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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: 9-125003528-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=125003528&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 125003528,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_173690.5",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "c.904C>G",
"hgvs_p": "p.Gln302Glu",
"transcript": "NM_001144877.3",
"protein_id": "NP_001138349.1",
"transcript_support_level": null,
"aa_start": 302,
"aa_end": null,
"aa_length": 606,
"cds_start": 904,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000336505.11",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001144877.3"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "c.904C>G",
"hgvs_p": "p.Gln302Glu",
"transcript": "ENST00000336505.11",
"protein_id": "ENSP00000336756.6",
"transcript_support_level": 1,
"aa_start": 302,
"aa_end": null,
"aa_length": 606,
"cds_start": 904,
"cds_end": null,
"cds_length": 1821,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001144877.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000336505.11"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "c.973C>G",
"hgvs_p": "p.Gln325Glu",
"transcript": "ENST00000373549.8",
"protein_id": "ENSP00000362650.4",
"transcript_support_level": 1,
"aa_start": 325,
"aa_end": null,
"aa_length": 629,
"cds_start": 973,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373549.8"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "c.973C>G",
"hgvs_p": "p.Gln325Glu",
"transcript": "NM_173690.5",
"protein_id": "NP_775961.2",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 629,
"cds_start": 973,
"cds_end": null,
"cds_length": 1890,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_173690.5"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "c.904C>G",
"hgvs_p": "p.Gln302Glu",
"transcript": "ENST00000858987.1",
"protein_id": "ENSP00000529046.1",
"transcript_support_level": null,
"aa_start": 302,
"aa_end": null,
"aa_length": 600,
"cds_start": 904,
"cds_end": null,
"cds_length": 1803,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858987.1"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "c.808C>G",
"hgvs_p": "p.Gln270Glu",
"transcript": "ENST00000858986.1",
"protein_id": "ENSP00000529045.1",
"transcript_support_level": null,
"aa_start": 270,
"aa_end": null,
"aa_length": 574,
"cds_start": 808,
"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": "ENST00000858986.1"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "c.772C>G",
"hgvs_p": "p.Gln258Glu",
"transcript": "ENST00000858985.1",
"protein_id": "ENSP00000529044.1",
"transcript_support_level": null,
"aa_start": 258,
"aa_end": null,
"aa_length": 562,
"cds_start": 772,
"cds_end": null,
"cds_length": 1689,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000858985.1"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "c.721C>G",
"hgvs_p": "p.Gln241Glu",
"transcript": "ENST00000923997.1",
"protein_id": "ENSP00000594056.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 545,
"cds_start": 721,
"cds_end": null,
"cds_length": 1638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000923997.1"
},
{
"aa_ref": "Q",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "c.718C>G",
"hgvs_p": "p.Gln240Glu",
"transcript": "ENST00000952247.1",
"protein_id": "ENSP00000622306.1",
"transcript_support_level": null,
"aa_start": 240,
"aa_end": null,
"aa_length": 544,
"cds_start": 718,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952247.1"
},
{
"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": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "n.904C>G",
"hgvs_p": null,
"transcript": "ENST00000477186.5",
"protein_id": "ENSP00000419576.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000477186.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "n.163C>G",
"hgvs_p": null,
"transcript": "ENST00000487795.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000487795.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "n.1064C>G",
"hgvs_p": null,
"transcript": "XR_007061281.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007061281.1"
},
{
"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": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "n.995C>G",
"hgvs_p": null,
"transcript": "XR_007061282.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007061282.1"
},
{
"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": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "n.995C>G",
"hgvs_p": null,
"transcript": "XR_007061283.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_007061283.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"hgvs_c": "n.1064C>G",
"hgvs_p": null,
"transcript": "XR_929768.2",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_929768.2"
}
],
"gene_symbol": "SCAI",
"gene_hgnc_id": 26709,
"dbsnp": null,
"frequency_reference_population": 6.844027e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84403e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8097331523895264,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.469,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7621,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.16,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.516,
"phylop100way_prediction": "Pathogenic",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_173690.5",
"gene_symbol": "SCAI",
"hgnc_id": 26709,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.973C>G",
"hgvs_p": "p.Gln325Glu"
}
],
"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
}