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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: 3-38252824-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=38252824&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 38252824,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_005109.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSR1",
"gene_hgnc_id": 8508,
"hgvs_c": "c.1517G>A",
"hgvs_p": "p.Gly506Asp",
"transcript": "NM_005109.3",
"protein_id": "NP_005100.1",
"transcript_support_level": null,
"aa_start": 506,
"aa_end": null,
"aa_length": 527,
"cds_start": 1517,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000311806.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005109.3"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSR1",
"gene_hgnc_id": 8508,
"hgvs_c": "c.1517G>A",
"hgvs_p": "p.Gly506Asp",
"transcript": "ENST00000311806.8",
"protein_id": "ENSP00000311713.3",
"transcript_support_level": 1,
"aa_start": 506,
"aa_end": null,
"aa_length": 527,
"cds_start": 1517,
"cds_end": null,
"cds_length": 1584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005109.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000311806.8"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSR1",
"gene_hgnc_id": 8508,
"hgvs_c": "c.1481G>A",
"hgvs_p": "p.Gly494Asp",
"transcript": "ENST00000855343.1",
"protein_id": "ENSP00000525402.1",
"transcript_support_level": null,
"aa_start": 494,
"aa_end": null,
"aa_length": 515,
"cds_start": 1481,
"cds_end": null,
"cds_length": 1548,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855343.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSR1",
"gene_hgnc_id": 8508,
"hgvs_c": "c.1394G>A",
"hgvs_p": "p.Gly465Asp",
"transcript": "ENST00000855344.1",
"protein_id": "ENSP00000525403.1",
"transcript_support_level": null,
"aa_start": 465,
"aa_end": null,
"aa_length": 486,
"cds_start": 1394,
"cds_end": null,
"cds_length": 1461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000855344.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSR1",
"gene_hgnc_id": 8508,
"hgvs_c": "c.1676G>A",
"hgvs_p": "p.Gly559Asp",
"transcript": "XM_011534331.3",
"protein_id": "XP_011532633.1",
"transcript_support_level": null,
"aa_start": 559,
"aa_end": null,
"aa_length": 580,
"cds_start": 1676,
"cds_end": null,
"cds_length": 1743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011534331.3"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSR1",
"gene_hgnc_id": 8508,
"hgvs_c": "c.1640G>A",
"hgvs_p": "p.Gly547Asp",
"transcript": "XM_017007601.2",
"protein_id": "XP_016863090.1",
"transcript_support_level": null,
"aa_start": 547,
"aa_end": null,
"aa_length": 568,
"cds_start": 1640,
"cds_end": null,
"cds_length": 1707,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017007601.2"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSR1",
"gene_hgnc_id": 8508,
"hgvs_c": "c.1481G>A",
"hgvs_p": "p.Gly494Asp",
"transcript": "XM_047449386.1",
"protein_id": "XP_047305342.1",
"transcript_support_level": null,
"aa_start": 494,
"aa_end": null,
"aa_length": 515,
"cds_start": 1481,
"cds_end": null,
"cds_length": 1548,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449386.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSR1",
"gene_hgnc_id": 8508,
"hgvs_c": "c.1316G>A",
"hgvs_p": "p.Gly439Asp",
"transcript": "XM_047449387.1",
"protein_id": "XP_047305343.1",
"transcript_support_level": null,
"aa_start": 439,
"aa_end": null,
"aa_length": 460,
"cds_start": 1316,
"cds_end": null,
"cds_length": 1383,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449387.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSR1",
"gene_hgnc_id": 8508,
"hgvs_c": "c.1280G>A",
"hgvs_p": "p.Gly427Asp",
"transcript": "XM_047449388.1",
"protein_id": "XP_047305344.1",
"transcript_support_level": null,
"aa_start": 427,
"aa_end": null,
"aa_length": 448,
"cds_start": 1280,
"cds_end": null,
"cds_length": 1347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047449388.1"
},
{
"aa_ref": "G",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "OXSR1",
"gene_hgnc_id": 8508,
"hgvs_c": "c.941G>A",
"hgvs_p": "p.Gly314Asp",
"transcript": "XM_024453852.2",
"protein_id": "XP_024309620.1",
"transcript_support_level": null,
"aa_start": 314,
"aa_end": null,
"aa_length": 335,
"cds_start": 941,
"cds_end": null,
"cds_length": 1008,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024453852.2"
}
],
"gene_symbol": "OXSR1",
"gene_hgnc_id": 8508,
"dbsnp": "rs1433135948",
"frequency_reference_population": 0.0000020544257,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000205443,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7523378133773804,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.678,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6732,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.836,
"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_005109.3",
"gene_symbol": "OXSR1",
"hgnc_id": 8508,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1517G>A",
"hgvs_p": "p.Gly506Asp"
}
],
"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
}