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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: 3-184187938-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=184187938&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 184187938,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_018358.3",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.524C>T",
"hgvs_p": "p.Ser175Phe",
"transcript": "NM_018358.3",
"protein_id": "NP_060828.2",
"transcript_support_level": null,
"aa_start": 175,
"aa_end": null,
"aa_length": 709,
"cds_start": 524,
"cds_end": null,
"cds_length": 2130,
"cdna_start": 533,
"cdna_end": null,
"cdna_length": 2446,
"mane_select": "ENST00000429586.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.524C>T",
"hgvs_p": "p.Ser175Phe",
"transcript": "ENST00000429586.7",
"protein_id": "ENSP00000411471.2",
"transcript_support_level": 1,
"aa_start": 175,
"aa_end": null,
"aa_length": 709,
"cds_start": 524,
"cds_end": null,
"cds_length": 2130,
"cdna_start": 533,
"cdna_end": null,
"cdna_length": 2446,
"mane_select": "NM_018358.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.506C>T",
"hgvs_p": "p.Ser169Phe",
"transcript": "NM_001351298.2",
"protein_id": "NP_001338227.1",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 703,
"cds_start": 506,
"cds_end": null,
"cds_length": 2112,
"cdna_start": 515,
"cdna_end": null,
"cdna_length": 2428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.506C>T",
"hgvs_p": "p.Ser169Phe",
"transcript": "ENST00000292808.5",
"protein_id": "ENSP00000292808.4",
"transcript_support_level": 2,
"aa_start": 169,
"aa_end": null,
"aa_length": 703,
"cds_start": 506,
"cds_end": null,
"cds_length": 2112,
"cdna_start": 540,
"cdna_end": null,
"cdna_length": 2453,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "n.*245C>T",
"hgvs_p": null,
"transcript": "ENST00000421340.5",
"protein_id": "ENSP00000415704.1",
"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": 690,
"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": 4,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "n.917C>T",
"hgvs_p": null,
"transcript": "ENST00000473311.5",
"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": 2844,
"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": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "n.635C>T",
"hgvs_p": null,
"transcript": "ENST00000498136.5",
"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": 1014,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.-140C>T",
"hgvs_p": null,
"transcript": "NM_001351300.2",
"protein_id": "NP_001338229.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 488,
"cds_start": -4,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2479,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.-213C>T",
"hgvs_p": null,
"transcript": "NM_001351299.2",
"protein_id": "NP_001338228.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 466,
"cds_start": -4,
"cds_end": null,
"cds_length": 1401,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.-140C>T",
"hgvs_p": null,
"transcript": "XM_047448515.1",
"protein_id": "XP_047304471.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 488,
"cds_start": -4,
"cds_end": null,
"cds_length": 1467,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2250,
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "n.*245C>T",
"hgvs_p": null,
"transcript": "ENST00000421340.5",
"protein_id": "ENSP00000415704.1",
"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": 690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "n.*37C>T",
"hgvs_p": null,
"transcript": "ENST00000478288.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 754,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"dbsnp": "rs766606565",
"frequency_reference_population": 0.0000012394307,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.8425e-7,
"gnomad_genomes_af": 0.00000657073,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8135155439376831,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.10000000149011612,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.751,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.7461,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 6.14,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.1,
"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": "NM_018358.3",
"gene_symbol": "ABCF3",
"hgnc_id": 72,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.524C>T",
"hgvs_p": "p.Ser175Phe"
}
],
"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
}