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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-153694553-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153694553&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 153694553,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000253122.10",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1516G>A",
"hgvs_p": "p.Asp506Asn",
"transcript": "NM_005629.4",
"protein_id": "NP_005620.1",
"transcript_support_level": null,
"aa_start": 506,
"aa_end": null,
"aa_length": 635,
"cds_start": 1516,
"cds_end": null,
"cds_length": 1908,
"cdna_start": 2165,
"cdna_end": null,
"cdna_length": 3931,
"mane_select": "ENST00000253122.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1516G>A",
"hgvs_p": "p.Asp506Asn",
"transcript": "ENST00000253122.10",
"protein_id": "ENSP00000253122.5",
"transcript_support_level": 1,
"aa_start": 506,
"aa_end": null,
"aa_length": 635,
"cds_start": 1516,
"cds_end": null,
"cds_length": 1908,
"cdna_start": 2165,
"cdna_end": null,
"cdna_length": 3931,
"mane_select": "NM_005629.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1486G>A",
"hgvs_p": "p.Asp496Asn",
"transcript": "NM_001142805.2",
"protein_id": "NP_001136277.1",
"transcript_support_level": null,
"aa_start": 496,
"aa_end": null,
"aa_length": 625,
"cds_start": 1486,
"cds_end": null,
"cds_length": 1878,
"cdna_start": 2135,
"cdna_end": null,
"cdna_length": 3901,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1171G>A",
"hgvs_p": "p.Asp391Asn",
"transcript": "NM_001142806.1",
"protein_id": "NP_001136278.1",
"transcript_support_level": null,
"aa_start": 391,
"aa_end": null,
"aa_length": 520,
"cds_start": 1171,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 1343,
"cdna_end": null,
"cdna_length": 3114,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.1171G>A",
"hgvs_p": "p.Asp391Asn",
"transcript": "ENST00000430077.6",
"protein_id": "ENSP00000403041.2",
"transcript_support_level": 2,
"aa_start": 391,
"aa_end": null,
"aa_length": 520,
"cds_start": 1171,
"cds_end": null,
"cds_length": 1563,
"cdna_start": 1387,
"cdna_end": null,
"cdna_length": 1892,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC6A8",
"gene_hgnc_id": 11055,
"hgvs_c": "c.445G>A",
"hgvs_p": "p.Asp149Asn",
"transcript": "ENST00000413787.1",
"protein_id": "ENSP00000400463.1",
"transcript_support_level": 5,
"aa_start": 149,
"aa_end": null,
"aa_length": 155,
"cds_start": 445,
"cds_end": null,
"cds_length": 468,
"cdna_start": 445,
"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.1823G>A",
"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.*133G>A",
"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": "rs201526436",
"frequency_reference_population": 0.0003810666,
"hom_count_reference_population": 151,
"allele_count_reference_population": 460,
"gnomad_exomes_af": 0.000382894,
"gnomad_genomes_af": 0.000362884,
"gnomad_exomes_ac": 420,
"gnomad_genomes_ac": 40,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.02288493514060974,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.228,
"revel_prediction": "Benign",
"alphamissense_score": 0.495,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.44,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.438,
"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": -16,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS2",
"acmg_by_gene": [
{
"score": -16,
"benign_score": 16,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000253122.10",
"gene_symbol": "SLC6A8",
"hgnc_id": 11055,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.1516G>A",
"hgvs_p": "p.Asp506Asn"
}
],
"clinvar_disease": "Creatine transporter deficiency,Inborn genetic diseases,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:5",
"phenotype_combined": "not specified|not provided|Inborn genetic diseases|Creatine transporter deficiency",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}