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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: 5-169654394-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=169654394&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 5,
"criteria": [
"PM2",
"BP4_Strong",
"BP6"
],
"effects": [
"intron_variant"
],
"gene_symbol": "DOCK2",
"hgnc_id": 2988,
"hgvs_c": "c.44-9G>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -3,
"transcript": "NM_004946.3",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6",
"acmg_score": -3,
"allele_count_reference_population": 118,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.81,
"chr": "5",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_disease": "DOCK2 deficiency",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.8100000023841858,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1830,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6069,
"cdna_start": null,
"cds_end": null,
"cds_length": 5493,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 52,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_004946.3",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"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": null,
"aa_end": null,
"aa_length": 1830,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6069,
"cdna_start": null,
"cds_end": null,
"cds_length": 5493,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 52,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000520908.7",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"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": [
"intron_variant"
],
"exon_count": 53,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000524185.5",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "n.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"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": null,
"aa_end": null,
"aa_length": 1817,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6031,
"cdna_start": null,
"cds_end": null,
"cds_length": 5454,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 52,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000961039.1",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"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": null,
"aa_end": null,
"aa_length": 1802,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6006,
"cdna_start": null,
"cds_end": null,
"cds_length": 5409,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 51,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000961038.1",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"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": null,
"aa_end": null,
"aa_length": 1797,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5971,
"cdna_start": null,
"cds_end": null,
"cds_length": 5394,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 51,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000961040.1",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"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": 957,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3019,
"cdna_start": null,
"cds_end": null,
"cds_length": 2874,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 28,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000519628.2",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000428841.2",
"strand": true,
"transcript": "ENST00000519628.2",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 960,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6849,
"cdna_start": null,
"cds_end": null,
"cds_length": 2883,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 28,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011534448.3",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011532750.1",
"strand": true,
"transcript": "XM_011534448.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 957,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3071,
"cdna_start": null,
"cds_end": null,
"cds_length": 2874,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 28,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011534449.3",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011532751.1",
"strand": true,
"transcript": "XM_011534449.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 955,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3518,
"cdna_start": null,
"cds_end": null,
"cds_length": 2868,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 28,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011534450.3",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011532752.1",
"strand": true,
"transcript": "XM_011534450.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 951,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5419,
"cdna_start": null,
"cds_end": null,
"cds_length": 2856,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 28,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017009190.3",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016864679.1",
"strand": true,
"transcript": "XM_017009190.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 946,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11238,
"cdna_start": null,
"cds_end": null,
"cds_length": 2841,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 28,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_011534451.3",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011532753.1",
"strand": true,
"transcript": "XM_011534451.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 939,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3036,
"cdna_start": null,
"cds_end": null,
"cds_length": 2820,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 28,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_005265830.5",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "c.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005265887.1",
"strand": true,
"transcript": "XM_005265830.5",
"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": [
"intron_variant"
],
"exon_count": 52,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000522138.2",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "n.44-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"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": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 506,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000648741.1",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "n.103-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000648741.1",
"transcript_support_level": null
},
{
"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": [
"intron_variant"
],
"exon_count": 53,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_156756.1",
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"hgvs_c": "n.96-9G>A",
"hgvs_p": null,
"intron_rank": 1,
"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
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.0000485093301315266,
"dbsnp": "rs778542070",
"effect": "intron_variant",
"frequency_reference_population": 0.00007311083,
"gene_hgnc_id": 2988,
"gene_symbol": "DOCK2",
"gnomad_exomes_ac": 113,
"gnomad_exomes_af": 0.0000773027,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 5,
"gnomad_genomes_af": 0.0000328511,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"phenotype_combined": "DOCK2 deficiency",
"phylop100way_prediction": "Benign",
"phylop100way_score": -1.034,
"pos": 169654394,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_004946.3"
}
]
}