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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: 10-99836193-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=99836193&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 99836193,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_000392.5",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"hgvs_c": "c.3517A>T",
"hgvs_p": "p.Ile1173Phe",
"transcript": "NM_000392.5",
"protein_id": "NP_000383.2",
"transcript_support_level": null,
"aa_start": 1173,
"aa_end": null,
"aa_length": 1545,
"cds_start": 3517,
"cds_end": null,
"cds_length": 4638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000647814.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000392.5"
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"hgvs_c": "c.3517A>T",
"hgvs_p": "p.Ile1173Phe",
"transcript": "ENST00000647814.1",
"protein_id": "ENSP00000497274.1",
"transcript_support_level": null,
"aa_start": 1173,
"aa_end": null,
"aa_length": 1545,
"cds_start": 3517,
"cds_end": null,
"cds_length": 4638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000392.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000647814.1"
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"hgvs_c": "c.2821A>T",
"hgvs_p": "p.Ile941Phe",
"transcript": "XM_006717630.4",
"protein_id": "XP_006717693.1",
"transcript_support_level": null,
"aa_start": 941,
"aa_end": null,
"aa_length": 1313,
"cds_start": 2821,
"cds_end": null,
"cds_length": 3942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_006717630.4"
},
{
"aa_ref": "I",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"hgvs_c": "c.3517A>T",
"hgvs_p": "p.Ile1173Phe",
"transcript": "XM_047424598.1",
"protein_id": "XP_047280554.1",
"transcript_support_level": null,
"aa_start": 1173,
"aa_end": null,
"aa_length": 1209,
"cds_start": 3517,
"cds_end": null,
"cds_length": 3630,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047424598.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"hgvs_c": "n.3722A>T",
"hgvs_p": null,
"transcript": "XR_945604.4",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "XR_945604.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000295976",
"gene_hgnc_id": null,
"hgvs_c": "n.51-2014T>A",
"hgvs_p": null,
"transcript": "ENST00000734671.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000734671.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000295976",
"gene_hgnc_id": null,
"hgvs_c": "n.523-2014T>A",
"hgvs_p": null,
"transcript": "ENST00000734672.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000734672.1"
}
],
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"dbsnp": "rs72558201",
"frequency_reference_population": 0.000013010427,
"hom_count_reference_population": 0,
"allele_count_reference_population": 21,
"gnomad_exomes_af": 0.0000136809,
"gnomad_genomes_af": 0.00000657047,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.988064169883728,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.932,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8835,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.45,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.292,
"phylop100way_prediction": "Uncertain_significance",
"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": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_000392.5",
"gene_symbol": "ABCC2",
"hgnc_id": 53,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3517A>T",
"hgvs_p": "p.Ile1173Phe"
},
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000734671.1",
"gene_symbol": "ENSG00000295976",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.51-2014T>A",
"hgvs_p": null
}
],
"clinvar_disease": "Dubin-Johnson syndrome,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5",
"phenotype_combined": "Dubin-Johnson syndrome|not provided",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}