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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: 19-45179787-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=45179787&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 45179787,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000433642.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S3",
"gene_hgnc_id": 20914,
"hgvs_c": "c.491G>A",
"hgvs_p": "p.Arg164His",
"transcript": "NM_212550.5",
"protein_id": "NP_997715.1",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 202,
"cds_start": 491,
"cds_end": null,
"cds_length": 609,
"cdna_start": 548,
"cdna_end": null,
"cdna_length": 2561,
"mane_select": "ENST00000433642.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S3",
"gene_hgnc_id": 20914,
"hgvs_c": "c.491G>A",
"hgvs_p": "p.Arg164His",
"transcript": "ENST00000433642.3",
"protein_id": "ENSP00000393840.1",
"transcript_support_level": 2,
"aa_start": 164,
"aa_end": null,
"aa_length": 202,
"cds_start": 491,
"cds_end": null,
"cds_length": 609,
"cdna_start": 548,
"cdna_end": null,
"cdna_length": 2561,
"mane_select": "NM_212550.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S3",
"gene_hgnc_id": 20914,
"hgvs_c": "c.491G>A",
"hgvs_p": "p.Arg164His",
"transcript": "ENST00000587722.1",
"protein_id": "ENSP00000468281.1",
"transcript_support_level": 6,
"aa_start": 164,
"aa_end": null,
"aa_length": 202,
"cds_start": 491,
"cds_end": null,
"cds_length": 609,
"cdna_start": 565,
"cdna_end": null,
"cdna_length": 732,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S3",
"gene_hgnc_id": 20914,
"hgvs_c": "c.119G>A",
"hgvs_p": "p.Arg40His",
"transcript": "ENST00000592910.1",
"protein_id": "ENSP00000466798.1",
"transcript_support_level": 2,
"aa_start": 40,
"aa_end": null,
"aa_length": 78,
"cds_start": 119,
"cds_end": null,
"cds_length": 237,
"cdna_start": 119,
"cdna_end": null,
"cdna_length": 469,
"mane_select": null,
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S3",
"gene_hgnc_id": 20914,
"hgvs_c": "n.1004G>A",
"hgvs_p": null,
"transcript": "XR_001753683.2",
"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": 1733,
"mane_select": null,
"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": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S3",
"gene_hgnc_id": 20914,
"hgvs_c": "n.548G>A",
"hgvs_p": null,
"transcript": "XR_007066810.1",
"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": 3791,
"mane_select": null,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S3",
"gene_hgnc_id": 20914,
"hgvs_c": "n.1004G>A",
"hgvs_p": null,
"transcript": "XR_007066811.1",
"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": 1934,
"mane_select": null,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S3",
"gene_hgnc_id": 20914,
"hgvs_c": "n.1004G>A",
"hgvs_p": null,
"transcript": "XR_007066812.1",
"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": 2094,
"mane_select": null,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S3",
"gene_hgnc_id": 20914,
"hgvs_c": "n.1004G>A",
"hgvs_p": null,
"transcript": "XR_007066813.1",
"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": 1906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "MARK4",
"gene_hgnc_id": 13538,
"hgvs_c": "c.-276-79202G>A",
"hgvs_p": null,
"transcript": "ENST00000587566.5",
"protein_id": "ENSP00000465414.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 61,
"cds_start": -4,
"cds_end": null,
"cds_length": 187,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 553,
"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": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S3",
"gene_hgnc_id": 20914,
"hgvs_c": "n.-127G>A",
"hgvs_p": null,
"transcript": "ENST00000588362.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 473,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BLOC1S3",
"gene_hgnc_id": 20914,
"hgvs_c": "n.-35G>A",
"hgvs_p": null,
"transcript": "ENST00000593083.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 550,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "BLOC1S3",
"gene_hgnc_id": 20914,
"dbsnp": "rs200567085",
"frequency_reference_population": 0.00020341664,
"hom_count_reference_population": 2,
"allele_count_reference_population": 321,
"gnomad_exomes_af": 0.0000974897,
"gnomad_genomes_af": 0.0011954,
"gnomad_exomes_ac": 139,
"gnomad_genomes_ac": 182,
"gnomad_exomes_homalt": 2,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008386164903640747,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.109,
"revel_prediction": "Benign",
"alphamissense_score": 0.2752,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.15,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.942,
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000433642.3",
"gene_symbol": "BLOC1S3",
"hgnc_id": 20914,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.491G>A",
"hgvs_p": "p.Arg164His"
},
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000587566.5",
"gene_symbol": "MARK4",
"hgnc_id": 13538,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.-276-79202G>A",
"hgvs_p": null
}
],
"clinvar_disease": "BLOC1S3-related disorder,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:3 B:1",
"phenotype_combined": "not specified|not provided|BLOC1S3-related disorder",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}