← Back to variant description
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: 17-50056003-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=50056003&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 18,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"5_prime_UTR_variant"
],
"gene_symbol": "ITGA3",
"hgnc_id": 6139,
"hgvs_c": "c.-16G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -18,
"transcript": "ENST00000876971.1",
"verdict": "Benign"
},
{
"benign_score": 18,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"non_coding_transcript_exon_variant"
],
"gene_symbol": "PICART1",
"hgnc_id": 27576,
"hgvs_c": "n.16C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -18,
"transcript": "ENST00000691013.2",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BS1,BS2",
"acmg_score": -18,
"allele_count_reference_population": 2107,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.36,
"chr": "17",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.36000001430511475,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1051,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4608,
"cdna_start": null,
"cds_end": null,
"cds_length": 3156,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 27,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000876971.1",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "c.-16G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000547030.1",
"strand": true,
"transcript": "ENST00000876971.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1817,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 14,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000506401.6",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "n.-16G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000422826.2",
"strand": true,
"transcript": "ENST00000506401.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1359,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000691013.2",
"gene_hgnc_id": 27576,
"gene_symbol": "PICART1",
"hgvs_c": "n.16C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000691013.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1817,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 14,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000506401.6",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "n.-16G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000422826.2",
"strand": true,
"transcript": "ENST00000506401.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1051,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4889,
"cdna_start": null,
"cds_end": null,
"cds_length": 3156,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_002204.4",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "c.-437G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000320031.13",
"protein_coding": true,
"protein_id": "NP_002195.1",
"strand": true,
"transcript": "NM_002204.4",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1051,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4889,
"cdna_start": null,
"cds_end": null,
"cds_length": 3156,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000320031.13",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "c.-437G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_002204.4",
"protein_coding": true,
"protein_id": "ENSP00000315190.8",
"strand": true,
"transcript": "ENST00000320031.13",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1042,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4866,
"cdna_start": null,
"cds_end": null,
"cds_length": 3129,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000876973.1",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "c.-437G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000547032.1",
"strand": true,
"transcript": "ENST00000876973.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1031,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4851,
"cdna_start": null,
"cds_end": null,
"cds_length": 3096,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000876972.1",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "c.-437G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000547031.1",
"strand": true,
"transcript": "ENST00000876972.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 916,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4484,
"cdna_start": null,
"cds_end": null,
"cds_length": 2751,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_005257308.3",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "c.-437G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005257365.1",
"strand": true,
"transcript": "XM_005257308.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 738,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2668,
"cdna_start": null,
"cds_end": null,
"cds_length": 2217,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047435922.1",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "c.-437G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047291878.1",
"strand": true,
"transcript": "XM_047435922.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 5479,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 24,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000505306.5",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "n.-65G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000505306.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 612,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000826198.1",
"gene_hgnc_id": 27576,
"gene_symbol": "PICART1",
"hgvs_c": "n.-239C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000826198.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 533,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000826203.1",
"gene_hgnc_id": 27576,
"gene_symbol": "PICART1",
"hgvs_c": "n.-239C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000826203.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 719,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000826204.1",
"gene_hgnc_id": 27576,
"gene_symbol": "PICART1",
"hgvs_c": "n.-239C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000826204.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs76105399",
"effect": "5_prime_UTR_variant",
"frequency_reference_population": 0.013361998,
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"gnomad_exomes_ac": 9,
"gnomad_exomes_af": 0.00167038,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2098,
"gnomad_genomes_af": 0.0137756,
"gnomad_genomes_homalt": 48,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 48,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.163,
"pos": 50056003,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "ENST00000876971.1"
}
]
}