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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: X-47586541-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=47586541&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 47586541,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000218388.9",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMP1",
"gene_hgnc_id": 11820,
"hgvs_c": "c.474C>T",
"hgvs_p": "p.Ile158Ile",
"transcript": "NM_003254.3",
"protein_id": "NP_003245.1",
"transcript_support_level": null,
"aa_start": 158,
"aa_end": null,
"aa_length": 207,
"cds_start": 474,
"cds_end": null,
"cds_length": 624,
"cdna_start": 521,
"cdna_end": null,
"cdna_length": 769,
"mane_select": "ENST00000218388.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMP1",
"gene_hgnc_id": 11820,
"hgvs_c": "c.474C>T",
"hgvs_p": "p.Ile158Ile",
"transcript": "ENST00000218388.9",
"protein_id": "ENSP00000218388.4",
"transcript_support_level": 1,
"aa_start": 158,
"aa_end": null,
"aa_length": 207,
"cds_start": 474,
"cds_end": null,
"cds_length": 624,
"cdna_start": 521,
"cdna_end": null,
"cdna_length": 769,
"mane_select": "NM_003254.3",
"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": 13,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.775-9040G>A",
"hgvs_p": null,
"transcript": "NM_006950.3",
"protein_id": "NP_008881.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 705,
"cds_start": -4,
"cds_end": null,
"cds_length": 2118,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3210,
"mane_select": "ENST00000295987.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.775-9040G>A",
"hgvs_p": null,
"transcript": "ENST00000295987.13",
"protein_id": "ENSP00000295987.7",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 705,
"cds_start": -4,
"cds_end": null,
"cds_length": 2118,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3210,
"mane_select": "NM_006950.3",
"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": 13,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.775-9040G>A",
"hgvs_p": null,
"transcript": "ENST00000340666.5",
"protein_id": "ENSP00000343206.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 669,
"cds_start": -4,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3172,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMP1",
"gene_hgnc_id": 11820,
"hgvs_c": "c.345C>T",
"hgvs_p": "p.Ile115Ile",
"transcript": "ENST00000445623.1",
"protein_id": "ENSP00000410983.1",
"transcript_support_level": 2,
"aa_start": 115,
"aa_end": null,
"aa_length": 164,
"cds_start": 345,
"cds_end": null,
"cds_length": 495,
"cdna_start": 347,
"cdna_end": null,
"cdna_length": 595,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMP1",
"gene_hgnc_id": 11820,
"hgvs_c": "c.282C>T",
"hgvs_p": "p.Ile94Ile",
"transcript": "ENST00000377017.5",
"protein_id": "ENSP00000366216.1",
"transcript_support_level": 2,
"aa_start": 94,
"aa_end": null,
"aa_length": 143,
"cds_start": 282,
"cds_end": null,
"cds_length": 432,
"cdna_start": 378,
"cdna_end": null,
"cdna_length": 626,
"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": 13,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.775-9040G>A",
"hgvs_p": null,
"transcript": "NM_133499.2",
"protein_id": "NP_598006.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 669,
"cds_start": -4,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3172,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "ENSG00000283743",
"gene_hgnc_id": null,
"hgvs_c": "n.3231-9040G>A",
"hgvs_p": null,
"transcript": "ENST00000638776.2",
"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": 3761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TIMP1",
"gene_hgnc_id": 11820,
"dbsnp": "rs11551797",
"frequency_reference_population": 0.027063584,
"hom_count_reference_population": 12040,
"allele_count_reference_population": 32754,
"gnomad_exomes_af": 0.0265008,
"gnomad_genomes_af": 0.0325536,
"gnomad_exomes_ac": 29091,
"gnomad_genomes_ac": 3663,
"gnomad_exomes_homalt": 1838,
"gnomad_genomes_homalt": 236,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.14900000393390656,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.03999999910593033,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.149,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.35,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.158,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.04,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP7,BA1",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000218388.9",
"gene_symbol": "TIMP1",
"hgnc_id": 11820,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.474C>T",
"hgvs_p": "p.Ile158Ile"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000295987.13",
"gene_symbol": "SYN1",
"hgnc_id": 11494,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.775-9040G>A",
"hgvs_p": null
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000638776.2",
"gene_symbol": "ENSG00000283743",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.3231-9040G>A",
"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
}