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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: 17-50078061-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=50078061&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 50078061,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000320031.13",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.2155G>A",
"hgvs_p": "p.Ala719Thr",
"transcript": "NM_002204.4",
"protein_id": "NP_002195.1",
"transcript_support_level": null,
"aa_start": 719,
"aa_end": null,
"aa_length": 1051,
"cds_start": 2155,
"cds_end": null,
"cds_length": 3156,
"cdna_start": 2485,
"cdna_end": null,
"cdna_length": 4889,
"mane_select": "ENST00000320031.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.2155G>A",
"hgvs_p": "p.Ala719Thr",
"transcript": "ENST00000320031.13",
"protein_id": "ENSP00000315190.8",
"transcript_support_level": 1,
"aa_start": 719,
"aa_end": null,
"aa_length": 1051,
"cds_start": 2155,
"cds_end": null,
"cds_length": 3156,
"cdna_start": 2485,
"cdna_end": null,
"cdna_length": 4889,
"mane_select": "NM_002204.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.2155G>A",
"hgvs_p": "p.Ala719Thr",
"transcript": "ENST00000007722.11",
"protein_id": "ENSP00000007722.7",
"transcript_support_level": 5,
"aa_start": 719,
"aa_end": null,
"aa_length": 1066,
"cds_start": 2155,
"cds_end": null,
"cds_length": 3201,
"cdna_start": 2155,
"cdna_end": null,
"cdna_length": 3665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.289G>A",
"hgvs_p": "p.Ala97Thr",
"transcript": "ENST00000506827.1",
"protein_id": "ENSP00000426142.1",
"transcript_support_level": 3,
"aa_start": 97,
"aa_end": null,
"aa_length": 220,
"cds_start": 289,
"cds_end": null,
"cds_length": 663,
"cdna_start": 290,
"cdna_end": null,
"cdna_length": 827,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.1750G>A",
"hgvs_p": "p.Ala584Thr",
"transcript": "XM_005257308.3",
"protein_id": "XP_005257365.1",
"transcript_support_level": null,
"aa_start": 584,
"aa_end": null,
"aa_length": 916,
"cds_start": 1750,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 2080,
"cdna_end": null,
"cdna_length": 4484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "c.2196G>A",
"hgvs_p": "p.Ser732Ser",
"transcript": "XM_047435922.1",
"protein_id": "XP_047291878.1",
"transcript_support_level": null,
"aa_start": 732,
"aa_end": null,
"aa_length": 738,
"cds_start": 2196,
"cds_end": null,
"cds_length": 2217,
"cdna_start": 2526,
"cdna_end": null,
"cdna_length": 2668,
"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": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "n.3076G>A",
"hgvs_p": null,
"transcript": "ENST00000505306.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 5479,
"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": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "n.64G>A",
"hgvs_p": null,
"transcript": "ENST00000507771.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 399,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"hgvs_c": "n.58G>A",
"hgvs_p": null,
"transcript": "ENST00000515147.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 535,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ITGA3",
"gene_hgnc_id": 6139,
"dbsnp": "rs2230392",
"frequency_reference_population": 0.10292158,
"hom_count_reference_population": 11729,
"allele_count_reference_population": 165755,
"gnomad_exomes_af": 0.103724,
"gnomad_genomes_af": 0.0952353,
"gnomad_exomes_ac": 151264,
"gnomad_genomes_ac": 14491,
"gnomad_exomes_homalt": 10647,
"gnomad_genomes_homalt": 1082,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0030632317066192627,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.043,
"revel_prediction": "Benign",
"alphamissense_score": 0.0866,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.52,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.533,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000320031.13",
"gene_symbol": "ITGA3",
"hgnc_id": 6139,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2155G>A",
"hgvs_p": "p.Ala719Thr"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}