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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: 16-57248536-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=57248536&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "16",
"pos": 57248536,
"ref": "G",
"alt": "C",
"effect": "splice_acceptor_variant,intron_variant",
"transcript": "ENST00000219204.8",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ARL2BP",
"gene_hgnc_id": 17146,
"hgvs_c": "c.101-1G>C",
"hgvs_p": null,
"transcript": "NM_012106.4",
"protein_id": "NP_036238.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 163,
"cds_start": -4,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1969,
"mane_select": "ENST00000219204.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ARL2BP",
"gene_hgnc_id": 17146,
"hgvs_c": "c.101-1G>C",
"hgvs_p": null,
"transcript": "ENST00000219204.8",
"protein_id": "ENSP00000219204.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 163,
"cds_start": -4,
"cds_end": null,
"cds_length": 492,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1969,
"mane_select": "NM_012106.4",
"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": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "LOC124903697",
"gene_hgnc_id": null,
"hgvs_c": "n.1525C>G",
"hgvs_p": null,
"transcript": "XR_007065082.1",
"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": 4246,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ARL2BP",
"gene_hgnc_id": 17146,
"hgvs_c": "c.92-1G>C",
"hgvs_p": null,
"transcript": "ENST00000563234.1",
"protein_id": "ENSP00000454237.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 170,
"cds_start": -4,
"cds_end": null,
"cds_length": 513,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1416,
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ARL2BP",
"gene_hgnc_id": 17146,
"hgvs_c": "c.101-1244G>C",
"hgvs_p": null,
"transcript": "ENST00000562023.5",
"protein_id": "ENSP00000457465.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 123,
"cds_start": -4,
"cds_end": null,
"cds_length": 372,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 547,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ARL2BP",
"gene_hgnc_id": 17146,
"hgvs_c": "c.5-1G>C",
"hgvs_p": null,
"transcript": "XM_047433883.1",
"protein_id": "XP_047289839.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 131,
"cds_start": -4,
"cds_end": null,
"cds_length": 396,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1841,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000260038",
"gene_hgnc_id": null,
"hgvs_c": "n.*44G>C",
"hgvs_p": null,
"transcript": "ENST00000562409.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 358,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PLLP",
"gene_hgnc_id": 18553,
"hgvs_c": "n.*11C>G",
"hgvs_p": null,
"transcript": "ENST00000564376.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 400,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ARL2BP",
"gene_hgnc_id": 17146,
"dbsnp": "rs879255568",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2199999988079071,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9340000152587891,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.22,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.602,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.99,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999972853204913,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 11,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5",
"acmg_by_gene": [
{
"score": 11,
"benign_score": 0,
"pathogenic_score": 11,
"criteria": [
"PVS1",
"PM2",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000219204.8",
"gene_symbol": "ARL2BP",
"hgnc_id": 17146,
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.101-1G>C",
"hgvs_p": null
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "XR_007065082.1",
"gene_symbol": "LOC124903697",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1525C>G",
"hgvs_p": null
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000562409.1",
"gene_symbol": "ENSG00000260038",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*44G>C",
"hgvs_p": null
},
{
"score": 7,
"benign_score": 0,
"pathogenic_score": 7,
"criteria": [
"PM2",
"PP3_Strong",
"PP5"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000564376.1",
"gene_symbol": "PLLP",
"hgnc_id": 18553,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.*11C>G",
"hgvs_p": null
}
],
"clinvar_disease": "Autosomal recessive retinitis pigmentosa,Retinitis pigmentosa,Retinitis pigmentosa with or without situs inversus",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Retinitis pigmentosa with or without situs inversus|Retinitis pigmentosa|Autosomal recessive retinitis pigmentosa",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}