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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: 2-152126231-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=152126231&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 152126231,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005843.6",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAM2",
"gene_hgnc_id": 11358,
"hgvs_c": "c.1174A>G",
"hgvs_p": "p.Met392Val",
"transcript": "NM_005843.6",
"protein_id": "NP_005834.4",
"transcript_support_level": null,
"aa_start": 392,
"aa_end": null,
"aa_length": 525,
"cds_start": 1174,
"cds_end": null,
"cds_length": 1578,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000263904.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005843.6"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAM2",
"gene_hgnc_id": 11358,
"hgvs_c": "c.1174A>G",
"hgvs_p": "p.Met392Val",
"transcript": "ENST00000263904.5",
"protein_id": "ENSP00000263904.4",
"transcript_support_level": 1,
"aa_start": 392,
"aa_end": null,
"aa_length": 525,
"cds_start": 1174,
"cds_end": null,
"cds_length": 1578,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005843.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263904.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAM2",
"gene_hgnc_id": 11358,
"hgvs_c": "n.1261A>G",
"hgvs_p": null,
"transcript": "ENST00000482997.5",
"protein_id": null,
"transcript_support_level": 1,
"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": "retained_intron",
"feature": "ENST00000482997.5"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAM2",
"gene_hgnc_id": 11358,
"hgvs_c": "c.1228A>G",
"hgvs_p": "p.Met410Val",
"transcript": "ENST00000865052.1",
"protein_id": "ENSP00000535111.1",
"transcript_support_level": null,
"aa_start": 410,
"aa_end": null,
"aa_length": 543,
"cds_start": 1228,
"cds_end": null,
"cds_length": 1632,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865052.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAM2",
"gene_hgnc_id": 11358,
"hgvs_c": "c.1129A>G",
"hgvs_p": "p.Met377Val",
"transcript": "ENST00000968933.1",
"protein_id": "ENSP00000638992.1",
"transcript_support_level": null,
"aa_start": 377,
"aa_end": null,
"aa_length": 510,
"cds_start": 1129,
"cds_end": null,
"cds_length": 1533,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968933.1"
},
{
"aa_ref": "M",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STAM2",
"gene_hgnc_id": 11358,
"hgvs_c": "c.1075A>G",
"hgvs_p": "p.Met359Val",
"transcript": "ENST00000968932.1",
"protein_id": "ENSP00000638991.1",
"transcript_support_level": null,
"aa_start": 359,
"aa_end": null,
"aa_length": 492,
"cds_start": 1075,
"cds_end": null,
"cds_length": 1479,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000968932.1"
},
{
"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": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "STAM2",
"gene_hgnc_id": 11358,
"hgvs_c": "c.1026-5429A>G",
"hgvs_p": null,
"transcript": "ENST00000865053.1",
"protein_id": "ENSP00000535112.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 417,
"cds_start": null,
"cds_end": null,
"cds_length": 1254,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000865053.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000304591",
"gene_hgnc_id": null,
"hgvs_c": "n.181+685T>C",
"hgvs_p": null,
"transcript": "ENST00000804854.1",
"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": "ENST00000804854.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000304591",
"gene_hgnc_id": null,
"hgvs_c": "n.152+685T>C",
"hgvs_p": null,
"transcript": "ENST00000804855.1",
"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": "ENST00000804855.1"
}
],
"gene_symbol": "STAM2",
"gene_hgnc_id": 11358,
"dbsnp": "rs61754878",
"frequency_reference_population": 0.0024935487,
"hom_count_reference_population": 31,
"allele_count_reference_population": 3954,
"gnomad_exomes_af": 0.00239577,
"gnomad_genomes_af": 0.00341364,
"gnomad_exomes_ac": 3434,
"gnomad_genomes_ac": 520,
"gnomad_exomes_homalt": 25,
"gnomad_genomes_homalt": 6,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.003157585859298706,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.062,
"revel_prediction": "Benign",
"alphamissense_score": 0.049,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.7,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.256,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_005843.6",
"gene_symbol": "STAM2",
"hgnc_id": 11358,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1174A>G",
"hgvs_p": "p.Met392Val"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000804854.1",
"gene_symbol": "ENSG00000304591",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.181+685T>C",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}