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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: 20-48921847-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=48921847&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 48921847,
"ref": "G",
"alt": "A",
"effect": "5_prime_UTR_variant",
"transcript": "NM_006420.3",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARFGEF2",
"gene_hgnc_id": 15853,
"hgvs_c": "c.-43G>A",
"hgvs_p": null,
"transcript": "NM_006420.3",
"protein_id": "NP_006411.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1785,
"cds_start": -4,
"cds_end": null,
"cds_length": 5358,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9031,
"mane_select": "ENST00000371917.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARFGEF2",
"gene_hgnc_id": 15853,
"hgvs_c": "c.-43G>A",
"hgvs_p": null,
"transcript": "ENST00000371917.5",
"protein_id": "ENSP00000360985.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1785,
"cds_start": -4,
"cds_end": null,
"cds_length": 5358,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9031,
"mane_select": "NM_006420.3",
"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": 1,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARFGEF2",
"gene_hgnc_id": 15853,
"hgvs_c": "n.-43G>A",
"hgvs_p": null,
"transcript": "ENST00000681399.1",
"protein_id": "ENSP00000506363.1",
"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": 8731,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARFGEF2",
"gene_hgnc_id": 15853,
"hgvs_c": "c.-43G>A",
"hgvs_p": null,
"transcript": "NM_001410846.1",
"protein_id": "NP_001397775.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1784,
"cds_start": -4,
"cds_end": null,
"cds_length": 5355,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 9028,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARFGEF2",
"gene_hgnc_id": 15853,
"hgvs_c": "n.-43G>A",
"hgvs_p": null,
"transcript": "ENST00000681399.1",
"protein_id": "ENSP00000506363.1",
"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": 8731,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARFGEF2",
"gene_hgnc_id": 15853,
"hgvs_c": "c.-452G>A",
"hgvs_p": null,
"transcript": "XM_047439832.1",
"protein_id": "XP_047295788.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1597,
"cds_start": -4,
"cds_end": null,
"cds_length": 4794,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8876,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294533",
"gene_hgnc_id": null,
"hgvs_c": "n.62+504C>T",
"hgvs_p": null,
"transcript": "ENST00000724190.1",
"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": 328,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 39,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARFGEF2",
"gene_hgnc_id": 15853,
"hgvs_c": "c.-43G>A",
"hgvs_p": null,
"transcript": "ENST00000679436.1",
"protein_id": "ENSP00000504888.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1784,
"cds_start": -4,
"cds_end": null,
"cds_length": 5355,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8828,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARFGEF2",
"gene_hgnc_id": 15853,
"hgvs_c": "c.-43G>A",
"hgvs_p": null,
"transcript": "ENST00000681021.1",
"protein_id": "ENSP00000505972.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1728,
"cds_start": -4,
"cds_end": null,
"cds_length": 5187,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARFGEF2",
"gene_hgnc_id": 15853,
"hgvs_c": "n.-43G>A",
"hgvs_p": null,
"transcript": "ENST00000680871.1",
"protein_id": "ENSP00000505042.1",
"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": 5206,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARFGEF2",
"gene_hgnc_id": 15853,
"hgvs_c": "n.-43G>A",
"hgvs_p": null,
"transcript": "ENST00000681656.1",
"protein_id": "ENSP00000505638.1",
"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": 5249,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 38,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ARFGEF2",
"gene_hgnc_id": 15853,
"hgvs_c": "n.-43G>A",
"hgvs_p": null,
"transcript": "ENST00000681885.1",
"protein_id": "ENSP00000505737.1",
"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": 5660,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000294546",
"gene_hgnc_id": null,
"hgvs_c": "n.-205C>T",
"hgvs_p": null,
"transcript": "ENST00000724320.1",
"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": 586,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ARFGEF2",
"gene_hgnc_id": 15853,
"dbsnp": "rs370864802",
"frequency_reference_population": 0.0006957974,
"hom_count_reference_population": 3,
"allele_count_reference_population": 1035,
"gnomad_exomes_af": 0.000709787,
"gnomad_genomes_af": 0.000572783,
"gnomad_exomes_ac": 948,
"gnomad_genomes_ac": 87,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7699999809265137,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.77,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.022,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_006420.3",
"gene_symbol": "ARFGEF2",
"hgnc_id": 15853,
"effects": [
"5_prime_UTR_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.-43G>A",
"hgvs_p": null
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000724190.1",
"gene_symbol": "ENSG00000294533",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.62+504C>T",
"hgvs_p": null
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000724320.1",
"gene_symbol": "ENSG00000294546",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-205C>T",
"hgvs_p": null
}
],
"clinvar_disease": " autosomal recessive,ARFGEF2-related disorder,Periventricular heterotopia with microcephaly,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"phenotype_combined": "Periventricular heterotopia with microcephaly, autosomal recessive|not provided|ARFGEF2-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}