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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: 3-183927395-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=183927395&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 183927395,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_005688.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC5",
"gene_hgnc_id": 56,
"hgvs_c": "c.3982G>A",
"hgvs_p": "p.Asp1328Asn",
"transcript": "NM_005688.4",
"protein_id": "NP_005679.2",
"transcript_support_level": null,
"aa_start": 1328,
"aa_end": null,
"aa_length": 1437,
"cds_start": 3982,
"cds_end": null,
"cds_length": 4314,
"cdna_start": 4092,
"cdna_end": null,
"cdna_length": 5790,
"mane_select": "ENST00000334444.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC5",
"gene_hgnc_id": 56,
"hgvs_c": "c.3982G>A",
"hgvs_p": "p.Asp1328Asn",
"transcript": "ENST00000334444.11",
"protein_id": "ENSP00000333926.6",
"transcript_support_level": 1,
"aa_start": 1328,
"aa_end": null,
"aa_length": 1437,
"cds_start": 3982,
"cds_end": null,
"cds_length": 4314,
"cdna_start": 4092,
"cdna_end": null,
"cdna_length": 5790,
"mane_select": "NM_005688.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 27,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC5",
"gene_hgnc_id": 56,
"hgvs_c": "c.3853G>A",
"hgvs_p": "p.Asp1285Asn",
"transcript": "ENST00000265586.10",
"protein_id": "ENSP00000265586.6",
"transcript_support_level": 5,
"aa_start": 1285,
"aa_end": null,
"aa_length": 1394,
"cds_start": 3853,
"cds_end": null,
"cds_length": 4185,
"cdna_start": 4018,
"cdna_end": null,
"cdna_length": 5712,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC5",
"gene_hgnc_id": 56,
"hgvs_c": "c.2566G>A",
"hgvs_p": "p.Asp856Asn",
"transcript": "NM_001320032.2",
"protein_id": "NP_001306961.1",
"transcript_support_level": null,
"aa_start": 856,
"aa_end": null,
"aa_length": 965,
"cds_start": 2566,
"cds_end": null,
"cds_length": 2898,
"cdna_start": 4207,
"cdna_end": null,
"cdna_length": 5905,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC5",
"gene_hgnc_id": 56,
"hgvs_c": "c.3982G>A",
"hgvs_p": "p.Asp1328Asn",
"transcript": "XM_005247059.6",
"protein_id": "XP_005247116.1",
"transcript_support_level": null,
"aa_start": 1328,
"aa_end": null,
"aa_length": 1437,
"cds_start": 3982,
"cds_end": null,
"cds_length": 4314,
"cdna_start": 4571,
"cdna_end": null,
"cdna_length": 6269,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC5",
"gene_hgnc_id": 56,
"hgvs_c": "c.3982G>A",
"hgvs_p": "p.Asp1328Asn",
"transcript": "XM_011512314.3",
"protein_id": "XP_011510616.1",
"transcript_support_level": null,
"aa_start": 1328,
"aa_end": null,
"aa_length": 1437,
"cds_start": 3982,
"cds_end": null,
"cds_length": 4314,
"cdna_start": 4611,
"cdna_end": null,
"cdna_length": 6309,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC5",
"gene_hgnc_id": 56,
"hgvs_c": "c.3982G>A",
"hgvs_p": "p.Asp1328Asn",
"transcript": "XM_047447098.1",
"protein_id": "XP_047303054.1",
"transcript_support_level": null,
"aa_start": 1328,
"aa_end": null,
"aa_length": 1437,
"cds_start": 3982,
"cds_end": null,
"cds_length": 4314,
"cdna_start": 6278,
"cdna_end": null,
"cdna_length": 7976,
"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": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC5",
"gene_hgnc_id": 56,
"hgvs_c": "n.*2675G>A",
"hgvs_p": null,
"transcript": "ENST00000437205.5",
"protein_id": "ENSP00000403510.1",
"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": 5852,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC5",
"gene_hgnc_id": 56,
"hgvs_c": "n.*213G>A",
"hgvs_p": null,
"transcript": "ENST00000443497.1",
"protein_id": "ENSP00000404302.1",
"transcript_support_level": 4,
"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": 550,
"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": 28,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC5",
"gene_hgnc_id": 56,
"hgvs_c": "n.*2675G>A",
"hgvs_p": null,
"transcript": "ENST00000437205.5",
"protein_id": "ENSP00000403510.1",
"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": 5852,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC5",
"gene_hgnc_id": 56,
"hgvs_c": "n.*213G>A",
"hgvs_p": null,
"transcript": "ENST00000443497.1",
"protein_id": "ENSP00000404302.1",
"transcript_support_level": 4,
"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": 550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC5",
"gene_hgnc_id": 56,
"hgvs_c": "c.*316G>A",
"hgvs_p": null,
"transcript": "XM_011512315.2",
"protein_id": "XP_011510617.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1364,
"cds_start": -4,
"cds_end": null,
"cds_length": 4095,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4466,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCC5",
"gene_hgnc_id": 56,
"dbsnp": "rs756477346",
"frequency_reference_population": 0.0000034210677,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000342107,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3114398717880249,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.452,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0987,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.904,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_005688.4",
"gene_symbol": "ABCC5",
"hgnc_id": 56,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.3982G>A",
"hgvs_p": "p.Asp1328Asn"
}
],
"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
}