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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: 15-50929079-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=50929079&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 50929079,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000261842.10",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.613C>A",
"hgvs_p": "p.His205Asn",
"transcript": "NM_007347.5",
"protein_id": "NP_031373.2",
"transcript_support_level": null,
"aa_start": 205,
"aa_end": null,
"aa_length": 1137,
"cds_start": 613,
"cds_end": null,
"cds_length": 3414,
"cdna_start": 709,
"cdna_end": null,
"cdna_length": 6743,
"mane_select": "ENST00000261842.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.613C>A",
"hgvs_p": "p.His205Asn",
"transcript": "ENST00000261842.10",
"protein_id": "ENSP00000261842.5",
"transcript_support_level": 1,
"aa_start": 205,
"aa_end": null,
"aa_length": 1137,
"cds_start": 613,
"cds_end": null,
"cds_length": 3414,
"cdna_start": 709,
"cdna_end": null,
"cdna_length": 6743,
"mane_select": "NM_007347.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.388C>A",
"hgvs_p": "p.His130Asn",
"transcript": "ENST00000560508.1",
"protein_id": "ENSP00000452976.1",
"transcript_support_level": 1,
"aa_start": 130,
"aa_end": null,
"aa_length": 1062,
"cds_start": 388,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 620,
"cdna_end": null,
"cdna_length": 6653,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "n.613C>A",
"hgvs_p": null,
"transcript": "ENST00000558439.5",
"protein_id": "ENSP00000452712.1",
"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": 4165,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "n.388C>A",
"hgvs_p": null,
"transcript": "ENST00000561393.5",
"protein_id": "ENSP00000452711.1",
"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": 4024,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.388C>A",
"hgvs_p": "p.His130Asn",
"transcript": "NM_001252127.2",
"protein_id": "NP_001239056.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 1062,
"cds_start": 388,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 732,
"cdna_end": null,
"cdna_length": 6766,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.388C>A",
"hgvs_p": "p.His130Asn",
"transcript": "XM_005254264.5",
"protein_id": "XP_005254321.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 1062,
"cds_start": 388,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 1615,
"cdna_end": null,
"cdna_length": 7649,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.388C>A",
"hgvs_p": "p.His130Asn",
"transcript": "XM_006720447.5",
"protein_id": "XP_006720510.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 1062,
"cds_start": 388,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 898,
"cdna_end": null,
"cdna_length": 6932,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.388C>A",
"hgvs_p": "p.His130Asn",
"transcript": "XM_047432324.1",
"protein_id": "XP_047288280.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 1062,
"cds_start": 388,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 600,
"cdna_end": null,
"cdna_length": 6634,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.388C>A",
"hgvs_p": "p.His130Asn",
"transcript": "XM_047432325.1",
"protein_id": "XP_047288281.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 1062,
"cds_start": 388,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 921,
"cdna_end": null,
"cdna_length": 6955,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "H",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.388C>A",
"hgvs_p": "p.His130Asn",
"transcript": "XM_047432326.1",
"protein_id": "XP_047288282.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 899,
"cds_start": 388,
"cds_end": null,
"cds_length": 2700,
"cdna_start": 600,
"cdna_end": null,
"cdna_length": 3007,
"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": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "n.613C>A",
"hgvs_p": null,
"transcript": "ENST00000561441.5",
"protein_id": "ENSP00000453112.1",
"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": 1603,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"dbsnp": "rs148499164",
"frequency_reference_population": 0.0007150922,
"hom_count_reference_population": 1,
"allele_count_reference_population": 1154,
"gnomad_exomes_af": 0.000737574,
"gnomad_genomes_af": 0.000499245,
"gnomad_exomes_ac": 1078,
"gnomad_genomes_ac": 76,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.20294415950775146,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.256,
"revel_prediction": "Benign",
"alphamissense_score": 0.2548,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.568,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS1_Supporting",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS1_Supporting"
],
"verdict": "Likely_benign",
"transcript": "ENST00000261842.10",
"gene_symbol": "AP4E1",
"hgnc_id": 573,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.613C>A",
"hgvs_p": "p.His205Asn"
}
],
"clinvar_disease": " 1, familial persistent,Hereditary spastic paraplegia,Hereditary spastic paraplegia 51,Inborn genetic diseases,Spastic paraplegia,Stuttering,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:8 LB:1",
"phenotype_combined": "not provided|Spastic paraplegia|Hereditary spastic paraplegia|Stuttering, familial persistent, 1;Hereditary spastic paraplegia 51|Inborn genetic diseases|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}