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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: 16-288128-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=288128&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP6_Moderate",
"BS2"
],
"effects": [
"synonymous_variant"
],
"gene_symbol": "AXIN1",
"hgnc_id": 903,
"hgvs_c": "c.2583G>A",
"hgvs_p": "p.Val861Val",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_003502.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP6_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 23,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"chr": "16",
"clinvar_classification": "Likely benign",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.49000000953674316,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 862,
"aa_ref": "V",
"aa_start": 861,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3707,
"cdna_start": 3019,
"cds_end": null,
"cds_length": 2589,
"cds_start": 2583,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "NM_003502.4",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.2583G>A",
"hgvs_p": "p.Val861Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000262320.8",
"protein_coding": true,
"protein_id": "NP_003493.1",
"strand": false,
"transcript": "NM_003502.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 862,
"aa_ref": "V",
"aa_start": 861,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3707,
"cdna_start": 3019,
"cds_end": null,
"cds_length": 2589,
"cds_start": 2583,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000262320.8",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.2583G>A",
"hgvs_p": "p.Val861Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_003502.4",
"protein_coding": true,
"protein_id": "ENSP00000262320.3",
"strand": false,
"transcript": "ENST00000262320.8",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 826,
"aa_ref": "V",
"aa_start": 825,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3324,
"cdna_start": 2637,
"cds_end": null,
"cds_length": 2481,
"cds_start": 2475,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000354866.7",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.2475G>A",
"hgvs_p": "p.Val825Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000346935.3",
"strand": false,
"transcript": "ENST00000354866.7",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 867,
"aa_ref": "V",
"aa_start": 866,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3728,
"cdna_start": 3041,
"cds_end": null,
"cds_length": 2604,
"cds_start": 2598,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000957925.1",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.2598G>A",
"hgvs_p": "p.Val866Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627984.1",
"strand": false,
"transcript": "ENST00000957925.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 861,
"aa_ref": "V",
"aa_start": 860,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3705,
"cdna_start": 3017,
"cds_end": null,
"cds_length": 2586,
"cds_start": 2580,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000911683.1",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.2580G>A",
"hgvs_p": "p.Val860Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581742.1",
"strand": false,
"transcript": "ENST00000911683.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 831,
"aa_ref": "V",
"aa_start": 830,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3579,
"cdna_start": 2891,
"cds_end": null,
"cds_length": 2496,
"cds_start": 2490,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000911684.1",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.2490G>A",
"hgvs_p": "p.Val830Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581743.1",
"strand": false,
"transcript": "ENST00000911684.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 826,
"aa_ref": "V",
"aa_start": 825,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3599,
"cdna_start": 2911,
"cds_end": null,
"cds_length": 2481,
"cds_start": 2475,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_181050.3",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.2475G>A",
"hgvs_p": "p.Val825Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_851393.1",
"strand": false,
"transcript": "NM_181050.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 824,
"aa_ref": "V",
"aa_start": 823,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3549,
"cdna_start": 2862,
"cds_end": null,
"cds_length": 2475,
"cds_start": 2469,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000911685.1",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.2469G>A",
"hgvs_p": "p.Val823Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581744.1",
"strand": false,
"transcript": "ENST00000911685.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 816,
"aa_ref": "V",
"aa_start": 815,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3527,
"cdna_start": 2839,
"cds_end": null,
"cds_length": 2451,
"cds_start": 2445,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000957926.1",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.2445G>A",
"hgvs_p": "p.Val815Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627985.1",
"strand": false,
"transcript": "ENST00000957926.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 779,
"aa_ref": "V",
"aa_start": 778,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3396,
"cdna_start": 2708,
"cds_end": null,
"cds_length": 2340,
"cds_start": 2334,
"consequences": [
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000957927.1",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.2334G>A",
"hgvs_p": "p.Val778Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627986.1",
"strand": false,
"transcript": "ENST00000957927.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 769,
"aa_ref": "V",
"aa_start": 768,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3382,
"cdna_start": 2694,
"cds_end": null,
"cds_length": 2310,
"cds_start": 2304,
"consequences": [
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000911686.1",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.2304G>A",
"hgvs_p": "p.Val768Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000581745.1",
"strand": false,
"transcript": "ENST00000911686.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 916,
"aa_ref": "V",
"aa_start": 915,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3722,
"cdna_start": 3034,
"cds_end": null,
"cds_length": 2751,
"cds_start": 2745,
"consequences": [
"synonymous_variant"
],
"exon_count": 11,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_011522682.3",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.2745G>A",
"hgvs_p": "p.Val915Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011520984.1",
"strand": false,
"transcript": "XM_011522682.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
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"aa_length": 880,
"aa_ref": "V",
"aa_start": 879,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3614,
"cdna_start": 2926,
"cds_end": null,
"cds_length": 2643,
"cds_start": 2637,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011522683.3",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.2637G>A",
"hgvs_p": "p.Val879Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011520985.1",
"strand": false,
"transcript": "XM_011522683.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 582,
"aa_ref": "V",
"aa_start": 581,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2629,
"cdna_start": 1941,
"cds_end": null,
"cds_length": 1749,
"cds_start": 1743,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_017023745.3",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.1743G>A",
"hgvs_p": "p.Val581Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016879234.1",
"strand": false,
"transcript": "XM_017023745.3",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 581,
"aa_ref": "V",
"aa_start": 580,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2443,
"cdna_start": 1755,
"cds_end": null,
"cds_length": 1746,
"cds_start": 1740,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_011522686.1",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.1740G>A",
"hgvs_p": "p.Val580Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011520988.1",
"strand": false,
"transcript": "XM_011522686.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 576,
"aa_ref": "V",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2428,
"cdna_start": 1740,
"cds_end": null,
"cds_length": 1731,
"cds_start": 1725,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047434731.1",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.1725G>A",
"hgvs_p": "p.Val575Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047290687.1",
"strand": false,
"transcript": "XM_047434731.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 540,
"aa_ref": "V",
"aa_start": 539,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3384,
"cdna_start": 2696,
"cds_end": null,
"cds_length": 1623,
"cds_start": 1617,
"consequences": [
"synonymous_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_047434732.1",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.1617G>A",
"hgvs_p": "p.Val539Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047290688.1",
"strand": false,
"transcript": "XM_047434732.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 512,
"aa_ref": "V",
"aa_start": 511,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3276,
"cdna_start": 2588,
"cds_end": null,
"cds_length": 1539,
"cds_start": 1533,
"consequences": [
"synonymous_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_017023746.2",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.1533G>A",
"hgvs_p": "p.Val511Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016879235.1",
"strand": false,
"transcript": "XM_017023746.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 6340,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000461023.5",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "n.5652G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000461023.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 3502,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NR_134879.2",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "n.2814G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_134879.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 101,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 334,
"cdna_start": null,
"cds_end": null,
"cds_length": 306,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000457798.1",
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"hgvs_c": "c.*88G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000416835.1",
"strand": true,
"transcript": "ENST00000457798.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs762766340",
"effect": "synonymous_variant",
"frequency_reference_population": 0.000014256687,
"gene_hgnc_id": 903,
"gene_symbol": "AXIN1",
"gnomad_exomes_ac": 16,
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"gnomad_genomes_ac": 7,
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"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.284,
"pos": 288128,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Uncertain_significance",
"splice_score_selected": 0.3499999940395355,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Uncertain_significance",
"spliceai_max_score": 0.35,
"transcript": "NM_003502.4"
}
]
}