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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: 7-73708626-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=73708626&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 73708626,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_004603.4",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.171G>A",
"hgvs_p": "p.Lys57Lys",
"transcript": "NM_004603.4",
"protein_id": "NP_004594.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 288,
"cds_start": 171,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000222812.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004603.4"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.171G>A",
"hgvs_p": "p.Lys57Lys",
"transcript": "ENST00000222812.8",
"protein_id": "ENSP00000222812.3",
"transcript_support_level": 1,
"aa_start": 57,
"aa_end": null,
"aa_length": 288,
"cds_start": 171,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004603.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000222812.8"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.171G>A",
"hgvs_p": "p.Lys57Lys",
"transcript": "ENST00000395156.7",
"protein_id": "ENSP00000378585.3",
"transcript_support_level": 1,
"aa_start": 57,
"aa_end": null,
"aa_length": 251,
"cds_start": 171,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395156.7"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.171G>A",
"hgvs_p": "p.Lys57Lys",
"transcript": "ENST00000929307.1",
"protein_id": "ENSP00000599366.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 326,
"cds_start": 171,
"cds_end": null,
"cds_length": 981,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000929307.1"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.171G>A",
"hgvs_p": "p.Lys57Lys",
"transcript": "ENST00000395154.7",
"protein_id": "ENSP00000378583.3",
"transcript_support_level": 3,
"aa_start": 57,
"aa_end": null,
"aa_length": 280,
"cds_start": 171,
"cds_end": null,
"cds_length": 843,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395154.7"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.93G>A",
"hgvs_p": "p.Lys31Lys",
"transcript": "ENST00000971340.1",
"protein_id": "ENSP00000641399.1",
"transcript_support_level": null,
"aa_start": 31,
"aa_end": null,
"aa_length": 262,
"cds_start": 93,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971340.1"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.171G>A",
"hgvs_p": "p.Lys57Lys",
"transcript": "ENST00000395155.3",
"protein_id": "ENSP00000378584.3",
"transcript_support_level": 2,
"aa_start": 57,
"aa_end": null,
"aa_length": 260,
"cds_start": 171,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000395155.3"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.171G>A",
"hgvs_p": "p.Lys57Lys",
"transcript": "NM_001165903.2",
"protein_id": "NP_001159375.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 251,
"cds_start": 171,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001165903.2"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.171G>A",
"hgvs_p": "p.Lys57Lys",
"transcript": "ENST00000910650.1",
"protein_id": "ENSP00000580709.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 251,
"cds_start": 171,
"cds_end": null,
"cds_length": 756,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000910650.1"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.171G>A",
"hgvs_p": "p.Lys57Lys",
"transcript": "XM_047420777.1",
"protein_id": "XP_047276733.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 280,
"cds_start": 171,
"cds_end": null,
"cds_length": 843,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420777.1"
},
{
"aa_ref": "K",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "c.171G>A",
"hgvs_p": "p.Lys57Lys",
"transcript": "XM_047420778.1",
"protein_id": "XP_047276734.1",
"transcript_support_level": null,
"aa_start": 57,
"aa_end": null,
"aa_length": 260,
"cds_start": 171,
"cds_end": null,
"cds_length": 783,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047420778.1"
},
{
"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": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "n.212G>A",
"hgvs_p": null,
"transcript": "ENST00000462135.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000462135.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"hgvs_c": "n.320G>A",
"hgvs_p": null,
"transcript": "ENST00000470878.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000470878.5"
}
],
"gene_symbol": "STX1A",
"gene_hgnc_id": 11433,
"dbsnp": "rs140052001",
"frequency_reference_population": 0.00029054857,
"hom_count_reference_population": 1,
"allele_count_reference_population": 469,
"gnomad_exomes_af": 0.000298259,
"gnomad_genomes_af": 0.000216578,
"gnomad_exomes_ac": 436,
"gnomad_genomes_ac": 33,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4300000071525574,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.43,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.575,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.06,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_004603.4",
"gene_symbol": "STX1A",
"hgnc_id": 11433,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.171G>A",
"hgvs_p": "p.Lys57Lys"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}