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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: X-153693470-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153693470&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153693470,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_005629.4",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr",
"transcript": "NM_005629.4",
"protein_id": "NP_005620.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 635,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1908,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000253122.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005629.4"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr",
"transcript": "ENST00000253122.10",
"protein_id": "ENSP00000253122.5",
"transcript_support_level": 1,
"aa_start": 342,
"aa_end": null,
"aa_length": 635,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1908,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005629.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000253122.10"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr",
"transcript": "ENST00000955775.1",
"protein_id": "ENSP00000625834.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 634,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1905,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955775.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr",
"transcript": "ENST00000922630.1",
"protein_id": "ENSP00000592689.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 632,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1899,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922630.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.977T>C",
"hgvs_p": "p.Ile326Thr",
"transcript": "ENST00000922632.1",
"protein_id": "ENSP00000592691.1",
"transcript_support_level": null,
"aa_start": 326,
"aa_end": null,
"aa_length": 619,
"cds_start": 977,
"cds_end": null,
"cds_length": 1860,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922632.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.914T>C",
"hgvs_p": "p.Ile305Thr",
"transcript": "ENST00000922633.1",
"protein_id": "ENSP00000592692.1",
"transcript_support_level": null,
"aa_start": 305,
"aa_end": null,
"aa_length": 598,
"cds_start": 914,
"cds_end": null,
"cds_length": 1797,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922633.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr",
"transcript": "ENST00000922631.1",
"protein_id": "ENSP00000592690.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 589,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1770,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922631.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr",
"transcript": "ENST00000955776.1",
"protein_id": "ENSP00000625835.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 582,
"cds_start": 1025,
"cds_end": null,
"cds_length": 1749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955776.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.680T>C",
"hgvs_p": "p.Ile227Thr",
"transcript": "NM_001142806.1",
"protein_id": "NP_001136278.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 520,
"cds_start": 680,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142806.1"
},
{
"aa_ref": "I",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.680T>C",
"hgvs_p": "p.Ile227Thr",
"transcript": "ENST00000430077.6",
"protein_id": "ENSP00000403041.2",
"transcript_support_level": 2,
"aa_start": 227,
"aa_end": null,
"aa_length": 520,
"cds_start": 680,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000430077.6"
},
{
"aa_ref": "H",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.9T>C",
"hgvs_p": "p.His3His",
"transcript": "ENST00000457723.1",
"protein_id": "ENSP00000394742.1",
"transcript_support_level": 5,
"aa_start": 3,
"aa_end": null,
"aa_length": 87,
"cds_start": 9,
"cds_end": null,
"cds_length": 266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000457723.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1017-22T>C",
"hgvs_p": null,
"transcript": "NM_001142805.2",
"protein_id": "NP_001136277.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 625,
"cds_start": null,
"cds_end": null,
"cds_length": 1878,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142805.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.99-22T>C",
"hgvs_p": null,
"transcript": "ENST00000442457.1",
"protein_id": "ENSP00000403682.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 172,
"cds_start": null,
"cds_end": null,
"cds_length": 521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000442457.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.163-22T>C",
"hgvs_p": null,
"transcript": "ENST00000413787.1",
"protein_id": "ENSP00000400463.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 155,
"cds_start": null,
"cds_end": null,
"cds_length": 468,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000413787.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "n.1058T>C",
"hgvs_p": null,
"transcript": "ENST00000485324.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000485324.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "n.146-22T>C",
"hgvs_p": null,
"transcript": "ENST00000467402.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "ENST00000467402.1"
}
],
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"dbsnp": "rs781962672",
"frequency_reference_population": 0.00004961917,
"hom_count_reference_population": 16,
"allele_count_reference_population": 60,
"gnomad_exomes_af": 0.0000491943,
"gnomad_genomes_af": 0.0000538015,
"gnomad_exomes_ac": 54,
"gnomad_genomes_ac": 6,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8894811868667603,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.64,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.385,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.01,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.467,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS2",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_005629.4",
"gene_symbol": "SLC6A8",
"hgnc_id": 11055,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1025T>C",
"hgvs_p": "p.Ile342Thr"
}
],
"clinvar_disease": "Creatine transporter deficiency,not provided,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "US:3 LB:2",
"phenotype_combined": "not specified|Creatine transporter deficiency|not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}