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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: 2-170859769-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=170859769&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 170859769,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000358196.8",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"hgvs_c": "c.1672C>T",
"hgvs_p": "p.Pro558Ser",
"transcript": "NM_000817.3",
"protein_id": "NP_000808.2",
"transcript_support_level": null,
"aa_start": 558,
"aa_end": null,
"aa_length": 594,
"cds_start": 1672,
"cds_end": null,
"cds_length": 1785,
"cdna_start": 1897,
"cdna_end": null,
"cdna_length": 3279,
"mane_select": "ENST00000358196.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"hgvs_c": "c.1672C>T",
"hgvs_p": "p.Pro558Ser",
"transcript": "ENST00000358196.8",
"protein_id": "ENSP00000350928.3",
"transcript_support_level": 1,
"aa_start": 558,
"aa_end": null,
"aa_length": 594,
"cds_start": 1672,
"cds_end": null,
"cds_length": 1785,
"cdna_start": 1897,
"cdna_end": null,
"cdna_length": 3279,
"mane_select": "NM_000817.3",
"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": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"hgvs_c": "n.772C>T",
"hgvs_p": null,
"transcript": "ENST00000488724.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 1256,
"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": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"hgvs_c": "n.*506C>T",
"hgvs_p": null,
"transcript": "ENST00000493875.5",
"protein_id": "ENSP00000434696.1",
"transcript_support_level": 1,
"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": 3988,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"hgvs_c": "n.*506C>T",
"hgvs_p": null,
"transcript": "ENST00000493875.5",
"protein_id": "ENSP00000434696.1",
"transcript_support_level": 1,
"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": 3988,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"hgvs_c": "c.1672C>T",
"hgvs_p": "p.Pro558Ser",
"transcript": "XM_011510922.1",
"protein_id": "XP_011509224.1",
"transcript_support_level": null,
"aa_start": 558,
"aa_end": null,
"aa_length": 594,
"cds_start": 1672,
"cds_end": null,
"cds_length": 1785,
"cdna_start": 1948,
"cdna_end": null,
"cdna_length": 3330,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"hgvs_c": "c.1672C>T",
"hgvs_p": "p.Pro558Ser",
"transcript": "XM_017003756.2",
"protein_id": "XP_016859245.1",
"transcript_support_level": null,
"aa_start": 558,
"aa_end": null,
"aa_length": 594,
"cds_start": 1672,
"cds_end": null,
"cds_length": 1785,
"cdna_start": 1898,
"cdna_end": null,
"cdna_length": 3280,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"hgvs_c": "c.1000C>T",
"hgvs_p": "p.Pro334Ser",
"transcript": "XM_047443874.1",
"protein_id": "XP_047299830.1",
"transcript_support_level": null,
"aa_start": 334,
"aa_end": null,
"aa_length": 370,
"cds_start": 1000,
"cds_end": null,
"cds_length": 1113,
"cdna_start": 1119,
"cdna_end": null,
"cdna_length": 2501,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"hgvs_c": "c.904C>T",
"hgvs_p": "p.Pro302Ser",
"transcript": "XM_024452783.2",
"protein_id": "XP_024308551.1",
"transcript_support_level": null,
"aa_start": 302,
"aa_end": null,
"aa_length": 338,
"cds_start": 904,
"cds_end": null,
"cds_length": 1017,
"cdna_start": 1395,
"cdna_end": null,
"cdna_length": 2777,
"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": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"hgvs_c": "n.*857C>T",
"hgvs_p": null,
"transcript": "ENST00000414527.6",
"protein_id": "ENSP00000403849.1",
"transcript_support_level": 5,
"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": 1780,
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"hgvs_c": "n.1794C>T",
"hgvs_p": null,
"transcript": "ENST00000478562.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 3172,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"hgvs_c": "c.*506C>T",
"hgvs_p": null,
"transcript": "ENST00000625689.2",
"protein_id": "ENSP00000486612.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 425,
"cds_start": -4,
"cds_end": null,
"cds_length": 1278,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3700,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"hgvs_c": "n.*857C>T",
"hgvs_p": null,
"transcript": "ENST00000414527.6",
"protein_id": "ENSP00000403849.1",
"transcript_support_level": 5,
"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": 1780,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GAD1",
"gene_hgnc_id": 4092,
"dbsnp": "rs774953382",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6907532811164856,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.428,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7455,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.1,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.568,
"phylop100way_prediction": "Pathogenic",
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP6_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP6_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000358196.8",
"gene_symbol": "GAD1",
"hgnc_id": 4092,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1672C>T",
"hgvs_p": "p.Pro558Ser"
}
],
"clinvar_disease": "Neurodevelopmental disorder with progressive spasticity and brain white matter abnormalities",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Neurodevelopmental disorder with progressive spasticity and brain white matter abnormalities",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}