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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: 17-45436075-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=45436075&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 45436075,
"ref": "C",
"alt": "T",
"effect": "3_prime_UTR_variant",
"transcript": "ENST00000430334.8",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.*1783G>A",
"hgvs_p": null,
"transcript": "NM_014798.3",
"protein_id": "NP_055613.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1056,
"cds_start": -4,
"cds_end": null,
"cds_length": 3171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5240,
"mane_select": "ENST00000430334.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.*1783G>A",
"hgvs_p": null,
"transcript": "ENST00000430334.8",
"protein_id": "ENSP00000389913.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1056,
"cds_start": -4,
"cds_end": null,
"cds_length": 3171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5240,
"mane_select": "NM_014798.3",
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "n.*4514G>A",
"hgvs_p": null,
"transcript": "ENST00000579197.5",
"protein_id": "ENSP00000462282.1",
"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": 4995,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "n.2456G>A",
"hgvs_p": null,
"transcript": "ENST00000580404.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 2628,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "n.4817G>A",
"hgvs_p": null,
"transcript": "NR_027774.2",
"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": 4992,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "n.4680G>A",
"hgvs_p": null,
"transcript": "NR_027782.2",
"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": 4855,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "n.*4514G>A",
"hgvs_p": null,
"transcript": "ENST00000579197.5",
"protein_id": "ENSP00000462282.1",
"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": 4995,
"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": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.*1783G>A",
"hgvs_p": null,
"transcript": "XM_017025451.2",
"protein_id": "XP_016880940.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1056,
"cds_start": -4,
"cds_end": null,
"cds_length": 3171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6655,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.*1783G>A",
"hgvs_p": null,
"transcript": "XM_011525525.1",
"protein_id": "XP_011523827.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1005,
"cds_start": -4,
"cds_end": null,
"cds_length": 3018,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5057,
"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": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.*1783G>A",
"hgvs_p": null,
"transcript": "XM_047437190.1",
"protein_id": "XP_047293146.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 989,
"cds_start": -4,
"cds_end": null,
"cds_length": 2970,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6454,
"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": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.*1783G>A",
"hgvs_p": null,
"transcript": "XM_017025452.2",
"protein_id": "XP_016880941.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 967,
"cds_start": -4,
"cds_end": null,
"cds_length": 2904,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6407,
"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": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.*1783G>A",
"hgvs_p": null,
"transcript": "XM_006722201.5",
"protein_id": "XP_006722264.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 926,
"cds_start": -4,
"cds_end": null,
"cds_length": 2781,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5083,
"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": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.*1783G>A",
"hgvs_p": null,
"transcript": "XM_047437192.1",
"protein_id": "XP_047293148.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 926,
"cds_start": -4,
"cds_end": null,
"cds_length": 2781,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4859,
"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": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.*1783G>A",
"hgvs_p": null,
"transcript": "XM_011525528.3",
"protein_id": "XP_011523830.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 535,
"cds_start": -4,
"cds_end": null,
"cds_length": 1608,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3616,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"hgvs_c": "c.*35-1725G>A",
"hgvs_p": null,
"transcript": "XM_047437188.1",
"protein_id": "XP_047293144.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1056,
"cds_start": -4,
"cds_end": null,
"cds_length": 3171,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4873,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PLEKHM1",
"gene_hgnc_id": 29017,
"dbsnp": "rs11012",
"frequency_reference_population": 0.13371857,
"hom_count_reference_population": 5159,
"allele_count_reference_population": 61046,
"gnomad_exomes_af": 0.135548,
"gnomad_genomes_af": 0.130064,
"gnomad_exomes_ac": 41237,
"gnomad_genomes_ac": 19809,
"gnomad_exomes_homalt": 3541,
"gnomad_genomes_homalt": 1618,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.10300000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.103,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.89,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.208,
"phylop100way_prediction": "Benign",
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BA1",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000430334.8",
"gene_symbol": "PLEKHM1",
"hgnc_id": 29017,
"effects": [
"3_prime_UTR_variant"
],
"inheritance_mode": "AR,AD,Unknown",
"hgvs_c": "c.*1783G>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}