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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: 5-169983126-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=169983126&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 10,
"criteria": [
"BP4_Moderate",
"BS1",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DOCK2",
"hgnc_id": 2988,
"hgvs_c": "c.2858C>T",
"hgvs_p": "p.Ser953Phe",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -10,
"transcript": "NM_004946.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BS1,BS2",
"acmg_score": -10,
"allele_count_reference_population": 227,
"alphamissense_prediction": null,
"alphamissense_score": 0.1322,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.23,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "DOCK2 deficiency,DOCK2-related disorder,Inborn genetic diseases,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.07096612453460693,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 1830,
"aa_ref": "S",
"aa_start": 953,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6069,
"cdna_start": 2910,
"cds_end": null,
"cds_length": 5493,
"cds_start": 2858,
"consequences": [
"missense_variant"
],
"exon_count": 52,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NM_004946.3",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.2858C>T",
"hgvs_p": "p.Ser953Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000520908.7",
"protein_coding": true,
"protein_id": "NP_004937.1",
"strand": true,
"transcript": "NM_004946.3",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 1830,
"aa_ref": "S",
"aa_start": 953,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6069,
"cdna_start": 2910,
"cds_end": null,
"cds_length": 5493,
"cds_start": 2858,
"consequences": [
"missense_variant"
],
"exon_count": 52,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000520908.7",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.2858C>T",
"hgvs_p": "p.Ser953Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_004946.3",
"protein_coding": true,
"protein_id": "ENSP00000429283.3",
"strand": true,
"transcript": "ENST00000520908.7",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 5656,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 53,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000524185.5",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "n.2858C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000428850.1",
"strand": true,
"transcript": "ENST00000524185.5",
"transcript_support_level": 1
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 1817,
"aa_ref": "S",
"aa_start": 940,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6031,
"cdna_start": 2877,
"cds_end": null,
"cds_length": 5454,
"cds_start": 2819,
"consequences": [
"missense_variant"
],
"exon_count": 52,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000961039.1",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.2819C>T",
"hgvs_p": "p.Ser940Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000631098.1",
"strand": true,
"transcript": "ENST00000961039.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 1802,
"aa_ref": "S",
"aa_start": 953,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6006,
"cdna_start": 2936,
"cds_end": null,
"cds_length": 5409,
"cds_start": 2858,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000961038.1",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.2858C>T",
"hgvs_p": "p.Ser953Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000631097.1",
"strand": true,
"transcript": "ENST00000961038.1",
"transcript_support_level": null
},
{
"aa_alt": "F",
"aa_end": null,
"aa_length": 1797,
"aa_ref": "S",
"aa_start": 920,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5971,
"cdna_start": 2817,
"cds_end": null,
"cds_length": 5394,
"cds_start": 2759,
"consequences": [
"missense_variant"
],
"exon_count": 51,
"exon_rank": 27,
"exon_rank_end": null,
"feature": "ENST00000961040.1",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.2759C>T",
"hgvs_p": "p.Ser920Phe",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000631099.1",
"strand": true,
"transcript": "ENST00000961040.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 6072,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 52,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000522138.2",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "n.*2368C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000512484.1",
"strand": true,
"transcript": "ENST00000522138.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 674,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000522994.1",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "n.19C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000522994.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 4654,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 38,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000523351.6",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "n.1498C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000523351.6",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 6120,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 53,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "NR_156756.1",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "n.2910C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "NR_156756.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 6072,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 52,
"exon_rank": 28,
"exon_rank_end": null,
"feature": "ENST00000522138.2",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "n.*2368C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000512484.1",
"strand": true,
"transcript": "ENST00000522138.2",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs35395501",
"effect": "missense_variant",
"frequency_reference_population": 0.00014063774,
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"gnomad_exomes_ac": 207,
"gnomad_exomes_af": 0.000141612,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_ac": 20,
"gnomad_genomes_af": 0.00013129,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 2,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "DOCK2 deficiency|DOCK2-related disorder|Inborn genetic diseases|not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": 2.63,
"pos": 169983126,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.142,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004946.3"
}
]
}