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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: 12-57613749-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=57613749&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 57613749,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001111270.3",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGEF25",
"gene_hgnc_id": 30275,
"hgvs_c": "c.541C>A",
"hgvs_p": "p.Gln181Lys",
"transcript": "NM_182947.4",
"protein_id": "NP_891992.3",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 580,
"cds_start": 541,
"cds_end": null,
"cds_length": 1743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000286494.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_182947.4"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGEF25",
"gene_hgnc_id": 30275,
"hgvs_c": "c.541C>A",
"hgvs_p": "p.Gln181Lys",
"transcript": "ENST00000286494.9",
"protein_id": "ENSP00000286494.4",
"transcript_support_level": 1,
"aa_start": 181,
"aa_end": null,
"aa_length": 580,
"cds_start": 541,
"cds_end": null,
"cds_length": 1743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_182947.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000286494.9"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGEF25",
"gene_hgnc_id": 30275,
"hgvs_c": "c.658C>A",
"hgvs_p": "p.Gln220Lys",
"transcript": "ENST00000333972.11",
"protein_id": "ENSP00000335560.7",
"transcript_support_level": 1,
"aa_start": 220,
"aa_end": null,
"aa_length": 619,
"cds_start": 658,
"cds_end": null,
"cds_length": 1860,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000333972.11"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000224713",
"gene_hgnc_id": 41260,
"hgvs_c": "n.839-40G>T",
"hgvs_p": null,
"transcript": "ENST00000444467.2",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000444467.2"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGEF25",
"gene_hgnc_id": 30275,
"hgvs_c": "c.658C>A",
"hgvs_p": "p.Gln220Lys",
"transcript": "NM_001111270.3",
"protein_id": "NP_001104740.2",
"transcript_support_level": null,
"aa_start": 220,
"aa_end": null,
"aa_length": 619,
"cds_start": 658,
"cds_end": null,
"cds_length": 1860,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001111270.3"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGEF25",
"gene_hgnc_id": 30275,
"hgvs_c": "c.541C>A",
"hgvs_p": "p.Gln181Lys",
"transcript": "ENST00000885362.1",
"protein_id": "ENSP00000555421.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 554,
"cds_start": 541,
"cds_end": null,
"cds_length": 1665,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885362.1"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGEF25",
"gene_hgnc_id": 30275,
"hgvs_c": "c.541C>A",
"hgvs_p": "p.Gln181Lys",
"transcript": "NM_001347933.2",
"protein_id": "NP_001334862.2",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 550,
"cds_start": 541,
"cds_end": null,
"cds_length": 1653,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001347933.2"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGEF25",
"gene_hgnc_id": 30275,
"hgvs_c": "c.541C>A",
"hgvs_p": "p.Gln181Lys",
"transcript": "ENST00000885360.1",
"protein_id": "ENSP00000555419.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 550,
"cds_start": 541,
"cds_end": null,
"cds_length": 1653,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885360.1"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGEF25",
"gene_hgnc_id": 30275,
"hgvs_c": "c.541C>A",
"hgvs_p": "p.Gln181Lys",
"transcript": "ENST00000885361.1",
"protein_id": "ENSP00000555420.1",
"transcript_support_level": null,
"aa_start": 181,
"aa_end": null,
"aa_length": 546,
"cds_start": 541,
"cds_end": null,
"cds_length": 1641,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000885361.1"
},
{
"aa_ref": "Q",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGEF25",
"gene_hgnc_id": 30275,
"hgvs_c": "c.223C>A",
"hgvs_p": "p.Gln75Lys",
"transcript": "ENST00000616622.1",
"protein_id": "ENSP00000484303.1",
"transcript_support_level": 2,
"aa_start": 75,
"aa_end": null,
"aa_length": 474,
"cds_start": 223,
"cds_end": null,
"cds_length": 1425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000616622.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGEF25",
"gene_hgnc_id": 30275,
"hgvs_c": "n.1031C>A",
"hgvs_p": null,
"transcript": "NR_046223.2",
"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_046223.2"
},
{
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000224713",
"gene_hgnc_id": 41260,
"hgvs_c": "n.764-40G>T",
"hgvs_p": null,
"transcript": "ENST00000356672.3",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000356672.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARHGEF25",
"gene_hgnc_id": 30275,
"hgvs_c": "n.-245C>A",
"hgvs_p": null,
"transcript": "ENST00000471370.5",
"protein_id": null,
"transcript_support_level": 5,
"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": "retained_intron",
"feature": "ENST00000471370.5"
}
],
"gene_symbol": "ARHGEF25",
"gene_hgnc_id": 30275,
"dbsnp": "rs147980194",
"frequency_reference_population": 0.000024782043,
"hom_count_reference_population": 0,
"allele_count_reference_population": 40,
"gnomad_exomes_af": 0.0000136817,
"gnomad_genomes_af": 0.000131347,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 20,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05223876237869263,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.072,
"revel_prediction": "Benign",
"alphamissense_score": 0.1259,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.4,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.171,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001111270.3",
"gene_symbol": "ARHGEF25",
"hgnc_id": 30275,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.658C>A",
"hgvs_p": "p.Gln220Lys"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000444467.2",
"gene_symbol": "ENSG00000224713",
"hgnc_id": 41260,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.839-40G>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
}