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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: 1-186674721-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=186674721&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 186674721,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000963.4",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTGS2",
"gene_hgnc_id": 9605,
"hgvs_c": "c.1447G>A",
"hgvs_p": "p.Asp483Asn",
"transcript": "NM_000963.4",
"protein_id": "NP_000954.1",
"transcript_support_level": null,
"aa_start": 483,
"aa_end": null,
"aa_length": 604,
"cds_start": 1447,
"cds_end": null,
"cds_length": 1815,
"cdna_start": 1580,
"cdna_end": null,
"cdna_length": 4510,
"mane_select": "ENST00000367468.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTGS2",
"gene_hgnc_id": 9605,
"hgvs_c": "c.1447G>A",
"hgvs_p": "p.Asp483Asn",
"transcript": "ENST00000367468.10",
"protein_id": "ENSP00000356438.5",
"transcript_support_level": 1,
"aa_start": 483,
"aa_end": null,
"aa_length": 604,
"cds_start": 1447,
"cds_end": null,
"cds_length": 1815,
"cdna_start": 1580,
"cdna_end": null,
"cdna_length": 4510,
"mane_select": "NM_000963.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTGS2",
"gene_hgnc_id": 9605,
"hgvs_c": "n.1862G>A",
"hgvs_p": null,
"transcript": "ENST00000490885.6",
"protein_id": null,
"transcript_support_level": 1,
"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": 3690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTGS2",
"gene_hgnc_id": 9605,
"hgvs_c": "n.*845G>A",
"hgvs_p": null,
"transcript": "ENST00000559627.1",
"protein_id": "ENSP00000454130.1",
"transcript_support_level": 1,
"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": 1705,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTGS2",
"gene_hgnc_id": 9605,
"hgvs_c": "n.*845G>A",
"hgvs_p": null,
"transcript": "ENST00000559627.1",
"protein_id": "ENSP00000454130.1",
"transcript_support_level": 1,
"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": 1705,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTGS2",
"gene_hgnc_id": 9605,
"hgvs_c": "c.1447G>A",
"hgvs_p": "p.Asp483Asn",
"transcript": "ENST00000680451.1",
"protein_id": "ENSP00000506242.1",
"transcript_support_level": null,
"aa_start": 483,
"aa_end": null,
"aa_length": 604,
"cds_start": 1447,
"cds_end": null,
"cds_length": 1815,
"cdna_start": 1779,
"cdna_end": null,
"cdna_length": 4709,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTGS2",
"gene_hgnc_id": 9605,
"hgvs_c": "n.663G>A",
"hgvs_p": null,
"transcript": "ENST00000466691.1",
"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": 888,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTGS2",
"gene_hgnc_id": 9605,
"hgvs_c": "n.*1119G>A",
"hgvs_p": null,
"transcript": "ENST00000681605.1",
"protein_id": "ENSP00000504900.1",
"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": 4506,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PTGS2",
"gene_hgnc_id": 9605,
"hgvs_c": "n.*1119G>A",
"hgvs_p": null,
"transcript": "ENST00000681605.1",
"protein_id": "ENSP00000504900.1",
"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": 4506,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PTGS2",
"gene_hgnc_id": 9605,
"dbsnp": "rs189679860",
"frequency_reference_population": 0.000043990796,
"hom_count_reference_population": 0,
"allele_count_reference_population": 71,
"gnomad_exomes_af": 0.0000431029,
"gnomad_genomes_af": 0.0000525093,
"gnomad_exomes_ac": 63,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.08886146545410156,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.282,
"revel_prediction": "Benign",
"alphamissense_score": 0.1207,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.019,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_000963.4",
"gene_symbol": "PTGS2",
"hgnc_id": 9605,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1447G>A",
"hgvs_p": "p.Asp483Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}