← Back to variant description
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: 20-62828755-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=62828755&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 62828755,
"ref": "T",
"alt": "C",
"effect": "intron_variant",
"transcript": "ENST00000649368.1",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "c.901-9T>C",
"hgvs_p": null,
"transcript": "NM_001853.4",
"protein_id": "NP_001844.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 684,
"cds_start": -4,
"cds_end": null,
"cds_length": 2055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2497,
"mane_select": "ENST00000649368.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "c.901-9T>C",
"hgvs_p": null,
"transcript": "ENST00000649368.1",
"protein_id": "ENSP00000496793.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 684,
"cds_start": -4,
"cds_end": null,
"cds_length": 2055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2497,
"mane_select": "NM_001853.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "n.609-9T>C",
"hgvs_p": null,
"transcript": "ENST00000463487.2",
"protein_id": null,
"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": 716,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 16,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "c.1078-9T>C",
"hgvs_p": null,
"transcript": "XM_047439893.1",
"protein_id": "XP_047295849.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 743,
"cds_start": -4,
"cds_end": null,
"cds_length": 2232,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2921,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "c.340-9T>C",
"hgvs_p": null,
"transcript": "XM_047439894.1",
"protein_id": "XP_047295850.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 497,
"cds_start": -4,
"cds_end": null,
"cds_length": 1494,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2509,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "c.901-9T>C",
"hgvs_p": null,
"transcript": "XM_017027666.2",
"protein_id": "XP_016883155.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 486,
"cds_start": -4,
"cds_end": null,
"cds_length": 1461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1554,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 28,
"intron_rank": 17,
"intron_rank_end": null,
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"hgvs_c": "c.901-9T>C",
"hgvs_p": null,
"transcript": "XM_047439895.1",
"protein_id": "XP_047295851.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 471,
"cds_start": -4,
"cds_end": null,
"cds_length": 1416,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL9A3",
"gene_hgnc_id": 2219,
"dbsnp": "rs74506912",
"frequency_reference_population": 0.0060399505,
"hom_count_reference_population": 517,
"allele_count_reference_population": 9740,
"gnomad_exomes_af": 0.00578236,
"gnomad_genomes_af": 0.00850997,
"gnomad_exomes_ac": 8444,
"gnomad_genomes_ac": 1296,
"gnomad_exomes_homalt": 445,
"gnomad_genomes_homalt": 72,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7400000095367432,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.017999999225139618,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.74,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.721,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000238490170055761,
"dbscsnv_ada_prediction": "Benign",
"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": "ENST00000649368.1",
"gene_symbol": "COL9A3",
"hgnc_id": 2219,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.901-9T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Connective tissue disorder,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:7",
"phenotype_combined": "not specified|not provided|Connective tissue disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}