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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: 17-50077122-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=50077122&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"splice_donor_variant",
"intron_variant"
],
"gene_symbol": "ITGA3",
"hgnc_id": 6139,
"hgvs_c": "c.2070+1G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_002204.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.24,
"chr": "17",
"clinvar_classification": "Pathogenic",
"clinvar_disease": " junctional 7, with interstitial lung disease and nephrotic syndrome,Epidermolysis bullosa",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.23999999463558197,
"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": 4889,
"cdna_start": null,
"cds_end": null,
"cds_length": 3156,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_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.2070+1G>A",
"hgvs_p": null,
"intron_rank": 15,
"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": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000320031.13",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "c.2070+1G>A",
"hgvs_p": null,
"intron_rank": 15,
"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": 1066,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3665,
"cdna_start": null,
"cds_end": null,
"cds_length": 3201,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 25,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000007722.11",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "c.2070+1G>A",
"hgvs_p": null,
"intron_rank": 15,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000007722.7",
"strand": true,
"transcript": "ENST00000007722.11",
"transcript_support_level": 5
},
{
"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": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 27,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000876971.1",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "c.2070+1G>A",
"hgvs_p": null,
"intron_rank": 16,
"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": 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": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000876973.1",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "c.2043+1G>A",
"hgvs_p": null,
"intron_rank": 15,
"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": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000876972.1",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "c.2010+1G>A",
"hgvs_p": null,
"intron_rank": 15,
"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": 220,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 827,
"cdna_start": null,
"cds_end": null,
"cds_length": 663,
"cds_start": null,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000506827.1",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "c.204+1G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000426142.1",
"strand": true,
"transcript": "ENST00000506827.1",
"transcript_support_level": 3
},
{
"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": [
"splice_donor_variant",
"intron_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.1665+1G>A",
"hgvs_p": null,
"intron_rank": 13,
"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": [
"splice_donor_variant",
"intron_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.2070+1G>A",
"hgvs_p": null,
"intron_rank": 15,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_count": 24,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000505306.5",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "n.2735G>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": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 1817,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 14,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000506401.6",
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"hgvs_c": "n.*1464G>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
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999980428708689,
"dbsnp": "rs797045048",
"effect": "splice_donor_variant,intron_variant",
"frequency_reference_population": 7.1945965e-7,
"gene_hgnc_id": 6139,
"gene_symbol": "ITGA3",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 7.1946e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Epidermolysis bullosa, junctional 7, with interstitial lung disease and nephrotic syndrome",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.176,
"pos": 50077122,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9319999814033508,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.99,
"transcript": "NM_002204.4"
}
]
}