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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: 3-184188314-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=184188314&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 184188314,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_018358.3",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.743C>A",
"hgvs_p": "p.Thr248Asn",
"transcript": "NM_018358.3",
"protein_id": "NP_060828.2",
"transcript_support_level": null,
"aa_start": 248,
"aa_end": null,
"aa_length": 709,
"cds_start": 743,
"cds_end": null,
"cds_length": 2130,
"cdna_start": 752,
"cdna_end": null,
"cdna_length": 2446,
"mane_select": "ENST00000429586.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.743C>A",
"hgvs_p": "p.Thr248Asn",
"transcript": "ENST00000429586.7",
"protein_id": "ENSP00000411471.2",
"transcript_support_level": 1,
"aa_start": 248,
"aa_end": null,
"aa_length": 709,
"cds_start": 743,
"cds_end": null,
"cds_length": 2130,
"cdna_start": 752,
"cdna_end": null,
"cdna_length": 2446,
"mane_select": "NM_018358.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.725C>A",
"hgvs_p": "p.Thr242Asn",
"transcript": "NM_001351298.2",
"protein_id": "NP_001338227.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 703,
"cds_start": 725,
"cds_end": null,
"cds_length": 2112,
"cdna_start": 734,
"cdna_end": null,
"cdna_length": 2428,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.725C>A",
"hgvs_p": "p.Thr242Asn",
"transcript": "ENST00000292808.5",
"protein_id": "ENSP00000292808.4",
"transcript_support_level": 2,
"aa_start": 242,
"aa_end": null,
"aa_length": 703,
"cds_start": 725,
"cds_end": null,
"cds_length": 2112,
"cdna_start": 759,
"cdna_end": null,
"cdna_length": 2453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.80C>A",
"hgvs_p": "p.Thr27Asn",
"transcript": "NM_001351300.2",
"protein_id": "NP_001338229.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 488,
"cds_start": 80,
"cds_end": null,
"cds_length": 1467,
"cdna_start": 785,
"cdna_end": null,
"cdna_length": 2479,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.7C>A",
"hgvs_p": "p.Leu3Ile",
"transcript": "NM_001351299.2",
"protein_id": "NP_001338228.1",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 466,
"cds_start": 7,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 752,
"cdna_end": null,
"cdna_length": 2453,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "c.80C>A",
"hgvs_p": "p.Thr27Asn",
"transcript": "XM_047448515.1",
"protein_id": "XP_047304471.1",
"transcript_support_level": null,
"aa_start": 27,
"aa_end": null,
"aa_length": 488,
"cds_start": 80,
"cds_end": null,
"cds_length": 1467,
"cdna_start": 556,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "n.1C>A",
"hgvs_p": null,
"transcript": "ENST00000471226.5",
"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": 650,
"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": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "n.1136C>A",
"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": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "n.854C>A",
"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": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"hgvs_c": "n.-20C>A",
"hgvs_p": null,
"transcript": "ENST00000472608.5",
"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": 657,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCF3",
"gene_hgnc_id": 72,
"dbsnp": "rs754647500",
"frequency_reference_population": 0.000002736405,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.0000027364,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7558401823043823,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.717,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.359,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.897,
"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": "NM_018358.3",
"gene_symbol": "ABCF3",
"hgnc_id": 72,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.743C>A",
"hgvs_p": "p.Thr248Asn"
}
],
"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
}