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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: 15-45368091-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=45368091&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 45368091,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000396659.8",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "c.654G>A",
"hgvs_p": "p.Met218Ile",
"transcript": "NM_001482.3",
"protein_id": "NP_001473.1",
"transcript_support_level": null,
"aa_start": 218,
"aa_end": null,
"aa_length": 423,
"cds_start": 654,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 745,
"cdna_end": null,
"cdna_length": 2348,
"mane_select": "ENST00000396659.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "c.654G>A",
"hgvs_p": "p.Met218Ile",
"transcript": "ENST00000396659.8",
"protein_id": "ENSP00000379895.3",
"transcript_support_level": 1,
"aa_start": 218,
"aa_end": null,
"aa_length": 423,
"cds_start": 654,
"cds_end": null,
"cds_length": 1272,
"cdna_start": 745,
"cdna_end": null,
"cdna_length": 2348,
"mane_select": "NM_001482.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "n.2310G>A",
"hgvs_p": null,
"transcript": "ENST00000558362.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 3911,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "c.594G>A",
"hgvs_p": "p.Met198Ile",
"transcript": "ENST00000675701.1",
"protein_id": "ENSP00000502671.1",
"transcript_support_level": null,
"aa_start": 198,
"aa_end": null,
"aa_length": 403,
"cds_start": 594,
"cds_end": null,
"cds_length": 1212,
"cdna_start": 855,
"cdna_end": null,
"cdna_length": 1909,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "c.654G>A",
"hgvs_p": "p.Met218Ile",
"transcript": "ENST00000558336.5",
"protein_id": "ENSP00000454008.1",
"transcript_support_level": 2,
"aa_start": 218,
"aa_end": null,
"aa_length": 391,
"cds_start": 654,
"cds_end": null,
"cds_length": 1176,
"cdna_start": 748,
"cdna_end": null,
"cdna_length": 1522,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "c.654G>A",
"hgvs_p": "p.Met218Ile",
"transcript": "ENST00000675323.1",
"protein_id": "ENSP00000502445.1",
"transcript_support_level": null,
"aa_start": 218,
"aa_end": null,
"aa_length": 391,
"cds_start": 654,
"cds_end": null,
"cds_length": 1176,
"cdna_start": 745,
"cdna_end": null,
"cdna_length": 3964,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "c.267G>A",
"hgvs_p": "p.Met89Ile",
"transcript": "NM_001321015.2",
"protein_id": "NP_001307944.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 294,
"cds_start": 267,
"cds_end": null,
"cds_length": 885,
"cdna_start": 1201,
"cdna_end": null,
"cdna_length": 2804,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "c.435G>A",
"hgvs_p": "p.Met145Ile",
"transcript": "ENST00000558163.1",
"protein_id": "ENSP00000453781.1",
"transcript_support_level": 4,
"aa_start": 145,
"aa_end": null,
"aa_length": 166,
"cds_start": 435,
"cds_end": null,
"cds_length": 503,
"cdna_start": 501,
"cdna_end": null,
"cdna_length": 569,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "c.813G>A",
"hgvs_p": "p.Met271Ile",
"transcript": "XM_047432385.1",
"protein_id": "XP_047288341.1",
"transcript_support_level": null,
"aa_start": 271,
"aa_end": null,
"aa_length": 476,
"cds_start": 813,
"cds_end": null,
"cds_length": 1431,
"cdna_start": 2409,
"cdna_end": null,
"cdna_length": 4012,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "c.702G>A",
"hgvs_p": "p.Met234Ile",
"transcript": "XM_047432386.1",
"protein_id": "XP_047288342.1",
"transcript_support_level": null,
"aa_start": 234,
"aa_end": null,
"aa_length": 439,
"cds_start": 702,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1211,
"cdna_end": null,
"cdna_length": 2814,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "c.702G>A",
"hgvs_p": "p.Met234Ile",
"transcript": "XM_047432387.1",
"protein_id": "XP_047288343.1",
"transcript_support_level": null,
"aa_start": 234,
"aa_end": null,
"aa_length": 439,
"cds_start": 702,
"cds_end": null,
"cds_length": 1320,
"cdna_start": 1171,
"cdna_end": null,
"cdna_length": 2774,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "c.267G>A",
"hgvs_p": "p.Met89Ile",
"transcript": "XM_047432388.1",
"protein_id": "XP_047288344.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 294,
"cds_start": 267,
"cds_end": null,
"cds_length": 885,
"cdna_start": 1010,
"cdna_end": null,
"cdna_length": 2613,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "n.552G>A",
"hgvs_p": null,
"transcript": "ENST00000558916.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 913,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "n.654G>A",
"hgvs_p": null,
"transcript": "ENST00000674905.1",
"protein_id": "ENSP00000502176.1",
"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": 2051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "n.654G>A",
"hgvs_p": null,
"transcript": "ENST00000675158.1",
"protein_id": "ENSP00000501737.1",
"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": 2142,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "n.745G>A",
"hgvs_p": null,
"transcript": "ENST00000675974.1",
"protein_id": null,
"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": 4323,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "n.*1385G>A",
"hgvs_p": null,
"transcript": "ENST00000676090.1",
"protein_id": "ENSP00000501630.1",
"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": 3551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"hgvs_c": "n.*1385G>A",
"hgvs_p": null,
"transcript": "ENST00000676090.1",
"protein_id": "ENSP00000501630.1",
"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": 3551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GATM",
"gene_hgnc_id": 4175,
"dbsnp": "rs1555384217",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7668993473052979,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.404,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9793,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.11,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.476,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000396659.8",
"gene_symbol": "GATM",
"hgnc_id": 4175,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.654G>A",
"hgvs_p": "p.Met218Ile"
}
],
"clinvar_disease": "Arginine:glycine amidinotransferase deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Arginine:glycine amidinotransferase deficiency",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}