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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: 19-39825806-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=39825806&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 39825806,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004714.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYRK1B",
"gene_hgnc_id": 3092,
"hgvs_c": "c.1799G>A",
"hgvs_p": "p.Arg600His",
"transcript": "NM_004714.3",
"protein_id": "NP_004705.1",
"transcript_support_level": null,
"aa_start": 600,
"aa_end": null,
"aa_length": 629,
"cds_start": 1799,
"cds_end": null,
"cds_length": 1890,
"cdna_start": 2040,
"cdna_end": null,
"cdna_length": 2496,
"mane_select": "ENST00000323039.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYRK1B",
"gene_hgnc_id": 3092,
"hgvs_c": "c.1799G>A",
"hgvs_p": "p.Arg600His",
"transcript": "ENST00000323039.10",
"protein_id": "ENSP00000312789.4",
"transcript_support_level": 1,
"aa_start": 600,
"aa_end": null,
"aa_length": 629,
"cds_start": 1799,
"cds_end": null,
"cds_length": 1890,
"cdna_start": 2040,
"cdna_end": null,
"cdna_length": 2496,
"mane_select": "NM_004714.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYRK1B",
"gene_hgnc_id": 3092,
"hgvs_c": "c.1979G>A",
"hgvs_p": "p.Arg660His",
"transcript": "ENST00000593685.5",
"protein_id": "ENSP00000469863.2",
"transcript_support_level": 5,
"aa_start": 660,
"aa_end": null,
"aa_length": 689,
"cds_start": 1979,
"cds_end": null,
"cds_length": 2070,
"cdna_start": 2268,
"cdna_end": null,
"cdna_length": 2724,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYRK1B",
"gene_hgnc_id": 3092,
"hgvs_c": "c.1715G>A",
"hgvs_p": "p.Arg572His",
"transcript": "NM_006484.3",
"protein_id": "NP_006475.1",
"transcript_support_level": null,
"aa_start": 572,
"aa_end": null,
"aa_length": 601,
"cds_start": 1715,
"cds_end": null,
"cds_length": 1806,
"cdna_start": 1956,
"cdna_end": null,
"cdna_length": 2412,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYRK1B",
"gene_hgnc_id": 3092,
"hgvs_c": "c.1715G>A",
"hgvs_p": "p.Arg572His",
"transcript": "ENST00000348817.7",
"protein_id": "ENSP00000221803.4",
"transcript_support_level": 5,
"aa_start": 572,
"aa_end": null,
"aa_length": 601,
"cds_start": 1715,
"cds_end": null,
"cds_length": 1806,
"cdna_start": 1995,
"cdna_end": null,
"cdna_length": 2448,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYRK1B",
"gene_hgnc_id": 3092,
"hgvs_c": "c.1715G>A",
"hgvs_p": "p.Arg572His",
"transcript": "ENST00000597639.5",
"protein_id": "ENSP00000472941.1",
"transcript_support_level": 5,
"aa_start": 572,
"aa_end": null,
"aa_length": 601,
"cds_start": 1715,
"cds_end": null,
"cds_length": 1806,
"cdna_start": 1715,
"cdna_end": null,
"cdna_length": 1806,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYRK1B",
"gene_hgnc_id": 3092,
"hgvs_c": "c.1679G>A",
"hgvs_p": "p.Arg560His",
"transcript": "NM_006483.3",
"protein_id": "NP_006474.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 589,
"cds_start": 1679,
"cds_end": null,
"cds_length": 1770,
"cdna_start": 1920,
"cdna_end": null,
"cdna_length": 2376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYRK1B",
"gene_hgnc_id": 3092,
"hgvs_c": "c.1679G>A",
"hgvs_p": "p.Arg560His",
"transcript": "ENST00000430012.6",
"protein_id": "ENSP00000403182.1",
"transcript_support_level": 5,
"aa_start": 560,
"aa_end": null,
"aa_length": 589,
"cds_start": 1679,
"cds_end": null,
"cds_length": 1770,
"cdna_start": 1916,
"cdna_end": null,
"cdna_length": 2007,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYRK1B",
"gene_hgnc_id": 3092,
"hgvs_c": "c.1979G>A",
"hgvs_p": "p.Arg660His",
"transcript": "XM_047439667.1",
"protein_id": "XP_047295623.1",
"transcript_support_level": null,
"aa_start": 660,
"aa_end": null,
"aa_length": 689,
"cds_start": 1979,
"cds_end": null,
"cds_length": 2070,
"cdna_start": 2282,
"cdna_end": null,
"cdna_length": 2738,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYRK1B",
"gene_hgnc_id": 3092,
"hgvs_c": "c.1895G>A",
"hgvs_p": "p.Arg632His",
"transcript": "XM_047439668.1",
"protein_id": "XP_047295624.1",
"transcript_support_level": null,
"aa_start": 632,
"aa_end": null,
"aa_length": 661,
"cds_start": 1895,
"cds_end": null,
"cds_length": 1986,
"cdna_start": 2198,
"cdna_end": null,
"cdna_length": 2654,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYRK1B",
"gene_hgnc_id": 3092,
"hgvs_c": "c.1859G>A",
"hgvs_p": "p.Arg620His",
"transcript": "XM_047439669.1",
"protein_id": "XP_047295625.1",
"transcript_support_level": null,
"aa_start": 620,
"aa_end": null,
"aa_length": 649,
"cds_start": 1859,
"cds_end": null,
"cds_length": 1950,
"cdna_start": 2162,
"cdna_end": null,
"cdna_length": 2618,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DYRK1B",
"gene_hgnc_id": 3092,
"hgvs_c": "c.1799G>A",
"hgvs_p": "p.Arg600His",
"transcript": "XM_005259398.5",
"protein_id": "XP_005259455.1",
"transcript_support_level": null,
"aa_start": 600,
"aa_end": null,
"aa_length": 629,
"cds_start": 1799,
"cds_end": null,
"cds_length": 1890,
"cdna_start": 2108,
"cdna_end": null,
"cdna_length": 2564,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DYRK1B",
"gene_hgnc_id": 3092,
"dbsnp": "rs1442897061",
"frequency_reference_population": 0.000009424017,
"hom_count_reference_population": 0,
"allele_count_reference_population": 15,
"gnomad_exomes_af": 0.00000764051,
"gnomad_genomes_af": 0.0000263186,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0904356837272644,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.062,
"revel_prediction": "Benign",
"alphamissense_score": 0.1137,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.356,
"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": -6,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_by_gene": [
{
"score": -6,
"benign_score": 6,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_004714.3",
"gene_symbol": "DYRK1B",
"hgnc_id": 3092,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1799G>A",
"hgvs_p": "p.Arg600His"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}