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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: 19-43543687-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=43543687&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 9,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7",
"BS2"
],
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"gene_symbol": "XRCC1",
"hgnc_id": 12828,
"hgvs_c": "c.1713G>A",
"hgvs_p": "p.Gly571Gly",
"inheritance_mode": "Unknown,AD",
"pathogenic_score": 0,
"score": -9,
"transcript": "NM_006297.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7,BS2",
"acmg_score": -9,
"allele_count_reference_population": 2575,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.45,
"chr": "19",
"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": -0.44999998807907104,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 633,
"aa_ref": "G",
"aa_start": 571,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2052,
"cdna_start": 1782,
"cds_end": null,
"cds_length": 1902,
"cds_start": 1713,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "NM_006297.3",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1713G>A",
"hgvs_p": "p.Gly571Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000262887.10",
"protein_coding": true,
"protein_id": "NP_006288.2",
"strand": false,
"transcript": "NM_006297.3",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 633,
"aa_ref": "G",
"aa_start": 571,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2052,
"cdna_start": 1782,
"cds_end": null,
"cds_length": 1902,
"cds_start": 1713,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000262887.10",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1713G>A",
"hgvs_p": "p.Gly571Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_006297.3",
"protein_coding": true,
"protein_id": "ENSP00000262887.5",
"strand": false,
"transcript": "ENST00000262887.10",
"transcript_support_level": 1
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 637,
"aa_ref": "G",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2060,
"cdna_start": 1791,
"cds_end": null,
"cds_length": 1914,
"cds_start": 1725,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000953258.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1725G>A",
"hgvs_p": "p.Gly575Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000623317.1",
"strand": false,
"transcript": "ENST00000953258.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 632,
"aa_ref": "G",
"aa_start": 570,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2102,
"cdna_start": 1827,
"cds_end": null,
"cds_length": 1899,
"cds_start": 1710,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000865401.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1710G>A",
"hgvs_p": "p.Gly570Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535460.1",
"strand": false,
"transcript": "ENST00000865401.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 632,
"aa_ref": "G",
"aa_start": 570,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2085,
"cdna_start": 1815,
"cds_end": null,
"cds_length": 1899,
"cds_start": 1710,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000865404.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1710G>A",
"hgvs_p": "p.Gly570Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535463.1",
"strand": false,
"transcript": "ENST00000865404.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 631,
"aa_ref": "G",
"aa_start": 569,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2137,
"cdna_start": 1867,
"cds_end": null,
"cds_length": 1896,
"cds_start": 1707,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000865400.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1707G>A",
"hgvs_p": "p.Gly569Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535459.1",
"strand": false,
"transcript": "ENST00000865400.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 631,
"aa_ref": "G",
"aa_start": 569,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2076,
"cdna_start": 1807,
"cds_end": null,
"cds_length": 1896,
"cds_start": 1707,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000865405.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1707G>A",
"hgvs_p": "p.Gly569Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535464.1",
"strand": false,
"transcript": "ENST00000865405.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 631,
"aa_ref": "G",
"aa_start": 569,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2140,
"cdna_start": 1870,
"cds_end": null,
"cds_length": 1896,
"cds_start": 1707,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000953254.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1707G>A",
"hgvs_p": "p.Gly569Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000623313.1",
"strand": false,
"transcript": "ENST00000953254.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 630,
"aa_ref": "G",
"aa_start": 568,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2083,
"cdna_start": 1813,
"cds_end": null,
"cds_length": 1893,
"cds_start": 1704,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000865403.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1704G>A",
"hgvs_p": "p.Gly568Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535462.1",
"strand": false,
"transcript": "ENST00000865403.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 630,
"aa_ref": "G",
"aa_start": 568,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2051,
"cdna_start": 1776,
"cds_end": null,
"cds_length": 1893,
"cds_start": 1704,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000953256.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1704G>A",
"hgvs_p": "p.Gly568Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000623315.1",
"strand": false,
"transcript": "ENST00000953256.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 623,
"aa_ref": "G",
"aa_start": 561,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2063,
"cdna_start": 1788,
"cds_end": null,
"cds_length": 1872,
"cds_start": 1683,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000934412.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1683G>A",
"hgvs_p": "p.Gly561Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604471.1",
"strand": false,
"transcript": "ENST00000934412.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 602,
"aa_ref": "G",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1994,
"cdna_start": 1725,
"cds_end": null,
"cds_length": 1809,
"cds_start": 1620,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000543982.5",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1620G>A",
"hgvs_p": "p.Gly540Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443671.1",
"strand": false,
"transcript": "ENST00000543982.5",
"transcript_support_level": 2
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 601,
"aa_ref": "G",
"aa_start": 539,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1987,
"cdna_start": 1717,
"cds_end": null,
"cds_length": 1806,
"cds_start": 1617,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000934413.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1617G>A",
"hgvs_p": "p.Gly539Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000604472.1",
"strand": false,
"transcript": "ENST00000934413.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 595,
"aa_ref": "G",
"aa_start": 533,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1983,
"cdna_start": 1708,
"cds_end": null,
"cds_length": 1788,
"cds_start": 1599,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000865402.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1599G>A",
"hgvs_p": "p.Gly533Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535461.1",
"strand": false,
"transcript": "ENST00000865402.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 594,
"aa_ref": "G",
"aa_start": 532,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1940,
"cdna_start": 1671,
"cds_end": null,
"cds_length": 1785,
"cds_start": 1596,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000953257.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1596G>A",
"hgvs_p": "p.Gly532Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000623316.1",
"strand": false,
"transcript": "ENST00000953257.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 580,
"aa_ref": "G",
"aa_start": 518,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2012,
"cdna_start": 1744,
"cds_end": null,
"cds_length": 1743,
"cds_start": 1554,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000865399.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1554G>A",
"hgvs_p": "p.Gly518Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000535458.1",
"strand": false,
"transcript": "ENST00000865399.1",
"transcript_support_level": null
},
{
"aa_alt": "G",
"aa_end": null,
"aa_length": 559,
"aa_ref": "G",
"aa_start": 497,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1848,
"cdna_start": 1581,
"cds_end": null,
"cds_length": 1680,
"cds_start": 1491,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000953255.1",
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"hgvs_c": "c.1491G>A",
"hgvs_p": "p.Gly497Gly",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000623314.1",
"strand": false,
"transcript": "ENST00000953255.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.000797384700535443,
"dbsnp": "rs2307182",
"effect": "splice_region_variant,synonymous_variant",
"frequency_reference_population": 0.001595512,
"gene_hgnc_id": 12828,
"gene_symbol": "XRCC1",
"gnomad_exomes_ac": 2391,
"gnomad_exomes_af": 0.00163564,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_ac": 184,
"gnomad_genomes_af": 0.00120981,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 5,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.199,
"pos": 43543687,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.10599999874830246,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.03,
"transcript": "NM_006297.3"
}
]
}