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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: 3-39184951-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=39184951&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 39184951,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000340369.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIRP1",
"gene_hgnc_id": 14301,
"hgvs_c": "c.4495G>A",
"hgvs_p": "p.Glu1499Lys",
"transcript": "NM_194293.4",
"protein_id": "NP_919269.2",
"transcript_support_level": null,
"aa_start": 1499,
"aa_end": null,
"aa_length": 1843,
"cds_start": 4495,
"cds_end": null,
"cds_length": 5532,
"cdna_start": 4725,
"cdna_end": null,
"cdna_length": 6461,
"mane_select": "ENST00000340369.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIRP1",
"gene_hgnc_id": 14301,
"hgvs_c": "c.4495G>A",
"hgvs_p": "p.Glu1499Lys",
"transcript": "ENST00000340369.4",
"protein_id": "ENSP00000343140.3",
"transcript_support_level": 1,
"aa_start": 1499,
"aa_end": null,
"aa_length": 1843,
"cds_start": 4495,
"cds_end": null,
"cds_length": 5532,
"cdna_start": 4725,
"cdna_end": null,
"cdna_length": 6461,
"mane_select": "NM_194293.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIRP1",
"gene_hgnc_id": 14301,
"hgvs_c": "c.544G>A",
"hgvs_p": "p.Glu182Lys",
"transcript": "ENST00000421646.1",
"protein_id": "ENSP00000391645.1",
"transcript_support_level": 1,
"aa_start": 182,
"aa_end": null,
"aa_length": 526,
"cds_start": 544,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 861,
"cdna_end": null,
"cdna_length": 2596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIRP1",
"gene_hgnc_id": 14301,
"hgvs_c": "c.*702G>A",
"hgvs_p": null,
"transcript": "ENST00000396251.1",
"protein_id": "ENSP00000379550.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1121,
"cds_start": -4,
"cds_end": null,
"cds_length": 3366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6040,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIRP1",
"gene_hgnc_id": 14301,
"hgvs_c": "c.544G>A",
"hgvs_p": "p.Glu182Lys",
"transcript": "NM_001351377.2",
"protein_id": "NP_001338306.1",
"transcript_support_level": null,
"aa_start": 182,
"aa_end": null,
"aa_length": 526,
"cds_start": 544,
"cds_end": null,
"cds_length": 1581,
"cdna_start": 861,
"cdna_end": null,
"cdna_length": 2597,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIRP1",
"gene_hgnc_id": 14301,
"hgvs_c": "c.4495G>A",
"hgvs_p": "p.Glu1499Lys",
"transcript": "XM_005264909.4",
"protein_id": "XP_005264966.1",
"transcript_support_level": null,
"aa_start": 1499,
"aa_end": null,
"aa_length": 1843,
"cds_start": 4495,
"cds_end": null,
"cds_length": 5532,
"cdna_start": 4649,
"cdna_end": null,
"cdna_length": 6385,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIRP1",
"gene_hgnc_id": 14301,
"hgvs_c": "c.*702G>A",
"hgvs_p": null,
"transcript": "NM_001198621.4",
"protein_id": "NP_001185550.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1121,
"cds_start": -4,
"cds_end": null,
"cds_length": 3366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6034,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XIRP1",
"gene_hgnc_id": 14301,
"hgvs_c": "c.*702G>A",
"hgvs_p": null,
"transcript": "XM_047447588.1",
"protein_id": "XP_047303544.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1121,
"cds_start": -4,
"cds_end": null,
"cds_length": 3366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "ENSG00000287620",
"gene_hgnc_id": null,
"hgvs_c": "n.141+7023C>T",
"hgvs_p": null,
"transcript": "ENST00000720013.1",
"protein_id": null,
"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": 659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "XIRP1",
"gene_hgnc_id": 14301,
"dbsnp": "rs369082457",
"frequency_reference_population": 0.00006174483,
"hom_count_reference_population": 0,
"allele_count_reference_population": 96,
"gnomad_exomes_af": 0.0000656006,
"gnomad_genomes_af": 0.0000262536,
"gnomad_exomes_ac": 92,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.33511659502983093,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.671,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.1296,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.45,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.047,
"phylop100way_prediction": "Uncertain_significance",
"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": "Likely_benign",
"acmg_criteria": "BP4,BP6_Moderate",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000340369.4",
"gene_symbol": "XIRP1",
"hgnc_id": 14301,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.4495G>A",
"hgvs_p": "p.Glu1499Lys"
},
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000720013.1",
"gene_symbol": "ENSG00000287620",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.141+7023C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Classical primary microcephaly,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Classical primary microcephaly|not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}