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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: 2-227164728-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=227164728&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 227164728,
"ref": "T",
"alt": "G",
"effect": "start_lost",
"transcript": "ENST00000396578.8",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "NM_000091.5",
"protein_id": "NP_000082.2",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1670,
"cds_start": 2,
"cds_end": null,
"cds_length": 5013,
"cdna_start": 105,
"cdna_end": null,
"cdna_length": 8038,
"mane_select": "ENST00000396578.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "ENST00000396578.8",
"protein_id": "ENSP00000379823.3",
"transcript_support_level": 1,
"aa_start": 1,
"aa_end": null,
"aa_length": 1670,
"cds_start": 2,
"cds_end": null,
"cds_length": 5013,
"cdna_start": 105,
"cdna_end": null,
"cdna_length": 8038,
"mane_select": "NM_000091.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_005246277.4",
"protein_id": "XP_005246334.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1635,
"cds_start": 2,
"cds_end": null,
"cds_length": 4908,
"cdna_start": 105,
"cdna_end": null,
"cdna_length": 7933,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_011510555.2",
"protein_id": "XP_011508857.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1609,
"cds_start": 2,
"cds_end": null,
"cds_length": 4830,
"cdna_start": 105,
"cdna_end": null,
"cdna_length": 5012,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 49,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_047443224.1",
"protein_id": "XP_047299180.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1498,
"cds_start": 2,
"cds_end": null,
"cds_length": 4497,
"cdna_start": 105,
"cdna_end": null,
"cdna_length": 4677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_006712245.4",
"protein_id": "XP_006712308.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1189,
"cds_start": 2,
"cds_end": null,
"cds_length": 3570,
"cdna_start": 105,
"cdna_end": null,
"cdna_length": 3759,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_017003295.2",
"protein_id": "XP_016858784.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1119,
"cds_start": 2,
"cds_end": null,
"cds_length": 3360,
"cdna_start": 105,
"cdna_end": null,
"cdna_length": 3898,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"start_lost"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?",
"transcript": "XM_005246280.4",
"protein_id": "XP_005246337.1",
"transcript_support_level": null,
"aa_start": 1,
"aa_end": null,
"aa_length": 1051,
"cds_start": 2,
"cds_end": null,
"cds_length": 3156,
"cdna_start": 105,
"cdna_end": null,
"cdna_length": 3357,
"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": 1,
"exon_rank_end": null,
"exon_count": 42,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"hgvs_c": "n.105T>G",
"hgvs_p": null,
"transcript": "XR_001738601.2",
"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": 4938,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.-434A>C",
"hgvs_p": null,
"transcript": "XM_005246281.4",
"protein_id": "XP_005246338.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1690,
"cds_start": -4,
"cds_end": null,
"cds_length": 5073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9878,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 48,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL4A4",
"gene_hgnc_id": 2206,
"hgvs_c": "c.-417A>C",
"hgvs_p": null,
"transcript": "XM_047443228.1",
"protein_id": "XP_047299184.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1690,
"cds_start": -4,
"cds_end": null,
"cds_length": 5073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9861,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL4A3",
"gene_hgnc_id": 2204,
"dbsnp": "rs1553725815",
"frequency_reference_population": 7.2558197e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 7.25582e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9822597503662109,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.55,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.25,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 0.421,
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PS1_Moderate,PM2",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PS1_Moderate",
"PM2"
],
"verdict": "Pathogenic",
"transcript": "ENST00000396578.8",
"gene_symbol": "COL4A3",
"hgnc_id": 2204,
"effects": [
"start_lost"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.2T>G",
"hgvs_p": "p.Met1?"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "XM_005246281.4",
"gene_symbol": "COL4A4",
"hgnc_id": 2206,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.-434A>C",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}