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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: 19-6822510-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=6822510&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "VAV1",
"hgnc_id": 12657,
"hgvs_c": "c.650A>G",
"hgvs_p": "p.Gln217Arg",
"inheritance_mode": "AD",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_005428.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 1389,
"alphamissense_prediction": null,
"alphamissense_score": 0.0983,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.37,
"chr": "19",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.11311262845993042,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 845,
"aa_ref": "Q",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2892,
"cdna_start": 750,
"cds_end": null,
"cds_length": 2538,
"cds_start": 650,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_005428.4",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "c.650A>G",
"hgvs_p": "p.Gln217Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000602142.6",
"protein_coding": true,
"protein_id": "NP_005419.2",
"strand": true,
"transcript": "NM_005428.4",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 845,
"aa_ref": "Q",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2892,
"cdna_start": 750,
"cds_end": null,
"cds_length": 2538,
"cds_start": 650,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000602142.6",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "c.650A>G",
"hgvs_p": "p.Gln217Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005428.4",
"protein_coding": true,
"protein_id": "ENSP00000472929.1",
"strand": true,
"transcript": "ENST00000602142.6",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 823,
"aa_ref": "Q",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2825,
"cdna_start": 744,
"cds_end": null,
"cds_length": 2472,
"cds_start": 650,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000304076.6",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "c.650A>G",
"hgvs_p": "p.Gln217Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000302269.2",
"strand": true,
"transcript": "ENST00000304076.6",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 790,
"aa_ref": "Q",
"aa_start": 162,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2717,
"cdna_start": 570,
"cds_end": null,
"cds_length": 2373,
"cds_start": 485,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000599806.5",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "c.485A>G",
"hgvs_p": "p.Gln162Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000472803.1",
"strand": true,
"transcript": "ENST00000599806.5",
"transcript_support_level": 1
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 843,
"aa_ref": "Q",
"aa_start": 215,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2836,
"cdna_start": 695,
"cds_end": null,
"cds_length": 2532,
"cds_start": 644,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000962219.1",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "c.644A>G",
"hgvs_p": "p.Gln215Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632278.1",
"strand": true,
"transcript": "ENST00000962219.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 834,
"aa_ref": "Q",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2859,
"cdna_start": 750,
"cds_end": null,
"cds_length": 2505,
"cds_start": 650,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000962218.1",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "c.650A>G",
"hgvs_p": "p.Gln217Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000632277.1",
"strand": true,
"transcript": "ENST00000962218.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 823,
"aa_ref": "Q",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2826,
"cdna_start": 750,
"cds_end": null,
"cds_length": 2472,
"cds_start": 650,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001258206.2",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "c.650A>G",
"hgvs_p": "p.Gln217Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001245135.1",
"strand": true,
"transcript": "NM_001258206.2",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 813,
"aa_ref": "Q",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2810,
"cdna_start": 764,
"cds_end": null,
"cds_length": 2442,
"cds_start": 650,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000908658.1",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "c.650A>G",
"hgvs_p": "p.Gln217Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578717.1",
"strand": true,
"transcript": "ENST00000908658.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 789,
"aa_ref": "Q",
"aa_start": 161,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2627,
"cdna_start": 482,
"cds_end": null,
"cds_length": 2370,
"cds_start": 482,
"consequences": [
"missense_variant"
],
"exon_count": 27,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000539284.2",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "c.482A>G",
"hgvs_p": "p.Gln161Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000443242.2",
"strand": true,
"transcript": "ENST00000539284.2",
"transcript_support_level": 5
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 821,
"aa_ref": "Q",
"aa_start": 217,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2777,
"cdna_start": 750,
"cds_end": null,
"cds_length": 2466,
"cds_start": 650,
"consequences": [
"missense_variant"
],
"exon_count": 26,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "XM_005259642.2",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "c.650A>G",
"hgvs_p": "p.Gln217Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005259699.1",
"strand": true,
"transcript": "XM_005259642.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 813,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2796,
"cdna_start": null,
"cds_end": null,
"cds_length": 2442,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001258207.2",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "c.558+181A>G",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001245136.1",
"strand": true,
"transcript": "NM_001258207.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 813,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2775,
"cdna_start": null,
"cds_end": null,
"cds_length": 2442,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 26,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000596764.5",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "c.558+181A>G",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000469450.1",
"strand": true,
"transcript": "ENST00000596764.5",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 734,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2539,
"cdna_start": null,
"cds_end": null,
"cds_length": 2205,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 23,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000908659.1",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "c.321+1692A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000578718.1",
"strand": true,
"transcript": "ENST00000908659.1",
"transcript_support_level": null
},
{
"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": 744,
"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": "ENST00000594082.1",
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"hgvs_c": "n.74A>G",
"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": "ENST00000594082.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs201002344",
"effect": "missense_variant",
"frequency_reference_population": 0.0008972231,
"gene_hgnc_id": 12657,
"gene_symbol": "VAV1",
"gnomad_exomes_ac": 1318,
"gnomad_exomes_af": 0.000944237,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 71,
"gnomad_genomes_af": 0.000466265,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not provided|not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.68,
"pos": 6822510,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.15,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_005428.4"
}
]
}