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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: 1-40301280-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=40301280&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 40301280,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000372748.8",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.1972G>A",
"hgvs_p": "p.Val658Met",
"transcript": "NM_001852.4",
"protein_id": "NP_001843.1",
"transcript_support_level": null,
"aa_start": 658,
"aa_end": null,
"aa_length": 689,
"cds_start": 1972,
"cds_end": null,
"cds_length": 2070,
"cdna_start": 2061,
"cdna_end": null,
"cdna_length": 2852,
"mane_select": "ENST00000372748.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.1972G>A",
"hgvs_p": "p.Val658Met",
"transcript": "ENST00000372748.8",
"protein_id": "ENSP00000361834.3",
"transcript_support_level": 1,
"aa_start": 658,
"aa_end": null,
"aa_length": 689,
"cds_start": 1972,
"cds_end": null,
"cds_length": 2070,
"cdna_start": 2061,
"cdna_end": null,
"cdna_length": 2852,
"mane_select": "NM_001852.4",
"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": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "n.2275G>A",
"hgvs_p": null,
"transcript": "ENST00000482722.5",
"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": 2887,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.1984G>A",
"hgvs_p": "p.Val662Met",
"transcript": "XM_017000332.2",
"protein_id": "XP_016855821.1",
"transcript_support_level": null,
"aa_start": 662,
"aa_end": null,
"aa_length": 693,
"cds_start": 1984,
"cds_end": null,
"cds_length": 2082,
"cdna_start": 2073,
"cdna_end": null,
"cdna_length": 2864,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 32,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.1702G>A",
"hgvs_p": "p.Val568Met",
"transcript": "XM_011540715.3",
"protein_id": "XP_011539017.1",
"transcript_support_level": null,
"aa_start": 568,
"aa_end": null,
"aa_length": 599,
"cds_start": 1702,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 2167,
"cdna_end": null,
"cdna_length": 2958,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.1702G>A",
"hgvs_p": "p.Val568Met",
"transcript": "XM_011540716.3",
"protein_id": "XP_011539018.1",
"transcript_support_level": null,
"aa_start": 568,
"aa_end": null,
"aa_length": 599,
"cds_start": 1702,
"cds_end": null,
"cds_length": 1800,
"cdna_start": 2013,
"cdna_end": null,
"cdna_length": 2804,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 31,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"hgvs_c": "c.1690G>A",
"hgvs_p": "p.Val564Met",
"transcript": "XM_017000333.2",
"protein_id": "XP_016855822.1",
"transcript_support_level": null,
"aa_start": 564,
"aa_end": null,
"aa_length": 595,
"cds_start": 1690,
"cds_end": null,
"cds_length": 1788,
"cdna_start": 2001,
"cdna_end": null,
"cdna_length": 2792,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL9A2",
"gene_hgnc_id": 2218,
"dbsnp": "rs773159349",
"frequency_reference_population": 0.000006197384,
"hom_count_reference_population": 0,
"allele_count_reference_population": 10,
"gnomad_exomes_af": 0.0000061586,
"gnomad_genomes_af": 0.0000065697,
"gnomad_exomes_ac": 9,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.22129538655281067,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.209,
"revel_prediction": "Benign",
"alphamissense_score": 0.0984,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.2,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.042,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000372748.8",
"gene_symbol": "COL9A2",
"hgnc_id": 2218,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.1972G>A",
"hgvs_p": "p.Val658Met"
}
],
"clinvar_disease": "Inborn genetic diseases,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Inborn genetic diseases|not specified|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}