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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: 4-3160307-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=3160307&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 3160307,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000355072.11",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTT",
"gene_hgnc_id": 4851,
"hgvs_c": "c.3779C>T",
"hgvs_p": "p.Thr1260Met",
"transcript": "NM_001388492.1",
"protein_id": "NP_001375421.1",
"transcript_support_level": null,
"aa_start": 1260,
"aa_end": null,
"aa_length": 3142,
"cds_start": 3779,
"cds_end": null,
"cds_length": 9429,
"cdna_start": 3924,
"cdna_end": null,
"cdna_length": 13472,
"mane_select": "ENST00000355072.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTT",
"gene_hgnc_id": 4851,
"hgvs_c": "c.3779C>T",
"hgvs_p": "p.Thr1260Met",
"transcript": "ENST00000355072.11",
"protein_id": "ENSP00000347184.5",
"transcript_support_level": 1,
"aa_start": 1260,
"aa_end": null,
"aa_length": 3142,
"cds_start": 3779,
"cds_end": null,
"cds_length": 9429,
"cdna_start": 3924,
"cdna_end": null,
"cdna_length": 13472,
"mane_select": "NM_001388492.1",
"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": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTT",
"gene_hgnc_id": 4851,
"hgvs_c": "n.3878C>T",
"hgvs_p": null,
"transcript": "ENST00000510626.5",
"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": 14438,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTT",
"gene_hgnc_id": 4851,
"hgvs_c": "c.3779C>T",
"hgvs_p": "p.Thr1260Met",
"transcript": "NM_002111.8",
"protein_id": "NP_002102.4",
"transcript_support_level": null,
"aa_start": 1260,
"aa_end": null,
"aa_length": 3142,
"cds_start": 3779,
"cds_end": null,
"cds_length": 9429,
"cdna_start": 3924,
"cdna_end": null,
"cdna_length": 13475,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 68,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTT",
"gene_hgnc_id": 4851,
"hgvs_c": "c.3521C>T",
"hgvs_p": "p.Thr1174Met",
"transcript": "ENST00000681528.1",
"protein_id": "ENSP00000506116.1",
"transcript_support_level": null,
"aa_start": 1174,
"aa_end": null,
"aa_length": 3086,
"cds_start": 3521,
"cds_end": null,
"cds_length": 9261,
"cdna_start": 4399,
"cdna_end": null,
"cdna_length": 14033,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTT",
"gene_hgnc_id": 4851,
"hgvs_c": "c.3521C>T",
"hgvs_p": "p.Thr1174Met",
"transcript": "ENST00000680956.1",
"protein_id": "ENSP00000506029.1",
"transcript_support_level": null,
"aa_start": 1174,
"aa_end": null,
"aa_length": 3056,
"cds_start": 3521,
"cds_end": null,
"cds_length": 9171,
"cdna_start": 4399,
"cdna_end": null,
"cdna_length": 13943,
"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": 29,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTT",
"gene_hgnc_id": 4851,
"hgvs_c": "n.3521C>T",
"hgvs_p": null,
"transcript": "ENST00000680239.1",
"protein_id": "ENSP00000506169.1",
"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": 13834,
"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": 29,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTT",
"gene_hgnc_id": 4851,
"hgvs_c": "n.3876C>T",
"hgvs_p": null,
"transcript": "ENST00000680291.1",
"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": 7184,
"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": 29,
"exon_rank_end": null,
"exon_count": 67,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTT",
"gene_hgnc_id": 4851,
"hgvs_c": "n.3521C>T",
"hgvs_p": null,
"transcript": "ENST00000680360.1",
"protein_id": "ENSP00000505014.1",
"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": 13984,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HTT",
"gene_hgnc_id": 4851,
"hgvs_c": "c.-56C>T",
"hgvs_p": null,
"transcript": "ENST00000509618.1",
"protein_id": "ENSP00000425743.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 111,
"cds_start": -4,
"cds_end": null,
"cds_length": 336,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 429,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HTT",
"gene_hgnc_id": 4851,
"dbsnp": "rs34315806",
"frequency_reference_population": 0.0047243284,
"hom_count_reference_population": 249,
"allele_count_reference_population": 7334,
"gnomad_exomes_af": 0.00280191,
"gnomad_genomes_af": 0.0224007,
"gnomad_exomes_ac": 3923,
"gnomad_genomes_ac": 3411,
"gnomad_exomes_homalt": 122,
"gnomad_genomes_homalt": 127,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.002370595932006836,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.106,
"revel_prediction": "Benign",
"alphamissense_score": 0.086,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.461,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000355072.11",
"gene_symbol": "HTT",
"hgnc_id": 4851,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.3779C>T",
"hgvs_p": "p.Thr1260Met"
}
],
"clinvar_disease": "Lopes-Maciel-Rodan syndrome,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:4",
"phenotype_combined": "Lopes-Maciel-Rodan syndrome|not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}