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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-153693368-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153693368&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153693368,
"ref": "T",
"alt": "C",
"effect": "splice_donor_variant,intron_variant",
"transcript": "NM_005629.4",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"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.1016+2T>C",
"hgvs_p": null,
"transcript": "NM_005629.4",
"protein_id": "NP_005620.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 635,
"cds_start": null,
"cds_end": null,
"cds_length": 1908,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3931,
"mane_select": "ENST00000253122.10",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005629.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"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.1016+2T>C",
"hgvs_p": null,
"transcript": "ENST00000253122.10",
"protein_id": "ENSP00000253122.5",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 635,
"cds_start": null,
"cds_end": null,
"cds_length": 1908,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3931,
"mane_select": "NM_005629.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000253122.10"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"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.1016+2T>C",
"hgvs_p": null,
"transcript": "ENST00000955775.1",
"protein_id": "ENSP00000625834.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 634,
"cds_start": null,
"cds_end": null,
"cds_length": 1905,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3920,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955775.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"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.1016+2T>C",
"hgvs_p": null,
"transcript": "ENST00000922630.1",
"protein_id": "ENSP00000592689.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 632,
"cds_start": null,
"cds_end": null,
"cds_length": 1899,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3924,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922630.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"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.1016+2T>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": 3901,
"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": [
"splice_donor_variant",
"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.968+2T>C",
"hgvs_p": null,
"transcript": "ENST00000922632.1",
"protein_id": "ENSP00000592691.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 619,
"cds_start": null,
"cds_end": null,
"cds_length": 1860,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3879,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922632.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"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.905+2T>C",
"hgvs_p": null,
"transcript": "ENST00000922633.1",
"protein_id": "ENSP00000592692.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 598,
"cds_start": null,
"cds_end": null,
"cds_length": 1797,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2638,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922633.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1016+2T>C",
"hgvs_p": null,
"transcript": "ENST00000922631.1",
"protein_id": "ENSP00000592690.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 589,
"cds_start": null,
"cds_end": null,
"cds_length": 1770,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3792,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000922631.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1016+2T>C",
"hgvs_p": null,
"transcript": "ENST00000955776.1",
"protein_id": "ENSP00000625835.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 582,
"cds_start": null,
"cds_end": null,
"cds_length": 1749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2460,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000955776.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"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.671+2T>C",
"hgvs_p": null,
"transcript": "NM_001142806.1",
"protein_id": "NP_001136278.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 520,
"cds_start": null,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3114,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001142806.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"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.671+2T>C",
"hgvs_p": null,
"transcript": "ENST00000430077.6",
"protein_id": "ENSP00000403041.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 520,
"cds_start": null,
"cds_end": null,
"cds_length": 1563,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1892,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000430077.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"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.98+2T>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": 523,
"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": [
"splice_donor_variant",
"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.162+2T>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": 468,
"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": [
"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.146-124T>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": 308,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000467402.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"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": "n.1049+2T>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": 2401,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000485324.1"
},
{
"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": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.-94T>C",
"hgvs_p": null,
"transcript": "ENST00000457723.1",
"protein_id": "ENSP00000394742.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 87,
"cds_start": null,
"cds_end": null,
"cds_length": 266,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 266,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000457723.1"
}
],
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"dbsnp": "rs1557045066",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.1899999976158142,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.5860000252723694,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.19,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 5.044,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.4,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.989732985218383,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PP4,PM2_Supporting",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PVS1",
"PP4",
"PM2_Supporting"
],
"verdict": "Pathogenic",
"transcript": "NM_005629.4",
"gene_symbol": "SLC6A8",
"hgnc_id": 11055,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1016+2T>C",
"hgvs_p": null
}
],
"clinvar_disease": "Creatine transporter deficiency,Inborn genetic diseases",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "reviewed by expert panel",
"clinvar_submissions_summary": "P:3 LP:1 O:1",
"phenotype_combined": "Inborn genetic diseases|Creatine transporter deficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}