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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: 20-63642257-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=63642257&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 63642257,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_015894.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STMN3",
"gene_hgnc_id": 15926,
"hgvs_c": "c.334G>A",
"hgvs_p": "p.Glu112Lys",
"transcript": "NM_015894.4",
"protein_id": "NP_056978.2",
"transcript_support_level": null,
"aa_start": 112,
"aa_end": null,
"aa_length": 180,
"cds_start": 334,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000370053.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015894.4"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STMN3",
"gene_hgnc_id": 15926,
"hgvs_c": "c.334G>A",
"hgvs_p": "p.Glu112Lys",
"transcript": "ENST00000370053.3",
"protein_id": "ENSP00000359070.1",
"transcript_support_level": 1,
"aa_start": 112,
"aa_end": null,
"aa_length": 180,
"cds_start": 334,
"cds_end": null,
"cds_length": 543,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_015894.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370053.3"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STMN3",
"gene_hgnc_id": 15926,
"hgvs_c": "c.508G>A",
"hgvs_p": "p.Glu170Lys",
"transcript": "ENST00000631920.1",
"protein_id": "ENSP00000487795.1",
"transcript_support_level": 2,
"aa_start": 170,
"aa_end": null,
"aa_length": 238,
"cds_start": 508,
"cds_end": null,
"cds_length": 717,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000631920.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STMN3",
"gene_hgnc_id": 15926,
"hgvs_c": "c.358G>A",
"hgvs_p": "p.Glu120Lys",
"transcript": "ENST00000860150.1",
"protein_id": "ENSP00000530209.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 188,
"cds_start": 358,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860150.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STMN3",
"gene_hgnc_id": 15926,
"hgvs_c": "c.334G>A",
"hgvs_p": "p.Glu112Lys",
"transcript": "ENST00000860151.1",
"protein_id": "ENSP00000530210.1",
"transcript_support_level": null,
"aa_start": 112,
"aa_end": null,
"aa_length": 188,
"cds_start": 334,
"cds_end": null,
"cds_length": 567,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000860151.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STMN3",
"gene_hgnc_id": 15926,
"hgvs_c": "c.334G>A",
"hgvs_p": "p.Glu112Lys",
"transcript": "ENST00000953346.1",
"protein_id": "ENSP00000623405.1",
"transcript_support_level": null,
"aa_start": 112,
"aa_end": null,
"aa_length": 179,
"cds_start": 334,
"cds_end": null,
"cds_length": 540,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953346.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STMN3",
"gene_hgnc_id": 15926,
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Glu101Lys",
"transcript": "NM_001276310.2",
"protein_id": "NP_001263239.1",
"transcript_support_level": null,
"aa_start": 101,
"aa_end": null,
"aa_length": 169,
"cds_start": 301,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001276310.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STMN3",
"gene_hgnc_id": 15926,
"hgvs_c": "c.301G>A",
"hgvs_p": "p.Glu101Lys",
"transcript": "ENST00000540534.5",
"protein_id": "ENSP00000439840.1",
"transcript_support_level": 2,
"aa_start": 101,
"aa_end": null,
"aa_length": 169,
"cds_start": 301,
"cds_end": null,
"cds_length": 510,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000540534.5"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STMN3",
"gene_hgnc_id": 15926,
"hgvs_c": "c.334G>A",
"hgvs_p": "p.Glu112Lys",
"transcript": "ENST00000940055.1",
"protein_id": "ENSP00000610114.1",
"transcript_support_level": null,
"aa_start": 112,
"aa_end": null,
"aa_length": 161,
"cds_start": 334,
"cds_end": null,
"cds_length": 486,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000940055.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STMN3",
"gene_hgnc_id": 15926,
"hgvs_c": "n.510G>A",
"hgvs_p": null,
"transcript": "NR_075070.2",
"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": "NR_075070.2"
}
],
"gene_symbol": "STMN3",
"gene_hgnc_id": 15926,
"dbsnp": "rs370557606",
"frequency_reference_population": 0.000022643228,
"hom_count_reference_population": 0,
"allele_count_reference_population": 35,
"gnomad_exomes_af": 0.0000229548,
"gnomad_genomes_af": 0.0000197798,
"gnomad_exomes_ac": 32,
"gnomad_genomes_ac": 3,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6885799169540405,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.211,
"revel_prediction": "Benign",
"alphamissense_score": 0.4357,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.11,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.641,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 0,
"pathogenic_score": 0,
"criteria": [],
"verdict": "Uncertain_significance",
"transcript": "NM_015894.4",
"gene_symbol": "STMN3",
"hgnc_id": 15926,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.334G>A",
"hgvs_p": "p.Glu112Lys"
}
],
"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
}