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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: 15-50941684-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=50941684&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "AP4E1",
"hgnc_id": 573,
"hgvs_c": "c.1085A>G",
"hgvs_p": "p.Tyr362Cys",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_007347.5",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_score": -20,
"allele_count_reference_population": 4035,
"alphamissense_prediction": null,
"alphamissense_score": 0.0879,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.45,
"chr": "15",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": " 1, familial persistent,Hereditary spastic paraplegia,Hereditary spastic paraplegia 51,Spastic paraplegia,Stuttering,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0053795576095581055,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1137,
"aa_ref": "Y",
"aa_start": 362,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6743,
"cdna_start": 1181,
"cds_end": null,
"cds_length": 3414,
"cds_start": 1085,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_007347.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.1085A>G",
"hgvs_p": "p.Tyr362Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000261842.10",
"protein_coding": true,
"protein_id": "NP_031373.2",
"strand": true,
"transcript": "NM_007347.5",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1137,
"aa_ref": "Y",
"aa_start": 362,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6743,
"cdna_start": 1181,
"cds_end": null,
"cds_length": 3414,
"cds_start": 1085,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000261842.10",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.1085A>G",
"hgvs_p": "p.Tyr362Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_007347.5",
"protein_coding": true,
"protein_id": "ENSP00000261842.5",
"strand": true,
"transcript": "ENST00000261842.10",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1062,
"aa_ref": "Y",
"aa_start": 287,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6653,
"cdna_start": 1092,
"cds_end": null,
"cds_length": 3189,
"cds_start": 860,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000560508.1",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.860A>G",
"hgvs_p": "p.Tyr287Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000452976.1",
"strand": true,
"transcript": "ENST00000560508.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 4165,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000558439.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "n.*207A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000452712.1",
"strand": true,
"transcript": "ENST00000558439.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 4024,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000561393.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "n.*129A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000452711.1",
"strand": true,
"transcript": "ENST00000561393.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 4165,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000558439.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "n.*207A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000452712.1",
"strand": true,
"transcript": "ENST00000558439.5",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": true,
"cdna_end": null,
"cdna_length": 4024,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 20,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000561393.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "n.*129A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000452711.1",
"strand": true,
"transcript": "ENST00000561393.5",
"transcript_support_level": 1
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1062,
"aa_ref": "Y",
"aa_start": 287,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6766,
"cdna_start": 1204,
"cds_end": null,
"cds_length": 3189,
"cds_start": 860,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001252127.2",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.860A>G",
"hgvs_p": "p.Tyr287Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001239056.1",
"strand": true,
"transcript": "NM_001252127.2",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1036,
"aa_ref": "Y",
"aa_start": 362,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3277,
"cdna_start": 1178,
"cds_end": null,
"cds_length": 3111,
"cds_start": 1085,
"consequences": [
"missense_variant"
],
"exon_count": 20,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000879007.1",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.1085A>G",
"hgvs_p": "p.Tyr362Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000549066.1",
"strand": true,
"transcript": "ENST00000879007.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1062,
"aa_ref": "Y",
"aa_start": 287,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7649,
"cdna_start": 2087,
"cds_end": null,
"cds_length": 3189,
"cds_start": 860,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_005254264.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.860A>G",
"hgvs_p": "p.Tyr287Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005254321.1",
"strand": true,
"transcript": "XM_005254264.5",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1062,
"aa_ref": "Y",
"aa_start": 287,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6932,
"cdna_start": 1370,
"cds_end": null,
"cds_length": 3189,
"cds_start": 860,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_006720447.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.860A>G",
"hgvs_p": "p.Tyr287Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_006720510.1",
"strand": true,
"transcript": "XM_006720447.5",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1062,
"aa_ref": "Y",
"aa_start": 287,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6634,
"cdna_start": 1072,
"cds_end": null,
"cds_length": 3189,
"cds_start": 860,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047432324.1",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.860A>G",
"hgvs_p": "p.Tyr287Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288280.1",
"strand": true,
"transcript": "XM_047432324.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 1062,
"aa_ref": "Y",
"aa_start": 287,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6955,
"cdna_start": 1393,
"cds_end": null,
"cds_length": 3189,
"cds_start": 860,
"consequences": [
"missense_variant"
],
"exon_count": 21,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047432325.1",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.860A>G",
"hgvs_p": "p.Tyr287Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288281.1",
"strand": true,
"transcript": "XM_047432325.1",
"transcript_support_level": null
},
{
"aa_alt": "C",
"aa_end": null,
"aa_length": 899,
"aa_ref": "Y",
"aa_start": 287,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3007,
"cdna_start": 1072,
"cds_end": null,
"cds_length": 2700,
"cds_start": 860,
"consequences": [
"missense_variant"
],
"exon_count": 19,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047432326.1",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "c.860A>G",
"hgvs_p": "p.Tyr287Cys",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288282.1",
"strand": true,
"transcript": "XM_047432326.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1603,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 13,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000561441.5",
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"hgvs_c": "n.1067-14A>G",
"hgvs_p": null,
"intron_rank": 9,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000453112.1",
"strand": true,
"transcript": "ENST00000561441.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs58909326",
"effect": "missense_variant",
"frequency_reference_population": 0.002500598,
"gene_hgnc_id": 573,
"gene_symbol": "AP4E1",
"gnomad_exomes_ac": 1995,
"gnomad_exomes_af": 0.00136519,
"gnomad_exomes_homalt": 37,
"gnomad_genomes_ac": 2040,
"gnomad_genomes_af": 0.013396,
"gnomad_genomes_homalt": 52,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 89,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "not specified|Spastic paraplegia|Hereditary spastic paraplegia|Stuttering, familial persistent, 1|Hereditary spastic paraplegia 51|not provided",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.923,
"pos": 50941684,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.052,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_007347.5"
}
]
}