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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: 19-43560950-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=43560950&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 43560950,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000262887.10",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC1",
"gene_hgnc_id": 12828,
"hgvs_c": "c.215T>C",
"hgvs_p": "p.Val72Ala",
"transcript": "NM_006297.3",
"protein_id": "NP_006288.2",
"transcript_support_level": null,
"aa_start": 72,
"aa_end": null,
"aa_length": 633,
"cds_start": 215,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 2052,
"mane_select": "ENST00000262887.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC1",
"gene_hgnc_id": 12828,
"hgvs_c": "c.215T>C",
"hgvs_p": "p.Val72Ala",
"transcript": "ENST00000262887.10",
"protein_id": "ENSP00000262887.5",
"transcript_support_level": 1,
"aa_start": 72,
"aa_end": null,
"aa_length": 633,
"cds_start": 215,
"cds_end": null,
"cds_length": 1902,
"cdna_start": 284,
"cdna_end": null,
"cdna_length": 2052,
"mane_select": "NM_006297.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000268361",
"gene_hgnc_id": null,
"hgvs_c": "c.239T>C",
"hgvs_p": "p.Val80Ala",
"transcript": "ENST00000594374.1",
"protein_id": "ENSP00000472698.1",
"transcript_support_level": 3,
"aa_start": 80,
"aa_end": null,
"aa_length": 129,
"cds_start": 239,
"cds_end": null,
"cds_length": 392,
"cdna_start": 240,
"cdna_end": null,
"cdna_length": 393,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC1",
"gene_hgnc_id": 12828,
"hgvs_c": "c.122T>C",
"hgvs_p": "p.Val41Ala",
"transcript": "ENST00000543982.5",
"protein_id": "ENSP00000443671.1",
"transcript_support_level": 2,
"aa_start": 41,
"aa_end": null,
"aa_length": 602,
"cds_start": 122,
"cds_end": null,
"cds_length": 1809,
"cdna_start": 227,
"cdna_end": null,
"cdna_length": 1994,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC1",
"gene_hgnc_id": 12828,
"hgvs_c": "c.236T>C",
"hgvs_p": "p.Val79Ala",
"transcript": "ENST00000598165.5",
"protein_id": "ENSP00000470045.1",
"transcript_support_level": 3,
"aa_start": 79,
"aa_end": null,
"aa_length": 291,
"cds_start": 236,
"cds_end": null,
"cds_length": 876,
"cdna_start": 273,
"cdna_end": null,
"cdna_length": 913,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC1",
"gene_hgnc_id": 12828,
"hgvs_c": "c.140T>C",
"hgvs_p": "p.Val47Ala",
"transcript": "ENST00000599693.5",
"protein_id": "ENSP00000472128.1",
"transcript_support_level": 3,
"aa_start": 47,
"aa_end": null,
"aa_length": 208,
"cds_start": 140,
"cds_end": null,
"cds_length": 627,
"cdna_start": 141,
"cdna_end": null,
"cdna_length": 628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC1",
"gene_hgnc_id": 12828,
"hgvs_c": "n.263T>C",
"hgvs_p": null,
"transcript": "ENST00000595789.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 1147,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "XRCC1",
"gene_hgnc_id": 12828,
"hgvs_c": "c.145-6146T>C",
"hgvs_p": null,
"transcript": "ENST00000594107.1",
"protein_id": "ENSP00000471159.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 171,
"cds_start": -4,
"cds_end": null,
"cds_length": 517,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "XRCC1",
"gene_hgnc_id": 12828,
"hgvs_c": "n.-2T>C",
"hgvs_p": null,
"transcript": "ENST00000597811.5",
"protein_id": "ENSP00000470391.1",
"transcript_support_level": 5,
"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": 809,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "XRCC1",
"gene_hgnc_id": 12828,
"dbsnp": "rs25496",
"frequency_reference_population": 0.0032016851,
"hom_count_reference_population": 139,
"allele_count_reference_population": 5168,
"gnomad_exomes_af": 0.00173133,
"gnomad_genomes_af": 0.0173184,
"gnomad_exomes_ac": 2531,
"gnomad_genomes_ac": 2637,
"gnomad_exomes_homalt": 65,
"gnomad_genomes_homalt": 74,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008586138486862183,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.13,
"revel_prediction": "Benign",
"alphamissense_score": 0.2019,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.397,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000262887.10",
"gene_symbol": "XRCC1",
"hgnc_id": 12828,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,Unknown",
"hgvs_c": "c.215T>C",
"hgvs_p": "p.Val72Ala"
},
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000594374.1",
"gene_symbol": "ENSG00000268361",
"hgnc_id": null,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.239T>C",
"hgvs_p": "p.Val80Ala"
}
],
"clinvar_disease": "XRCC1-related disorder,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided|XRCC1-related disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}