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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: 5-83258607-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=83258607&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 83258607,
"ref": "C",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000396027.9",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "NM_003401.5",
"protein_id": "NP_003392.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 334,
"cds_start": 823,
"cds_end": null,
"cds_length": 1005,
"cdna_start": 902,
"cdna_end": null,
"cdna_length": 1602,
"mane_select": "ENST00000396027.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "ENST00000396027.9",
"protein_id": "ENSP00000379344.4",
"transcript_support_level": 5,
"aa_start": 275,
"aa_end": null,
"aa_length": 334,
"cds_start": 823,
"cds_end": null,
"cds_length": 1005,
"cdna_start": 902,
"cdna_end": null,
"cdna_length": 1602,
"mane_select": "NM_003401.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "ENST00000511817.1",
"protein_id": "ENSP00000421491.1",
"transcript_support_level": 1,
"aa_start": 275,
"aa_end": null,
"aa_length": 336,
"cds_start": 823,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 903,
"cdna_end": null,
"cdna_length": 1636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "ENST00000282268.7",
"protein_id": "ENSP00000282268.3",
"transcript_support_level": 1,
"aa_start": 275,
"aa_end": null,
"aa_length": 334,
"cds_start": 823,
"cds_end": null,
"cds_length": 1005,
"cdna_start": 998,
"cdna_end": null,
"cdna_length": 1696,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "n.892C>T",
"hgvs_p": null,
"transcript": "ENST00000542685.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 1243,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "NM_001318012.3",
"protein_id": "NP_001304941.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 336,
"cds_start": 823,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 949,
"cdna_end": null,
"cdna_length": 1655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "NM_022406.5",
"protein_id": "NP_071801.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 336,
"cds_start": 823,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 902,
"cdna_end": null,
"cdna_length": 1608,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "ENST00000338635.10",
"protein_id": "ENSP00000342011.6",
"transcript_support_level": 2,
"aa_start": 275,
"aa_end": null,
"aa_length": 336,
"cds_start": 823,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 922,
"cdna_end": null,
"cdna_length": 1579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "NM_022550.4",
"protein_id": "NP_072044.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 334,
"cds_start": 823,
"cds_end": null,
"cds_length": 1005,
"cdna_start": 949,
"cdna_end": null,
"cdna_length": 1649,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "NM_001318013.2",
"protein_id": "NP_001304942.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 310,
"cds_start": 823,
"cds_end": null,
"cds_length": 933,
"cdna_start": 902,
"cdna_end": null,
"cdna_length": 1252,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "XM_011543626.2",
"protein_id": "XP_011541928.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 336,
"cds_start": 823,
"cds_end": null,
"cds_length": 1011,
"cdna_start": 946,
"cdna_end": null,
"cdna_length": 1652,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "XM_047417694.1",
"protein_id": "XP_047273650.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 334,
"cds_start": 823,
"cds_end": null,
"cds_length": 1005,
"cdna_start": 946,
"cdna_end": null,
"cdna_length": 1646,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "XM_017009827.3",
"protein_id": "XP_016865316.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 312,
"cds_start": 823,
"cds_end": null,
"cds_length": 939,
"cdna_start": 902,
"cdna_end": null,
"cdna_length": 1807,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "XM_047417695.1",
"protein_id": "XP_047273651.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 312,
"cds_start": 823,
"cds_end": null,
"cds_length": 939,
"cdna_start": 949,
"cdna_end": null,
"cdna_length": 1854,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "XM_047417696.1",
"protein_id": "XP_047273652.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 310,
"cds_start": 823,
"cds_end": null,
"cds_length": 933,
"cdna_start": 949,
"cdna_end": null,
"cdna_length": 1299,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "XM_017009828.3",
"protein_id": "XP_016865317.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 308,
"cds_start": 823,
"cds_end": null,
"cds_length": 927,
"cdna_start": 902,
"cdna_end": null,
"cdna_length": 2815,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*",
"transcript": "XM_047417697.1",
"protein_id": "XP_047273653.1",
"transcript_support_level": null,
"aa_start": 275,
"aa_end": null,
"aa_length": 308,
"cds_start": 823,
"cds_end": null,
"cds_length": 927,
"cdna_start": 949,
"cdna_end": null,
"cdna_length": 2862,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "n.835C>T",
"hgvs_p": null,
"transcript": "ENST00000509268.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 1567,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"hgvs_c": "c.*113C>T",
"hgvs_p": null,
"transcript": "XM_047417698.1",
"protein_id": "XP_047273654.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 261,
"cds_start": -4,
"cds_end": null,
"cds_length": 786,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1095,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "XRCC4",
"gene_hgnc_id": 12831,
"dbsnp": "rs797045016",
"frequency_reference_population": 0.000006855269,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.00000685527,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 10,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6200000047683716,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.62,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.958,
"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": "Pathogenic",
"acmg_criteria": "PVS1,PP5_Moderate",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000396027.9",
"gene_symbol": "XRCC4",
"hgnc_id": 12831,
"effects": [
"stop_gained"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.823C>T",
"hgvs_p": "p.Arg275*"
}
],
"clinvar_disease": " and endocrine dysfunction, microcephaly,Short stature",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Short stature, microcephaly, and endocrine dysfunction",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}