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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: 20-63346758-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=63346758&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 63346758,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_000744.7",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA4",
"gene_hgnc_id": 1958,
"hgvs_c": "c.1864T>C",
"hgvs_p": "p.Trp622Arg",
"transcript": "NM_000744.7",
"protein_id": "NP_000735.1",
"transcript_support_level": null,
"aa_start": 622,
"aa_end": null,
"aa_length": 627,
"cds_start": 1864,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 2048,
"cdna_end": null,
"cdna_length": 5583,
"mane_select": "ENST00000370263.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA4",
"gene_hgnc_id": 1958,
"hgvs_c": "c.1864T>C",
"hgvs_p": "p.Trp622Arg",
"transcript": "ENST00000370263.9",
"protein_id": "ENSP00000359285.4",
"transcript_support_level": 1,
"aa_start": 622,
"aa_end": null,
"aa_length": 627,
"cds_start": 1864,
"cds_end": null,
"cds_length": 1884,
"cdna_start": 2048,
"cdna_end": null,
"cdna_length": 5583,
"mane_select": "NM_000744.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA4",
"gene_hgnc_id": 1958,
"hgvs_c": "n.2512T>C",
"hgvs_p": null,
"transcript": "ENST00000463705.5",
"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": 5201,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "CHRNA4",
"gene_hgnc_id": 1958,
"hgvs_c": "n.1934T>C",
"hgvs_p": null,
"transcript": "ENST00000467563.3",
"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": 2098,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "CHRNA4",
"gene_hgnc_id": 1958,
"hgvs_c": "n.*1553T>C",
"hgvs_p": null,
"transcript": "ENST00000627000.1",
"protein_id": "ENSP00000486914.1",
"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": 2192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA4",
"gene_hgnc_id": 1958,
"hgvs_c": "n.*1553T>C",
"hgvs_p": null,
"transcript": "ENST00000627000.1",
"protein_id": "ENSP00000486914.1",
"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": 2192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA4",
"gene_hgnc_id": 1958,
"hgvs_c": "c.1336T>C",
"hgvs_p": "p.Trp446Arg",
"transcript": "NM_001256573.2",
"protein_id": "NP_001243502.1",
"transcript_support_level": null,
"aa_start": 446,
"aa_end": null,
"aa_length": 451,
"cds_start": 1336,
"cds_end": null,
"cds_length": 1356,
"cdna_start": 1979,
"cdna_end": null,
"cdna_length": 5514,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "CHRNA4",
"gene_hgnc_id": 1958,
"hgvs_c": "n.*1475T>C",
"hgvs_p": null,
"transcript": "ENST00000498043.6",
"protein_id": "ENSP00000429513.1",
"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": 2052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA4",
"gene_hgnc_id": 1958,
"hgvs_c": "n.178T>C",
"hgvs_p": null,
"transcript": "ENST00000631289.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "CHRNA4",
"gene_hgnc_id": 1958,
"hgvs_c": "n.2073T>C",
"hgvs_p": null,
"transcript": "NR_046317.2",
"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": 5608,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA4",
"gene_hgnc_id": 1958,
"hgvs_c": "n.*1475T>C",
"hgvs_p": null,
"transcript": "ENST00000498043.6",
"protein_id": "ENSP00000429513.1",
"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": 2052,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CHRNA4",
"gene_hgnc_id": 1958,
"dbsnp": null,
"frequency_reference_population": 6.8549775e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.85498e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8680539131164551,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.744,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8492,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.21,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 6.061,
"phylop100way_prediction": "Uncertain_significance",
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000744.7",
"gene_symbol": "CHRNA4",
"hgnc_id": 1958,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1864T>C",
"hgvs_p": "p.Trp622Arg"
}
],
"clinvar_disease": "Autosomal dominant nocturnal frontal lobe epilepsy",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Autosomal dominant nocturnal frontal lobe epilepsy",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}