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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: 19-44908979-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=44908979&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 44908979,
"ref": "G",
"alt": "A",
"effect": "stop_gained",
"transcript": "ENST00000252486.9",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOE",
"gene_hgnc_id": 613,
"hgvs_c": "c.683G>A",
"hgvs_p": "p.Trp228*",
"transcript": "NM_000041.4",
"protein_id": "NP_000032.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 317,
"cds_start": 683,
"cds_end": null,
"cds_length": 954,
"cdna_start": 752,
"cdna_end": null,
"cdna_length": 1166,
"mane_select": "ENST00000252486.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOE",
"gene_hgnc_id": 613,
"hgvs_c": "c.683G>A",
"hgvs_p": "p.Trp228*",
"transcript": "ENST00000252486.9",
"protein_id": "ENSP00000252486.3",
"transcript_support_level": 1,
"aa_start": 228,
"aa_end": null,
"aa_length": 317,
"cds_start": 683,
"cds_end": null,
"cds_length": 954,
"cdna_start": 752,
"cdna_end": null,
"cdna_length": 1166,
"mane_select": "NM_000041.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOE",
"gene_hgnc_id": 613,
"hgvs_c": "c.761G>A",
"hgvs_p": "p.Trp254*",
"transcript": "NM_001302688.2",
"protein_id": "NP_001289617.1",
"transcript_support_level": null,
"aa_start": 254,
"aa_end": null,
"aa_length": 343,
"cds_start": 761,
"cds_end": null,
"cds_length": 1032,
"cdna_start": 834,
"cdna_end": null,
"cdna_length": 1248,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOE",
"gene_hgnc_id": 613,
"hgvs_c": "c.683G>A",
"hgvs_p": "p.Trp228*",
"transcript": "NM_001302689.2",
"protein_id": "NP_001289618.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 317,
"cds_start": 683,
"cds_end": null,
"cds_length": 954,
"cdna_start": 730,
"cdna_end": null,
"cdna_length": 1144,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOE",
"gene_hgnc_id": 613,
"hgvs_c": "c.683G>A",
"hgvs_p": "p.Trp228*",
"transcript": "NM_001302690.2",
"protein_id": "NP_001289619.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 317,
"cds_start": 683,
"cds_end": null,
"cds_length": 954,
"cdna_start": 830,
"cdna_end": null,
"cdna_length": 1244,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOE",
"gene_hgnc_id": 613,
"hgvs_c": "c.683G>A",
"hgvs_p": "p.Trp228*",
"transcript": "NM_001302691.2",
"protein_id": "NP_001289620.1",
"transcript_support_level": null,
"aa_start": 228,
"aa_end": null,
"aa_length": 317,
"cds_start": 683,
"cds_end": null,
"cds_length": 954,
"cdna_start": 767,
"cdna_end": null,
"cdna_length": 1181,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOE",
"gene_hgnc_id": 613,
"hgvs_c": "c.761G>A",
"hgvs_p": "p.Trp254*",
"transcript": "ENST00000434152.5",
"protein_id": "ENSP00000413653.2",
"transcript_support_level": 2,
"aa_start": 254,
"aa_end": null,
"aa_length": 268,
"cds_start": 761,
"cds_end": null,
"cds_length": 807,
"cdna_start": 818,
"cdna_end": null,
"cdna_length": 864,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOE",
"gene_hgnc_id": 613,
"hgvs_c": "c.*25G>A",
"hgvs_p": null,
"transcript": "ENST00000425718.1",
"protein_id": "ENSP00000410423.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 218,
"cds_start": -4,
"cds_end": null,
"cds_length": 658,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 923,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "APOE",
"gene_hgnc_id": 613,
"hgvs_c": "c.*35G>A",
"hgvs_p": null,
"transcript": "ENST00000446996.5",
"protein_id": "ENSP00000413135.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 215,
"cds_start": -4,
"cds_end": null,
"cds_length": 648,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 737,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "APOE",
"gene_hgnc_id": 613,
"dbsnp": "rs121918396",
"frequency_reference_population": 0.000024155535,
"hom_count_reference_population": 0,
"allele_count_reference_population": 37,
"gnomad_exomes_af": 0.0000231937,
"gnomad_genomes_af": 0.0000328831,
"gnomad_exomes_ac": 32,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.07999999821186066,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 0.594,
"phylop100way_prediction": "Benign",
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PVS1_Strong,PP5_Moderate",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PVS1_Strong",
"PP5_Moderate"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000252486.9",
"gene_symbol": "APOE",
"hgnc_id": 613,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,AR,Unknown",
"hgvs_c": "c.683G>A",
"hgvs_p": "p.Trp228*"
}
],
"clinvar_disease": " ASSOCIATED WITH APOE3(WASHINGTON), TYPE III,Familial type 3 hyperlipoproteinemia,HYPERLIPOPROTEINEMIA,not provided",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Familial type 3 hyperlipoproteinemia|HYPERLIPOPROTEINEMIA, TYPE III, ASSOCIATED WITH APOE3(WASHINGTON)|not provided",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}