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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: 10-45826255-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=45826255&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 45826255,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001276343.3",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP4",
"gene_hgnc_id": 23459,
"hgvs_c": "c.1721A>T",
"hgvs_p": "p.Lys574Met",
"transcript": "NM_001276343.3",
"protein_id": "NP_001263272.2",
"transcript_support_level": null,
"aa_start": 574,
"aa_end": null,
"aa_length": 686,
"cds_start": 1721,
"cds_end": null,
"cds_length": 2061,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000616763.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001276343.3"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP4",
"gene_hgnc_id": 23459,
"hgvs_c": "c.1721A>T",
"hgvs_p": "p.Lys574Met",
"transcript": "ENST00000616763.6",
"protein_id": "ENSP00000483751.2",
"transcript_support_level": 1,
"aa_start": 574,
"aa_end": null,
"aa_length": 686,
"cds_start": 1721,
"cds_end": null,
"cds_length": 2061,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001276343.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000616763.6"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP4",
"gene_hgnc_id": 23459,
"hgvs_c": "c.1652A>T",
"hgvs_p": "p.Lys551Met",
"transcript": "ENST00000448048.7",
"protein_id": "ENSP00000392513.2",
"transcript_support_level": 1,
"aa_start": 551,
"aa_end": null,
"aa_length": 663,
"cds_start": 1652,
"cds_end": null,
"cds_length": 1992,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000448048.7"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP4",
"gene_hgnc_id": 23459,
"hgvs_c": "c.1715A>T",
"hgvs_p": "p.Lys572Met",
"transcript": "ENST00000970389.1",
"protein_id": "ENSP00000640448.1",
"transcript_support_level": null,
"aa_start": 572,
"aa_end": null,
"aa_length": 684,
"cds_start": 1715,
"cds_end": null,
"cds_length": 2055,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000970389.1"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP4",
"gene_hgnc_id": 23459,
"hgvs_c": "c.1652A>T",
"hgvs_p": "p.Lys551Met",
"transcript": "NM_133446.4",
"protein_id": "NP_597703.2",
"transcript_support_level": null,
"aa_start": 551,
"aa_end": null,
"aa_length": 663,
"cds_start": 1652,
"cds_end": null,
"cds_length": 1992,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_133446.4"
},
{
"aa_ref": "K",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP4",
"gene_hgnc_id": 23459,
"hgvs_c": "c.1604A>T",
"hgvs_p": "p.Lys535Met",
"transcript": "NM_001393377.1",
"protein_id": "NP_001380306.1",
"transcript_support_level": null,
"aa_start": 535,
"aa_end": null,
"aa_length": 647,
"cds_start": 1604,
"cds_end": null,
"cds_length": 1944,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001393377.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP4",
"gene_hgnc_id": 23459,
"hgvs_c": "c.*1174A>T",
"hgvs_p": null,
"transcript": "NM_001393378.1",
"protein_id": "NP_001380307.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 172,
"cds_start": null,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001393378.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARGP1-AGAP4",
"gene_hgnc_id": null,
"hgvs_c": "n.3658A>T",
"hgvs_p": null,
"transcript": "NR_160518.1",
"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": "NR_160518.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PARGP1-AGAP4",
"gene_hgnc_id": null,
"hgvs_c": "n.3747A>T",
"hgvs_p": null,
"transcript": "NR_160519.1",
"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": "NR_160519.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AGAP4",
"gene_hgnc_id": 23459,
"hgvs_c": "n.2852A>T",
"hgvs_p": null,
"transcript": "NR_171664.1",
"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": "NR_171664.1"
}
],
"gene_symbol": "AGAP4",
"gene_hgnc_id": 23459,
"dbsnp": "rs1428646434",
"frequency_reference_population": 0.0000068254726,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 0.00000344277,
"gnomad_genomes_af": 0.00000682547,
"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": 0.2653394639492035,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.19,
"revel_prediction": "Benign",
"alphamissense_score": 0.3892,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.411,
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001276343.3",
"gene_symbol": "AGAP4",
"hgnc_id": 23459,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1721A>T",
"hgvs_p": "p.Lys574Met"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NR_160518.1",
"gene_symbol": "PARGP1-AGAP4",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.3658A>T",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}