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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: 15-78601994-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=78601994&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 78601994,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_000743.5",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA3",
"gene_hgnc_id": 1957,
"hgvs_c": "c.648A>C",
"hgvs_p": "p.Lys216Asn",
"transcript": "NM_000743.5",
"protein_id": "NP_000734.2",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 505,
"cds_start": 648,
"cds_end": null,
"cds_length": 1518,
"cdna_start": 850,
"cdna_end": null,
"cdna_length": 3015,
"mane_select": "ENST00000326828.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA3",
"gene_hgnc_id": 1957,
"hgvs_c": "c.648A>C",
"hgvs_p": "p.Lys216Asn",
"transcript": "ENST00000326828.6",
"protein_id": "ENSP00000315602.5",
"transcript_support_level": 1,
"aa_start": 216,
"aa_end": null,
"aa_length": 505,
"cds_start": 648,
"cds_end": null,
"cds_length": 1518,
"cdna_start": 850,
"cdna_end": null,
"cdna_length": 3015,
"mane_select": "NM_000743.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA3",
"gene_hgnc_id": 1957,
"hgvs_c": "c.648A>C",
"hgvs_p": "p.Lys216Asn",
"transcript": "ENST00000348639.7",
"protein_id": "ENSP00000267951.4",
"transcript_support_level": 1,
"aa_start": 216,
"aa_end": null,
"aa_length": 489,
"cds_start": 648,
"cds_end": null,
"cds_length": 1470,
"cdna_start": 1149,
"cdna_end": null,
"cdna_length": 2030,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA3",
"gene_hgnc_id": 1957,
"hgvs_c": "c.648A>C",
"hgvs_p": "p.Lys216Asn",
"transcript": "NM_001166694.2",
"protein_id": "NP_001160166.1",
"transcript_support_level": null,
"aa_start": 216,
"aa_end": null,
"aa_length": 489,
"cds_start": 648,
"cds_end": null,
"cds_length": 1470,
"cdna_start": 850,
"cdna_end": null,
"cdna_length": 1731,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA3",
"gene_hgnc_id": 1957,
"hgvs_c": "c.447A>C",
"hgvs_p": "p.Lys149Asn",
"transcript": "XM_006720382.4",
"protein_id": "XP_006720445.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 438,
"cds_start": 447,
"cds_end": null,
"cds_length": 1317,
"cdna_start": 1193,
"cdna_end": null,
"cdna_length": 3358,
"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": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA3",
"gene_hgnc_id": 1957,
"hgvs_c": "n.355A>C",
"hgvs_p": null,
"transcript": "ENST00000558903.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 573,
"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": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA3",
"gene_hgnc_id": 1957,
"hgvs_c": "n.648A>C",
"hgvs_p": null,
"transcript": "ENST00000559658.5",
"protein_id": "ENSP00000452896.1",
"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": 1889,
"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": 5,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHRNA3",
"gene_hgnc_id": 1957,
"hgvs_c": "n.850A>C",
"hgvs_p": null,
"transcript": "NR_046313.2",
"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": 2022,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CHRNA3",
"gene_hgnc_id": 1957,
"dbsnp": "rs76821682",
"frequency_reference_population": 0.0000065801596,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000658016,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.7731729745864868,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.553,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9631,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.21,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.385,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_000743.5",
"gene_symbol": "CHRNA3",
"hgnc_id": 1957,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.648A>C",
"hgvs_p": "p.Lys216Asn"
}
],
"clinvar_disease": " atony of,SMOKING AS A QUANTITATIVE TRAIT LOCUS 3,Urinary bladder",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "SMOKING AS A QUANTITATIVE TRAIT LOCUS 3;Urinary bladder, atony of",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}