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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-153694445-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153694445&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153694445,
"ref": "C",
"alt": "G",
"effect": "stop_gained,splice_region_variant",
"transcript": "NM_005629.4",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1494C>G",
"hgvs_p": "p.Tyr498*",
"transcript": "NM_005629.4",
"protein_id": "NP_005620.1",
"transcript_support_level": null,
"aa_start": 498,
"aa_end": null,
"aa_length": 635,
"cds_start": 1494,
"cds_end": null,
"cds_length": 1908,
"cdna_start": 2143,
"cdna_end": null,
"cdna_length": 3931,
"mane_select": "ENST00000253122.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1494C>G",
"hgvs_p": "p.Tyr498*",
"transcript": "ENST00000253122.10",
"protein_id": "ENSP00000253122.5",
"transcript_support_level": 1,
"aa_start": 498,
"aa_end": null,
"aa_length": 635,
"cds_start": 1494,
"cds_end": null,
"cds_length": 1908,
"cdna_start": 2143,
"cdna_end": null,
"cdna_length": 3931,
"mane_select": "NM_005629.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1464C>G",
"hgvs_p": "p.Tyr488*",
"transcript": "NM_001142805.2",
"protein_id": "NP_001136277.1",
"transcript_support_level": null,
"aa_start": 488,
"aa_end": null,
"aa_length": 625,
"cds_start": 1464,
"cds_end": null,
"cds_length": 1878,
"cdna_start": 2113,
"cdna_end": null,
"cdna_length": 3901,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1149C>G",
"hgvs_p": "p.Tyr383*",
"transcript": "NM_001142806.1",
"protein_id": "NP_001136278.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 520,
"cds_start": 1149,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 1321,
"cdna_end": null,
"cdna_length": 3114,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1149C>G",
"hgvs_p": "p.Tyr383*",
"transcript": "ENST00000430077.6",
"protein_id": "ENSP00000403041.2",
"transcript_support_level": 2,
"aa_start": 383,
"aa_end": null,
"aa_length": 520,
"cds_start": 1149,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 1365,
"cdna_end": null,
"cdna_length": 1892,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.423C>G",
"hgvs_p": "p.Tyr141*",
"transcript": "ENST00000413787.1",
"protein_id": "ENSP00000400463.1",
"transcript_support_level": 5,
"aa_start": 141,
"aa_end": null,
"aa_length": 155,
"cds_start": 423,
"cds_end": null,
"cds_length": 468,
"cdna_start": 423,
"cdna_end": null,
"cdna_length": 468,
"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": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "n.1715C>G",
"hgvs_p": null,
"transcript": "ENST00000485324.1",
"protein_id": null,
"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": 2401,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.*25C>G",
"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": -4,
"cds_end": null,
"cds_length": 521,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 523,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"dbsnp": "rs143916832",
"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": 0.4300000071525574,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.1720000058412552,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.43,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": -2.531,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.46,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": 0.000553958489761831,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "NM_005629.4",
"gene_symbol": "SLC6A8",
"hgnc_id": 11055,
"effects": [
"stop_gained",
"splice_region_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1494C>G",
"hgvs_p": "p.Tyr498*"
}
],
"clinvar_disease": "Creatine transporter deficiency",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Creatine transporter deficiency",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}