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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: 15-50968263-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=50968263&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 50968263,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000261842.10",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.1852G>A",
"hgvs_p": "p.Val618Ile",
"transcript": "NM_007347.5",
"protein_id": "NP_031373.2",
"transcript_support_level": null,
"aa_start": 618,
"aa_end": null,
"aa_length": 1137,
"cds_start": 1852,
"cds_end": null,
"cds_length": 3414,
"cdna_start": 1948,
"cdna_end": null,
"cdna_length": 6743,
"mane_select": "ENST00000261842.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.1852G>A",
"hgvs_p": "p.Val618Ile",
"transcript": "ENST00000261842.10",
"protein_id": "ENSP00000261842.5",
"transcript_support_level": 1,
"aa_start": 618,
"aa_end": null,
"aa_length": 1137,
"cds_start": 1852,
"cds_end": null,
"cds_length": 3414,
"cdna_start": 1948,
"cdna_end": null,
"cdna_length": 6743,
"mane_select": "NM_007347.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Val543Ile",
"transcript": "ENST00000560508.1",
"protein_id": "ENSP00000452976.1",
"transcript_support_level": 1,
"aa_start": 543,
"aa_end": null,
"aa_length": 1062,
"cds_start": 1627,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 1859,
"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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "n.*976G>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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "n.*896G>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": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "n.*976G>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": [
"3_prime_UTR_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "n.*896G>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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Val543Ile",
"transcript": "NM_001252127.2",
"protein_id": "NP_001239056.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 1062,
"cds_start": 1627,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 1971,
"cdna_end": null,
"cdna_length": 6766,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Val543Ile",
"transcript": "XM_005254264.5",
"protein_id": "XP_005254321.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 1062,
"cds_start": 1627,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 2854,
"cdna_end": null,
"cdna_length": 7649,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Val543Ile",
"transcript": "XM_006720447.5",
"protein_id": "XP_006720510.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 1062,
"cds_start": 1627,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 2137,
"cdna_end": null,
"cdna_length": 6932,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Val543Ile",
"transcript": "XM_047432324.1",
"protein_id": "XP_047288280.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 1062,
"cds_start": 1627,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 1839,
"cdna_end": null,
"cdna_length": 6634,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Val543Ile",
"transcript": "XM_047432325.1",
"protein_id": "XP_047288281.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 1062,
"cds_start": 1627,
"cds_end": null,
"cds_length": 3189,
"cdna_start": 2160,
"cdna_end": null,
"cdna_length": 6955,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.1627G>A",
"hgvs_p": "p.Val543Ile",
"transcript": "XM_047432326.1",
"protein_id": "XP_047288282.1",
"transcript_support_level": null,
"aa_start": 543,
"aa_end": null,
"aa_length": 899,
"cds_start": 1627,
"cds_end": null,
"cds_length": 2700,
"cdna_start": 1839,
"cdna_end": null,
"cdna_length": 3007,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"hgvs_c": "c.502G>A",
"hgvs_p": "p.Val168Ile",
"transcript": "XM_047432327.1",
"protein_id": "XP_047288283.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 687,
"cds_start": 502,
"cds_end": null,
"cds_length": 2064,
"cdna_start": 623,
"cdna_end": null,
"cdna_length": 5418,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AP4E1",
"gene_hgnc_id": 573,
"dbsnp": "rs142215198",
"frequency_reference_population": 0.00034663532,
"hom_count_reference_population": 1,
"allele_count_reference_population": 557,
"gnomad_exomes_af": 0.000347804,
"gnomad_genomes_af": 0.000335451,
"gnomad_exomes_ac": 506,
"gnomad_genomes_ac": 51,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.19916179776191711,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.8199999928474426,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.149,
"revel_prediction": "Benign",
"alphamissense_score": 0.1101,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 8.34,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.1,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.996270479146199,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BP6,BS1",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 5,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP6",
"BS1"
],
"verdict": "Likely_benign",
"transcript": "ENST00000261842.10",
"gene_symbol": "AP4E1",
"hgnc_id": 573,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1852G>A",
"hgvs_p": "p.Val618Ile"
}
],
"clinvar_disease": "Hereditary spastic paraplegia 51,Spastic paraplegia,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:2 O:1",
"phenotype_combined": "Spastic paraplegia|not provided|Hereditary spastic paraplegia 51",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}