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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: 5-132897044-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=132897044&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 132897044,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000265343.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF4",
"gene_hgnc_id": 17869,
"hgvs_c": "c.1586C>T",
"hgvs_p": "p.Pro529Leu",
"transcript": "NM_014423.4",
"protein_id": "NP_055238.1",
"transcript_support_level": null,
"aa_start": 529,
"aa_end": null,
"aa_length": 1163,
"cds_start": 1586,
"cds_end": null,
"cds_length": 3492,
"cdna_start": 1966,
"cdna_end": null,
"cdna_length": 9536,
"mane_select": "ENST00000265343.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF4",
"gene_hgnc_id": 17869,
"hgvs_c": "c.1586C>T",
"hgvs_p": "p.Pro529Leu",
"transcript": "ENST00000265343.10",
"protein_id": "ENSP00000265343.5",
"transcript_support_level": 1,
"aa_start": 529,
"aa_end": null,
"aa_length": 1163,
"cds_start": 1586,
"cds_end": null,
"cds_length": 3492,
"cdna_start": 1966,
"cdna_end": null,
"cdna_length": 9536,
"mane_select": "NM_014423.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF4",
"gene_hgnc_id": 17869,
"hgvs_c": "c.1586C>T",
"hgvs_p": "p.Pro529Leu",
"transcript": "ENST00000378595.7",
"protein_id": "ENSP00000367858.3",
"transcript_support_level": 1,
"aa_start": 529,
"aa_end": null,
"aa_length": 900,
"cds_start": 1586,
"cds_end": null,
"cds_length": 2703,
"cdna_start": 1950,
"cdna_end": null,
"cdna_length": 3348,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF4",
"gene_hgnc_id": 17869,
"hgvs_c": "c.1586C>T",
"hgvs_p": "p.Pro529Leu",
"transcript": "XM_005271963.6",
"protein_id": "XP_005272020.1",
"transcript_support_level": null,
"aa_start": 529,
"aa_end": null,
"aa_length": 1163,
"cds_start": 1586,
"cds_end": null,
"cds_length": 3492,
"cdna_start": 2058,
"cdna_end": null,
"cdna_length": 9628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF4",
"gene_hgnc_id": 17869,
"hgvs_c": "c.1499C>T",
"hgvs_p": "p.Pro500Leu",
"transcript": "XM_006714587.5",
"protein_id": "XP_006714650.1",
"transcript_support_level": null,
"aa_start": 500,
"aa_end": null,
"aa_length": 1134,
"cds_start": 1499,
"cds_end": null,
"cds_length": 3405,
"cdna_start": 1879,
"cdna_end": null,
"cdna_length": 9449,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF4",
"gene_hgnc_id": 17869,
"hgvs_c": "c.1499C>T",
"hgvs_p": "p.Pro500Leu",
"transcript": "XM_047417103.1",
"protein_id": "XP_047273059.1",
"transcript_support_level": null,
"aa_start": 500,
"aa_end": null,
"aa_length": 1134,
"cds_start": 1499,
"cds_end": null,
"cds_length": 3405,
"cdna_start": 1971,
"cdna_end": null,
"cdna_length": 9541,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF4",
"gene_hgnc_id": 17869,
"hgvs_c": "c.452C>T",
"hgvs_p": "p.Pro151Leu",
"transcript": "XM_005271964.5",
"protein_id": "XP_005272021.1",
"transcript_support_level": null,
"aa_start": 151,
"aa_end": null,
"aa_length": 785,
"cds_start": 452,
"cds_end": null,
"cds_length": 2358,
"cdna_start": 712,
"cdna_end": null,
"cdna_length": 8282,
"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": "AFF4",
"gene_hgnc_id": 17869,
"hgvs_c": "n.664C>T",
"hgvs_p": null,
"transcript": "ENST00000478588.5",
"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": 897,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF4",
"gene_hgnc_id": 17869,
"hgvs_c": "c.*160C>T",
"hgvs_p": null,
"transcript": "ENST00000425658.1",
"protein_id": "ENSP00000409069.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 169,
"cds_start": -4,
"cds_end": null,
"cds_length": 511,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 513,
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AFF4",
"gene_hgnc_id": 17869,
"hgvs_c": "n.*160C>T",
"hgvs_p": null,
"transcript": "ENST00000378593.6",
"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": 430,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AFF4",
"gene_hgnc_id": 17869,
"dbsnp": "rs188073736",
"frequency_reference_population": 0.0002527668,
"hom_count_reference_population": 1,
"allele_count_reference_population": 408,
"gnomad_exomes_af": 0.000266779,
"gnomad_genomes_af": 0.000118227,
"gnomad_exomes_ac": 390,
"gnomad_genomes_ac": 18,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.21659597754478455,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.388,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0868,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.16,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.317,
"phylop100way_prediction": "Pathogenic",
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000265343.10",
"gene_symbol": "AFF4",
"hgnc_id": 17869,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1586C>T",
"hgvs_p": "p.Pro529Leu"
}
],
"clinvar_disease": "AFF4-related disorder,Cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome,Inborn genetic diseases,not provided,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:4",
"phenotype_combined": "not specified|Inborn genetic diseases|not provided|Cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome|AFF4-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}