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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: 5-132892356-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=132892356&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 17,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "AFF4",
"hgnc_id": 17869,
"hgvs_c": "c.2445C>T",
"hgvs_p": "p.Pro815Pro",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -17,
"transcript": "NM_014423.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS2",
"acmg_score": -17,
"allele_count_reference_population": 411,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.48,
"chr": "5",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "AFF4-related disorder,Cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.47999998927116394,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1163,
"aa_ref": "P",
"aa_start": 815,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9536,
"cdna_start": 2825,
"cds_end": null,
"cds_length": 3492,
"cds_start": 2445,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_014423.4",
"gene_hgnc_id": 17869,
"gene_symbol": "AFF4",
"hgvs_c": "c.2445C>T",
"hgvs_p": "p.Pro815Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000265343.10",
"protein_coding": true,
"protein_id": "NP_055238.1",
"strand": false,
"transcript": "NM_014423.4",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1163,
"aa_ref": "P",
"aa_start": 815,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 9536,
"cdna_start": 2825,
"cds_end": null,
"cds_length": 3492,
"cds_start": 2445,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000265343.10",
"gene_hgnc_id": 17869,
"gene_symbol": "AFF4",
"hgvs_c": "c.2445C>T",
"hgvs_p": "p.Pro815Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014423.4",
"protein_coding": true,
"protein_id": "ENSP00000265343.5",
"strand": false,
"transcript": "ENST00000265343.10",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 900,
"aa_ref": "P",
"aa_start": 815,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3348,
"cdna_start": 2809,
"cds_end": null,
"cds_length": 2703,
"cds_start": 2445,
"consequences": [
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000378595.7",
"gene_hgnc_id": 17869,
"gene_symbol": "AFF4",
"hgvs_c": "c.2445C>T",
"hgvs_p": "p.Pro815Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000367858.3",
"strand": false,
"transcript": "ENST00000378595.7",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1173,
"aa_ref": "P",
"aa_start": 825,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4867,
"cdna_start": 2821,
"cds_end": null,
"cds_length": 3522,
"cds_start": 2475,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000944867.1",
"gene_hgnc_id": 17869,
"gene_symbol": "AFF4",
"hgvs_c": "c.2475C>T",
"hgvs_p": "p.Pro825Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000614926.1",
"strand": false,
"transcript": "ENST00000944867.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 857,
"aa_ref": "P",
"aa_start": 509,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4542,
"cdna_start": 1802,
"cds_end": null,
"cds_length": 2574,
"cds_start": 1527,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000909435.1",
"gene_hgnc_id": 17869,
"gene_symbol": "AFF4",
"hgvs_c": "c.1527C>T",
"hgvs_p": "p.Pro509Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000579494.1",
"strand": false,
"transcript": "ENST00000909435.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1163,
"aa_ref": "P",
"aa_start": 815,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9628,
"cdna_start": 2917,
"cds_end": null,
"cds_length": 3492,
"cds_start": 2445,
"consequences": [
"synonymous_variant"
],
"exon_count": 22,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_005271963.6",
"gene_hgnc_id": 17869,
"gene_symbol": "AFF4",
"hgvs_c": "c.2445C>T",
"hgvs_p": "p.Pro815Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005272020.1",
"strand": false,
"transcript": "XM_005271963.6",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1134,
"aa_ref": "P",
"aa_start": 786,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9449,
"cdna_start": 2738,
"cds_end": null,
"cds_length": 3405,
"cds_start": 2358,
"consequences": [
"synonymous_variant"
],
"exon_count": 20,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_006714587.5",
"gene_hgnc_id": 17869,
"gene_symbol": "AFF4",
"hgvs_c": "c.2358C>T",
"hgvs_p": "p.Pro786Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006714650.1",
"strand": false,
"transcript": "XM_006714587.5",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 1134,
"aa_ref": "P",
"aa_start": 786,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 9541,
"cdna_start": 2830,
"cds_end": null,
"cds_length": 3405,
"cds_start": 2358,
"consequences": [
"synonymous_variant"
],
"exon_count": 21,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "XM_047417103.1",
"gene_hgnc_id": 17869,
"gene_symbol": "AFF4",
"hgvs_c": "c.2358C>T",
"hgvs_p": "p.Pro786Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047273059.1",
"strand": false,
"transcript": "XM_047417103.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 785,
"aa_ref": "P",
"aa_start": 437,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 8282,
"cdna_start": 1571,
"cds_end": null,
"cds_length": 2358,
"cds_start": 1311,
"consequences": [
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_005271964.5",
"gene_hgnc_id": 17869,
"gene_symbol": "AFF4",
"hgvs_c": "c.1311C>T",
"hgvs_p": "p.Pro437Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005272021.1",
"strand": false,
"transcript": "XM_005271964.5",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs138116584",
"effect": "synonymous_variant",
"frequency_reference_population": 0.0002546645,
"gene_hgnc_id": 17869,
"gene_symbol": "AFF4",
"gnomad_exomes_ac": 386,
"gnomad_exomes_af": 0.000264076,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 25,
"gnomad_genomes_af": 0.000164271,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "not specified|AFF4-related disorder|Cognitive impairment - coarse facies - heart defects - obesity - pulmonary involvement - short stature - skeletal dysplasia syndrome",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.006,
"pos": 132892356,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_014423.4"
}
]
}