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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: 9-137020766-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=137020766&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 137020766,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000341511.11",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"hgvs_c": "c.1193C>T",
"hgvs_p": "p.Thr398Met",
"transcript": "NM_001606.5",
"protein_id": "NP_001597.2",
"transcript_support_level": null,
"aa_start": 398,
"aa_end": null,
"aa_length": 2436,
"cds_start": 1193,
"cds_end": null,
"cds_length": 7311,
"cdna_start": 1290,
"cdna_end": null,
"cdna_length": 8103,
"mane_select": "ENST00000341511.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"hgvs_c": "c.1193C>T",
"hgvs_p": "p.Thr398Met",
"transcript": "ENST00000341511.11",
"protein_id": "ENSP00000344155.6",
"transcript_support_level": 5,
"aa_start": 398,
"aa_end": null,
"aa_length": 2436,
"cds_start": 1193,
"cds_end": null,
"cds_length": 7311,
"cdna_start": 1290,
"cdna_end": null,
"cdna_length": 8103,
"mane_select": "NM_001606.5",
"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": 8,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"hgvs_c": "n.1323C>T",
"hgvs_p": null,
"transcript": "ENST00000459850.5",
"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": 8073,
"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": 8,
"exon_rank_end": null,
"exon_count": 47,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"hgvs_c": "n.1280C>T",
"hgvs_p": null,
"transcript": "ENST00000487109.5",
"protein_id": "ENSP00000418662.1",
"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": 8031,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"hgvs_c": "c.1283C>T",
"hgvs_p": "p.Thr428Met",
"transcript": "NM_212533.3",
"protein_id": "NP_997698.1",
"transcript_support_level": null,
"aa_start": 428,
"aa_end": null,
"aa_length": 2466,
"cds_start": 1283,
"cds_end": null,
"cds_length": 7401,
"cdna_start": 1333,
"cdna_end": null,
"cdna_length": 8146,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"hgvs_c": "c.1283C>T",
"hgvs_p": "p.Thr428Met",
"transcript": "ENST00000614293.5",
"protein_id": "ENSP00000481105.2",
"transcript_support_level": 5,
"aa_start": 428,
"aa_end": null,
"aa_length": 2466,
"cds_start": 1283,
"cds_end": null,
"cds_length": 7401,
"cdna_start": 1289,
"cdna_end": null,
"cdna_length": 8102,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"hgvs_c": "c.1190C>T",
"hgvs_p": "p.Thr397Met",
"transcript": "NM_001411042.1",
"protein_id": "NP_001397971.1",
"transcript_support_level": null,
"aa_start": 397,
"aa_end": null,
"aa_length": 2435,
"cds_start": 1190,
"cds_end": null,
"cds_length": 7308,
"cdna_start": 1287,
"cdna_end": null,
"cdna_length": 8100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"hgvs_c": "c.1190C>T",
"hgvs_p": "p.Thr397Met",
"transcript": "ENST00000371605.7",
"protein_id": "ENSP00000360666.3",
"transcript_support_level": 2,
"aa_start": 397,
"aa_end": null,
"aa_length": 2435,
"cds_start": 1190,
"cds_end": null,
"cds_length": 7308,
"cdna_start": 1338,
"cdna_end": null,
"cdna_length": 8151,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"hgvs_c": "c.1280C>T",
"hgvs_p": "p.Thr427Met",
"transcript": "XM_047422921.1",
"protein_id": "XP_047278877.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 2465,
"cds_start": 1280,
"cds_end": null,
"cds_length": 7398,
"cdna_start": 1330,
"cdna_end": null,
"cdna_length": 8143,
"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": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"hgvs_c": "n.2296C>T",
"hgvs_p": null,
"transcript": "ENST00000464876.5",
"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": 3438,
"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": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"hgvs_c": "n.38C>T",
"hgvs_p": null,
"transcript": "ENST00000470535.2",
"protein_id": "ENSP00000420289.2",
"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": 586,
"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": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"hgvs_c": "n.1296C>T",
"hgvs_p": null,
"transcript": "ENST00000492260.5",
"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": 2062,
"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": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"hgvs_c": "n.1237C>T",
"hgvs_p": null,
"transcript": "ENST00000494046.5",
"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": 1622,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCA2",
"gene_hgnc_id": 32,
"dbsnp": "rs143473036",
"frequency_reference_population": 0.000032567903,
"hom_count_reference_population": 0,
"allele_count_reference_population": 52,
"gnomad_exomes_af": 0.000027695,
"gnomad_genomes_af": 0.0000787619,
"gnomad_exomes_ac": 40,
"gnomad_genomes_ac": 12,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.04062226414680481,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.188,
"revel_prediction": "Benign",
"alphamissense_score": 0.0926,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.234,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000341511.11",
"gene_symbol": "ABCA2",
"hgnc_id": 32,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.1193C>T",
"hgvs_p": "p.Thr398Met"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}