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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: 10-99818820-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=99818820&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 99818820,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000647814.1",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"hgvs_c": "c.2302C>T",
"hgvs_p": "p.Arg768Trp",
"transcript": "NM_000392.5",
"protein_id": "NP_000383.2",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 1545,
"cds_start": 2302,
"cds_end": null,
"cds_length": 4638,
"cdna_start": 2507,
"cdna_end": null,
"cdna_length": 5806,
"mane_select": "ENST00000647814.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"hgvs_c": "c.2302C>T",
"hgvs_p": "p.Arg768Trp",
"transcript": "ENST00000647814.1",
"protein_id": "ENSP00000497274.1",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 1545,
"cds_start": 2302,
"cds_end": null,
"cds_length": 4638,
"cdna_start": 2507,
"cdna_end": null,
"cdna_length": 5806,
"mane_select": "NM_000392.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"hgvs_c": "c.1606C>T",
"hgvs_p": "p.Arg536Trp",
"transcript": "XM_006717630.4",
"protein_id": "XP_006717693.1",
"transcript_support_level": null,
"aa_start": 536,
"aa_end": null,
"aa_length": 1313,
"cds_start": 1606,
"cds_end": null,
"cds_length": 3942,
"cdna_start": 4040,
"cdna_end": null,
"cdna_length": 7339,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"hgvs_c": "c.2302C>T",
"hgvs_p": "p.Arg768Trp",
"transcript": "XM_047424598.1",
"protein_id": "XP_047280554.1",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 1209,
"cds_start": 2302,
"cds_end": null,
"cds_length": 3630,
"cdna_start": 2507,
"cdna_end": null,
"cdna_length": 3918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"hgvs_c": "c.2302C>T",
"hgvs_p": "p.Arg768Trp",
"transcript": "XM_011539291.4",
"protein_id": "XP_011537593.1",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 916,
"cds_start": 2302,
"cds_end": null,
"cds_length": 2751,
"cdna_start": 2507,
"cdna_end": null,
"cdna_length": 3036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"hgvs_c": "c.2302C>T",
"hgvs_p": "p.Arg768Trp",
"transcript": "XM_006717631.5",
"protein_id": "XP_006717694.1",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 895,
"cds_start": 2302,
"cds_end": null,
"cds_length": 2688,
"cdna_start": 2507,
"cdna_end": null,
"cdna_length": 3030,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"hgvs_c": "c.2302C>T",
"hgvs_p": "p.Arg768Trp",
"transcript": "XM_017015675.3",
"protein_id": "XP_016871164.1",
"transcript_support_level": null,
"aa_start": 768,
"aa_end": null,
"aa_length": 892,
"cds_start": 2302,
"cds_end": null,
"cds_length": 2679,
"cdna_start": 2507,
"cdna_end": null,
"cdna_length": 2931,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"hgvs_c": "n.2507C>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4379,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ABCC2",
"gene_hgnc_id": 53,
"dbsnp": "rs56199535",
"frequency_reference_population": 0.000105321065,
"hom_count_reference_population": 0,
"allele_count_reference_population": 170,
"gnomad_exomes_af": 0.000106713,
"gnomad_genomes_af": 0.0000919576,
"gnomad_exomes_ac": 156,
"gnomad_genomes_ac": 14,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9760457277297974,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.1599999964237213,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.922,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9763,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.45,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.673,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.16,
"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": "ENST00000647814.1",
"gene_symbol": "ABCC2",
"hgnc_id": 53,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2302C>T",
"hgvs_p": "p.Arg768Trp"
}
],
"clinvar_disease": "ABCC2-related disorder,Dubin-Johnson syndrome,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 LP:2",
"phenotype_combined": "Dubin-Johnson syndrome|not provided|ABCC2-related disorder",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}