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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: 1-40271975-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=40271975&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 40271975,
"ref": "G",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000372759.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZMPSTE24",
"gene_hgnc_id": 12877,
"hgvs_c": "c.709G>T",
"hgvs_p": "p.Glu237*",
"transcript": "NM_005857.5",
"protein_id": "NP_005848.2",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 475,
"cds_start": 709,
"cds_end": null,
"cds_length": 1428,
"cdna_start": 745,
"cdna_end": null,
"cdna_length": 2975,
"mane_select": "ENST00000372759.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZMPSTE24",
"gene_hgnc_id": 12877,
"hgvs_c": "c.709G>T",
"hgvs_p": "p.Glu237*",
"transcript": "ENST00000372759.4",
"protein_id": "ENSP00000361845.3",
"transcript_support_level": 1,
"aa_start": 237,
"aa_end": null,
"aa_length": 475,
"cds_start": 709,
"cds_end": null,
"cds_length": 1428,
"cdna_start": 745,
"cdna_end": null,
"cdna_length": 2975,
"mane_select": "NM_005857.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZMPSTE24",
"gene_hgnc_id": 12877,
"hgvs_c": "c.460G>T",
"hgvs_p": "p.Glu154*",
"transcript": "XM_047427582.1",
"protein_id": "XP_047283538.1",
"transcript_support_level": null,
"aa_start": 154,
"aa_end": null,
"aa_length": 392,
"cds_start": 460,
"cds_end": null,
"cds_length": 1179,
"cdna_start": 584,
"cdna_end": null,
"cdna_length": 2814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZMPSTE24",
"gene_hgnc_id": 12877,
"hgvs_c": "c.709G>T",
"hgvs_p": "p.Glu237*",
"transcript": "XM_047427590.1",
"protein_id": "XP_047283546.1",
"transcript_support_level": null,
"aa_start": 237,
"aa_end": null,
"aa_length": 315,
"cds_start": 709,
"cds_end": null,
"cds_length": 948,
"cdna_start": 745,
"cdna_end": null,
"cdna_length": 1936,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZMPSTE24",
"gene_hgnc_id": 12877,
"hgvs_c": "n.*550G>T",
"hgvs_p": null,
"transcript": "ENST00000674703.1",
"protein_id": "ENSP00000501674.1",
"transcript_support_level": null,
"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": 3263,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZMPSTE24",
"gene_hgnc_id": 12877,
"hgvs_c": "n.*451G>T",
"hgvs_p": null,
"transcript": "ENST00000675754.1",
"protein_id": "ENSP00000502555.1",
"transcript_support_level": null,
"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": 3082,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZMPSTE24",
"gene_hgnc_id": 12877,
"hgvs_c": "n.709G>T",
"hgvs_p": null,
"transcript": "ENST00000675937.1",
"protein_id": "ENSP00000502683.1",
"transcript_support_level": null,
"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": 3357,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZMPSTE24",
"gene_hgnc_id": 12877,
"hgvs_c": "n.*550G>T",
"hgvs_p": null,
"transcript": "ENST00000674703.1",
"protein_id": "ENSP00000501674.1",
"transcript_support_level": null,
"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": 3263,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZMPSTE24",
"gene_hgnc_id": 12877,
"hgvs_c": "n.*451G>T",
"hgvs_p": null,
"transcript": "ENST00000675754.1",
"protein_id": "ENSP00000502555.1",
"transcript_support_level": null,
"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": 3082,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ZMPSTE24",
"gene_hgnc_id": 12877,
"dbsnp": "rs281875370",
"frequency_reference_population": 0.000006198429,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000615959,
"gnomad_genomes_af": 0.00000657134,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6000000238418579,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.6,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.975,
"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": 16,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 16,
"benign_score": 0,
"pathogenic_score": 16,
"criteria": [
"PVS1",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000372759.4",
"gene_symbol": "ZMPSTE24",
"hgnc_id": 12877,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.709G>T",
"hgvs_p": "p.Glu237*"
}
],
"clinvar_disease": "Lethal tight skin contracture syndrome,Mandibuloacral dysplasia with type B lipodystrophy,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2 LP:1 O:1",
"phenotype_combined": "not provided|Mandibuloacral dysplasia with type B lipodystrophy;Lethal tight skin contracture syndrome",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}