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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: 4-97981258-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=97981258&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 97981258,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_174952.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STPG2",
"gene_hgnc_id": 28712,
"hgvs_c": "c.673G>A",
"hgvs_p": "p.Ala225Thr",
"transcript": "NM_174952.3",
"protein_id": "NP_777612.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 459,
"cds_start": 673,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000295268.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_174952.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STPG2",
"gene_hgnc_id": 28712,
"hgvs_c": "c.673G>A",
"hgvs_p": "p.Ala225Thr",
"transcript": "ENST00000295268.4",
"protein_id": "ENSP00000295268.3",
"transcript_support_level": 1,
"aa_start": 225,
"aa_end": null,
"aa_length": 459,
"cds_start": 673,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_174952.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295268.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STPG2",
"gene_hgnc_id": 28712,
"hgvs_c": "c.940G>A",
"hgvs_p": "p.Ala314Thr",
"transcript": "XM_011531886.4",
"protein_id": "XP_011530188.1",
"transcript_support_level": null,
"aa_start": 314,
"aa_end": null,
"aa_length": 574,
"cds_start": 940,
"cds_end": null,
"cds_length": 1725,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531886.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STPG2",
"gene_hgnc_id": 28712,
"hgvs_c": "c.715G>A",
"hgvs_p": "p.Ala239Thr",
"transcript": "XM_017008049.3",
"protein_id": "XP_016863538.1",
"transcript_support_level": null,
"aa_start": 239,
"aa_end": null,
"aa_length": 499,
"cds_start": 715,
"cds_end": null,
"cds_length": 1500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017008049.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STPG2",
"gene_hgnc_id": 28712,
"hgvs_c": "c.673G>A",
"hgvs_p": "p.Ala225Thr",
"transcript": "XM_047450118.1",
"protein_id": "XP_047306074.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 485,
"cds_start": 673,
"cds_end": null,
"cds_length": 1458,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047450118.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STPG2",
"gene_hgnc_id": 28712,
"hgvs_c": "c.673G>A",
"hgvs_p": "p.Ala225Thr",
"transcript": "XM_047450119.1",
"protein_id": "XP_047306075.1",
"transcript_support_level": null,
"aa_start": 225,
"aa_end": null,
"aa_length": 446,
"cds_start": 673,
"cds_end": null,
"cds_length": 1341,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047450119.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STPG2",
"gene_hgnc_id": 28712,
"hgvs_c": "c.607G>A",
"hgvs_p": "p.Ala203Thr",
"transcript": "XM_047450120.1",
"protein_id": "XP_047306076.1",
"transcript_support_level": null,
"aa_start": 203,
"aa_end": null,
"aa_length": 424,
"cds_start": 607,
"cds_end": null,
"cds_length": 1275,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047450120.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STPG2",
"gene_hgnc_id": 28712,
"hgvs_c": "c.112G>A",
"hgvs_p": "p.Ala38Thr",
"transcript": "XM_017008051.3",
"protein_id": "XP_016863540.1",
"transcript_support_level": null,
"aa_start": 38,
"aa_end": null,
"aa_length": 298,
"cds_start": 112,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017008051.3"
}
],
"gene_symbol": "STPG2",
"gene_hgnc_id": 28712,
"dbsnp": "rs750242856",
"frequency_reference_population": 0.0000117728705,
"hom_count_reference_population": 0,
"allele_count_reference_population": 19,
"gnomad_exomes_af": 0.0000116301,
"gnomad_genomes_af": 0.0000131444,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1423620879650116,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.131,
"revel_prediction": "Benign",
"alphamissense_score": 0.1227,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.842,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_174952.3",
"gene_symbol": "STPG2",
"hgnc_id": 28712,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.673G>A",
"hgvs_p": "p.Ala225Thr"
}
],
"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
}