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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: 12-5494564-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=5494564&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 5494564,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_001102654.2",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "S",
"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": "NTF3",
"gene_hgnc_id": 8023,
"hgvs_c": "c.389T>C",
"hgvs_p": "p.Leu130Ser",
"transcript": "NM_001102654.2",
"protein_id": "NP_001096124.1",
"transcript_support_level": null,
"aa_start": 130,
"aa_end": null,
"aa_length": 270,
"cds_start": 389,
"cds_end": null,
"cds_length": 813,
"cdna_start": 606,
"cdna_end": null,
"cdna_length": 1341,
"mane_select": "ENST00000423158.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"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": "NTF3",
"gene_hgnc_id": 8023,
"hgvs_c": "c.389T>C",
"hgvs_p": "p.Leu130Ser",
"transcript": "ENST00000423158.4",
"protein_id": "ENSP00000397297.2",
"transcript_support_level": 1,
"aa_start": 130,
"aa_end": null,
"aa_length": 270,
"cds_start": 389,
"cds_end": null,
"cds_length": 813,
"cdna_start": 606,
"cdna_end": null,
"cdna_length": 1341,
"mane_select": "NM_001102654.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"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": "NTF3",
"gene_hgnc_id": 8023,
"hgvs_c": "c.350T>C",
"hgvs_p": "p.Leu117Ser",
"transcript": "NM_002527.5",
"protein_id": "NP_002518.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 257,
"cds_start": 350,
"cds_end": null,
"cds_length": 774,
"cdna_start": 433,
"cdna_end": null,
"cdna_length": 1168,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"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": "NTF3",
"gene_hgnc_id": 8023,
"hgvs_c": "c.350T>C",
"hgvs_p": "p.Leu117Ser",
"transcript": "ENST00000331010.7",
"protein_id": "ENSP00000328738.6",
"transcript_support_level": 6,
"aa_start": 117,
"aa_end": null,
"aa_length": 257,
"cds_start": 350,
"cds_end": null,
"cds_length": 774,
"cdna_start": 433,
"cdna_end": null,
"cdna_length": 1028,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"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": "NTF3",
"gene_hgnc_id": 8023,
"hgvs_c": "c.350T>C",
"hgvs_p": "p.Leu117Ser",
"transcript": "XM_011520963.3",
"protein_id": "XP_011519265.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 257,
"cds_start": 350,
"cds_end": null,
"cds_length": 774,
"cdna_start": 435,
"cdna_end": null,
"cdna_length": 1170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"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": "NTF3",
"gene_hgnc_id": 8023,
"hgvs_c": "c.350T>C",
"hgvs_p": "p.Leu117Ser",
"transcript": "XM_047428901.1",
"protein_id": "XP_047284857.1",
"transcript_support_level": null,
"aa_start": 117,
"aa_end": null,
"aa_length": 257,
"cds_start": 350,
"cds_end": null,
"cds_length": 774,
"cdna_start": 1233,
"cdna_end": null,
"cdna_length": 1968,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "NTF3",
"gene_hgnc_id": 8023,
"hgvs_c": "n.232-12001T>C",
"hgvs_p": null,
"transcript": "ENST00000535299.5",
"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": 875,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NTF3",
"gene_hgnc_id": 8023,
"hgvs_c": "n.*63T>C",
"hgvs_p": null,
"transcript": "ENST00000543548.1",
"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": 516,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NTF3",
"gene_hgnc_id": 8023,
"dbsnp": "rs771891372",
"frequency_reference_population": 0.000048328337,
"hom_count_reference_population": 0,
"allele_count_reference_population": 78,
"gnomad_exomes_af": 0.0000506202,
"gnomad_genomes_af": 0.0000262999,
"gnomad_exomes_ac": 74,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8056209087371826,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.482,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.699,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.08,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.988,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PP3,BS2",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 4,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001102654.2",
"gene_symbol": "NTF3",
"hgnc_id": 8023,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.389T>C",
"hgvs_p": "p.Leu130Ser"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}