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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: 9-39085813-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=39085813&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 39085813,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_033655.5",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTNAP3",
"gene_hgnc_id": 13834,
"hgvs_c": "c.3365G>A",
"hgvs_p": "p.Ser1122Asn",
"transcript": "NM_033655.5",
"protein_id": "NP_387504.2",
"transcript_support_level": null,
"aa_start": 1122,
"aa_end": null,
"aa_length": 1288,
"cds_start": 3365,
"cds_end": null,
"cds_length": 3867,
"cdna_start": 3468,
"cdna_end": null,
"cdna_length": 13150,
"mane_select": "ENST00000297668.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTNAP3",
"gene_hgnc_id": 13834,
"hgvs_c": "c.3365G>A",
"hgvs_p": "p.Ser1122Asn",
"transcript": "ENST00000297668.11",
"protein_id": "ENSP00000297668.6",
"transcript_support_level": 1,
"aa_start": 1122,
"aa_end": null,
"aa_length": 1288,
"cds_start": 3365,
"cds_end": null,
"cds_length": 3867,
"cdna_start": 3468,
"cdna_end": null,
"cdna_length": 13150,
"mane_select": "NM_033655.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTNAP3",
"gene_hgnc_id": 13834,
"hgvs_c": "c.3122G>A",
"hgvs_p": "p.Ser1041Asn",
"transcript": "ENST00000377656.6",
"protein_id": "ENSP00000366884.2",
"transcript_support_level": 1,
"aa_start": 1041,
"aa_end": null,
"aa_length": 1207,
"cds_start": 3122,
"cds_end": null,
"cds_length": 3624,
"cdna_start": 3361,
"cdna_end": null,
"cdna_length": 4986,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTNAP3",
"gene_hgnc_id": 13834,
"hgvs_c": "c.3122G>A",
"hgvs_p": "p.Ser1041Asn",
"transcript": "NM_001393379.1",
"protein_id": "NP_001380308.1",
"transcript_support_level": null,
"aa_start": 1041,
"aa_end": null,
"aa_length": 1207,
"cds_start": 3122,
"cds_end": null,
"cds_length": 3624,
"cdna_start": 3225,
"cdna_end": null,
"cdna_length": 12907,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTNAP3",
"gene_hgnc_id": 13834,
"hgvs_c": "n.111G>A",
"hgvs_p": null,
"transcript": "ENST00000477002.1",
"protein_id": null,
"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": 291,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTNAP3",
"gene_hgnc_id": 13834,
"hgvs_c": "n.196G>A",
"hgvs_p": null,
"transcript": "ENST00000493965.5",
"protein_id": null,
"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": 765,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CNTNAP3",
"gene_hgnc_id": 13834,
"hgvs_c": "c.*873G>A",
"hgvs_p": null,
"transcript": "ENST00000358144.6",
"protein_id": "ENSP00000350863.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1039,
"cds_start": -4,
"cds_end": null,
"cds_length": 3120,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4885,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CNTNAP3",
"gene_hgnc_id": 13834,
"dbsnp": "rs372421268",
"frequency_reference_population": 0.00012212571,
"hom_count_reference_population": 7,
"allele_count_reference_population": 190,
"gnomad_exomes_af": 0.000124495,
"gnomad_genomes_af": 0.0000999334,
"gnomad_exomes_ac": 175,
"gnomad_genomes_ac": 15,
"gnomad_exomes_homalt": 7,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0354437530040741,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.105,
"revel_prediction": "Benign",
"alphamissense_score": 0.0682,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.231,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_033655.5",
"gene_symbol": "CNTNAP3",
"hgnc_id": 13834,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3365G>A",
"hgvs_p": "p.Ser1122Asn"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}