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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: 6-131582720-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=131582720&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 131582720,
"ref": "G",
"alt": "A",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000368087.8",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.560+5G>A",
"hgvs_p": null,
"transcript": "NM_000045.4",
"protein_id": "NP_000036.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 322,
"cds_start": -4,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1447,
"mane_select": "ENST00000368087.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.560+5G>A",
"hgvs_p": null,
"transcript": "ENST00000368087.8",
"protein_id": "ENSP00000357066.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 322,
"cds_start": -4,
"cds_end": null,
"cds_length": 969,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1447,
"mane_select": "NM_000045.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 30,
"intron_rank_end": null,
"gene_symbol": "MED23",
"gene_hgnc_id": 2372,
"hgvs_c": "c.4095+4989C>T",
"hgvs_p": null,
"transcript": "ENST00000354577.8",
"protein_id": "ENSP00000346588.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1365,
"cds_start": -4,
"cds_end": null,
"cds_length": 4098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.584+5G>A",
"hgvs_p": null,
"transcript": "ENST00000356962.2",
"protein_id": "ENSP00000349446.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 330,
"cds_start": -4,
"cds_end": null,
"cds_length": 993,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1468,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 30,
"intron_rank_end": null,
"gene_symbol": "MED23",
"gene_hgnc_id": 2372,
"hgvs_c": "c.4095+4989C>T",
"hgvs_p": null,
"transcript": "NM_015979.4",
"protein_id": "NP_057063.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1365,
"cds_start": -4,
"cds_end": null,
"cds_length": 4098,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4618,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": 29,
"intron_rank_end": null,
"gene_symbol": "MED23",
"gene_hgnc_id": 2372,
"hgvs_c": "c.4077+4989C>T",
"hgvs_p": null,
"transcript": "NM_001270521.2",
"protein_id": "NP_001257450.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1359,
"cds_start": -4,
"cds_end": null,
"cds_length": 4080,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4600,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.584+5G>A",
"hgvs_p": null,
"transcript": "NM_001244438.2",
"protein_id": "NP_001231367.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 330,
"cds_start": -4,
"cds_end": null,
"cds_length": 993,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1471,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.506+5G>A",
"hgvs_p": null,
"transcript": "ENST00000672233.1",
"protein_id": "ENSP00000499826.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 304,
"cds_start": -4,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1059,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.306-340G>A",
"hgvs_p": null,
"transcript": "NM_001369020.1",
"protein_id": "NP_001355949.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 237,
"cds_start": -4,
"cds_end": null,
"cds_length": 714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "c.306-340G>A",
"hgvs_p": null,
"transcript": "ENST00000673427.1",
"protein_id": "ENSP00000500160.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 237,
"cds_start": -4,
"cds_end": null,
"cds_length": 714,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "n.544+5G>A",
"hgvs_p": null,
"transcript": "ENST00000275196.5",
"protein_id": null,
"transcript_support_level": 5,
"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": 693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "n.*447+5G>A",
"hgvs_p": null,
"transcript": "ENST00000673234.1",
"protein_id": "ENSP00000499885.1",
"transcript_support_level": null,
"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": 1230,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"hgvs_c": "n.544+5G>A",
"hgvs_p": null,
"transcript": "NR_160934.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1374,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ARG1",
"gene_hgnc_id": 663,
"dbsnp": "rs763312659",
"frequency_reference_population": 0.0000024801434,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000205376,
"gnomad_genomes_af": 0.00000657566,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.15000000596046448,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 1,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.15,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.672,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.72,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999967107592878,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000368087.8",
"gene_symbol": "ARG1",
"hgnc_id": 663,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.560+5G>A",
"hgvs_p": null
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_015979.4",
"gene_symbol": "MED23",
"hgnc_id": 2372,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4095+4989C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Arginase deficiency,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Arginase deficiency|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}