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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: 19-9966377-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=9966377&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": [
"synonymous_variant"
],
"gene_symbol": "COL5A3",
"hgnc_id": 14864,
"hgvs_c": "c.4719G>A",
"hgvs_p": "p.Arg1573Arg",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -9,
"transcript": "NM_015719.4",
"verdict": "Benign"
},
{
"benign_score": 8,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000295554",
"hgnc_id": null,
"hgvs_c": "n.74-17673C>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -8,
"transcript": "ENST00000730923.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7,BS2",
"acmg_score": -9,
"allele_count_reference_population": 7094,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.28,
"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": -0.2800000011920929,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 1745,
"aa_ref": "R",
"aa_start": 1573,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6207,
"cdna_start": 4838,
"cds_end": null,
"cds_length": 5238,
"cds_start": 4719,
"consequences": [
"synonymous_variant"
],
"exon_count": 67,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "NM_015719.4",
"gene_hgnc_id": 14864,
"gene_symbol": "COL5A3",
"hgvs_c": "c.4719G>A",
"hgvs_p": "p.Arg1573Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000264828.4",
"protein_coding": true,
"protein_id": "NP_056534.2",
"strand": false,
"transcript": "NM_015719.4",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 1745,
"aa_ref": "R",
"aa_start": 1573,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6207,
"cdna_start": 4838,
"cds_end": null,
"cds_length": 5238,
"cds_start": 4719,
"consequences": [
"synonymous_variant"
],
"exon_count": 67,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "ENST00000264828.4",
"gene_hgnc_id": 14864,
"gene_symbol": "COL5A3",
"hgvs_c": "c.4719G>A",
"hgvs_p": "p.Arg1573Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015719.4",
"protein_coding": true,
"protein_id": "ENSP00000264828.3",
"strand": false,
"transcript": "ENST00000264828.4",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 1744,
"aa_ref": "R",
"aa_start": 1572,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6204,
"cdna_start": 4835,
"cds_end": null,
"cds_length": 5235,
"cds_start": 4716,
"consequences": [
"synonymous_variant"
],
"exon_count": 67,
"exon_rank": 64,
"exon_rank_end": null,
"feature": "XM_011528042.3",
"gene_hgnc_id": 14864,
"gene_symbol": "COL5A3",
"hgvs_c": "c.4716G>A",
"hgvs_p": "p.Arg1572Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011526344.1",
"strand": false,
"transcript": "XM_011528042.3",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 966,
"aa_ref": "R",
"aa_start": 794,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3874,
"cdna_start": 2505,
"cds_end": null,
"cds_length": 2901,
"cds_start": 2382,
"consequences": [
"synonymous_variant"
],
"exon_count": 40,
"exon_rank": 37,
"exon_rank_end": null,
"feature": "XM_017026849.2",
"gene_hgnc_id": 14864,
"gene_symbol": "COL5A3",
"hgvs_c": "c.2382G>A",
"hgvs_p": "p.Arg794Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016882338.1",
"strand": false,
"transcript": "XM_017026849.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 644,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000730923.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000295554",
"hgvs_c": "n.74-17673C>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000730923.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs139736960",
"effect": "synonymous_variant",
"frequency_reference_population": 0.004405954,
"gene_hgnc_id": 14864,
"gene_symbol": "COL5A3",
"gnomad_exomes_ac": 6306,
"gnomad_exomes_af": 0.00432565,
"gnomad_exomes_homalt": 45,
"gnomad_genomes_ac": 788,
"gnomad_genomes_af": 0.00517468,
"gnomad_genomes_homalt": 17,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 62,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Likely benign",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.666,
"pos": 9966377,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.10999999940395355,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.11,
"transcript": "NM_015719.4"
}
]
}