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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: 2-237361837-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=237361837&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 237361837,
"ref": "G",
"alt": "C",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000295550.9",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.6064-6C>G",
"hgvs_p": null,
"transcript": "NM_004369.4",
"protein_id": "NP_004360.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 3177,
"cds_start": -4,
"cds_end": null,
"cds_length": 9534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10532,
"mane_select": "ENST00000295550.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": 14,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.6064-6C>G",
"hgvs_p": null,
"transcript": "ENST00000295550.9",
"protein_id": "ENSP00000295550.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 3177,
"cds_start": -4,
"cds_end": null,
"cds_length": 9534,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 10532,
"mane_select": "NM_004369.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.4243-6C>G",
"hgvs_p": null,
"transcript": "ENST00000472056.5",
"protein_id": "ENSP00000418285.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2570,
"cds_start": -4,
"cds_end": null,
"cds_length": 7713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8628,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.5446-6C>G",
"hgvs_p": null,
"transcript": "NM_057167.4",
"protein_id": "NP_476508.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2971,
"cds_start": -4,
"cds_end": null,
"cds_length": 8916,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9914,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 43,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.5446-6C>G",
"hgvs_p": null,
"transcript": "ENST00000353578.9",
"protein_id": "ENSP00000315873.4",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 2971,
"cds_start": -4,
"cds_end": null,
"cds_length": 8916,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"hgvs_c": "c.4243-6C>G",
"hgvs_p": null,
"transcript": "NM_057166.5",
"protein_id": "NP_476507.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2570,
"cds_start": -4,
"cds_end": null,
"cds_length": 7713,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8711,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "COL6A3",
"gene_hgnc_id": 2213,
"dbsnp": "rs202091342",
"frequency_reference_population": 0.000003721198,
"hom_count_reference_population": 0,
"allele_count_reference_population": 6,
"gnomad_exomes_af": 0.00000342419,
"gnomad_genomes_af": 0.00000657091,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8399999737739563,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.012000000104308128,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.84,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.28,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000211005223365634,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000295550.9",
"gene_symbol": "COL6A3",
"hgnc_id": 2213,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AD,AR,SD",
"hgvs_c": "c.6064-6C>G",
"hgvs_p": null
}
],
"clinvar_disease": "Bethlem myopathy 1A",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Bethlem myopathy 1A",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}