3030,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000494055.5"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2407A>G",
"hgvs_p": "p.Ile803Val",
"transcript": "NM_001318934.2",
"protein_id": "NP_001305863.1",
"transcript_support_level": null,
"aa_start": 803,
"aa_end": null,
"aa_length": 1008,
"cds_start": 2407,
"cds_end": null,
"cds_length": 3027,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318934.2"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.814A>G",
"hgvs_p": "p.Ile272Val",
"transcript": "ENST00000467858.1",
"protein_id": "ENSP00000420106.1",
"transcript_support_level": 5,
"aa_start": 272,
"aa_end": null,
"aa_length": 424,
"cds_start": 814,
"cds_end": null,
"cds_length": 1276,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000467858.1"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2422A>G",
"hgvs_p": "p.Ile808Val",
"transcript": "XM_011513091.3",
"protein_id": "XP_011511393.1",
"transcript_support_level": null,
"aa_start": 808,
"aa_end": null,
"aa_length": 1013,
"cds_start": 2422,
"cds_end": null,
"cds_length": 3042,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513091.3"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2422A>G",
"hgvs_p": "p.Ile808Val",
"transcript": "XM_011513092.3",
"protein_id": "XP_011511394.1",
"transcript_support_level": null,
"aa_start": 808,
"aa_end": null,
"aa_length": 1013,
"cds_start": 2422,
"cds_end": null,
"cds_length": 3042,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513092.3"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2419A>G",
"hgvs_p": "p.Ile807Val",
"transcript": "XM_011513093.3",
"protein_id": "XP_011511395.1",
"transcript_support_level": null,
"aa_start": 807,
"aa_end": null,
"aa_length": 1012,
"cds_start": 2419,
"cds_end": null,
"cds_length": 3039,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011513093.3"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2419A>G",
"hgvs_p": "p.Ile807Val",
"transcript": "XM_017007078.2",
"protein_id": "XP_016862567.1",
"transcript_support_level": null,
"aa_start": 807,
"aa_end": null,
"aa_length": 1012,
"cds_start": 2419,
"cds_end": null,
"cds_length": 3039,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017007078.2"
},
{
"aa_ref": "I",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "c.2407A>G",
"hgvs_p": "p.Ile803Val",
"transcript": "XM_017007079.3",
"protein_id": "XP_016862568.1",
"transcript_support_level": null,
"aa_start": 803,
"aa_end": null,
"aa_length": 1008,
"cds_start": 2407,
"cds_end": null,
"cds_length": 3027,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017007079.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "n.137A>G",
"hgvs_p": null,
"transcript": "ENST00000472830.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000472830.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"hgvs_c": "n.*19A>G",
"hgvs_p": null,
"transcript": "ENST00000497427.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000497427.1"
}
],
"gene_symbol": "HLTF",
"gene_hgnc_id": 11099,
"dbsnp": "rs777075595",
"frequency_reference_population": 0.000013673174,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000144149,
"gnomad_genomes_af": 0.00000657177,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0975552499294281,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.142,
"revel_prediction": "Benign",
"alphamissense_score": 0.1155,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.592,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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_003071.4",
"gene_symbol": "HLTF",
"hgnc_id": 11099,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2410A>G",
"hgvs_p": "p.Ile804Val"
}
],
"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
}