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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-153695180-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153695180&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SLC6A8",
"hgnc_id": 11055,
"hgvs_c": "c.1874G>A",
"hgvs_p": "p.Ser625Asn",
"inheritance_mode": "XL",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_005629.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 60,
"alphamissense_prediction": null,
"alphamissense_score": 0.0977,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.66,
"chr": "X",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Creatine deficiency syndrome 1,Creatine transporter deficiency,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.09410133957862854,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 635,
"aa_ref": "S",
"aa_start": 625,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3931,
"cdna_start": 2523,
"cds_end": null,
"cds_length": 1908,
"cds_start": 1874,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_005629.4",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1874G>A",
"hgvs_p": "p.Ser625Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000253122.10",
"protein_coding": true,
"protein_id": "NP_005620.1",
"strand": true,
"transcript": "NM_005629.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 635,
"aa_ref": "S",
"aa_start": 625,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3931,
"cdna_start": 2523,
"cds_end": null,
"cds_length": 1908,
"cds_start": 1874,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000253122.10",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1874G>A",
"hgvs_p": "p.Ser625Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005629.4",
"protein_coding": true,
"protein_id": "ENSP00000253122.5",
"strand": true,
"transcript": "ENST00000253122.10",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 634,
"aa_ref": "S",
"aa_start": 624,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3920,
"cdna_start": 2518,
"cds_end": null,
"cds_length": 1905,
"cds_start": 1871,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000955775.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1871G>A",
"hgvs_p": "p.Ser624Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625834.1",
"strand": true,
"transcript": "ENST00000955775.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 632,
"aa_ref": "S",
"aa_start": 622,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3924,
"cdna_start": 2513,
"cds_end": null,
"cds_length": 1899,
"cds_start": 1865,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000922630.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1865G>A",
"hgvs_p": "p.Ser622Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592689.1",
"strand": true,
"transcript": "ENST00000922630.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 625,
"aa_ref": "S",
"aa_start": 615,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3901,
"cdna_start": 2493,
"cds_end": null,
"cds_length": 1878,
"cds_start": 1844,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001142805.2",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1844G>A",
"hgvs_p": "p.Ser615Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001136277.1",
"strand": true,
"transcript": "NM_001142805.2",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 619,
"aa_ref": "S",
"aa_start": 609,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3879,
"cdna_start": 2471,
"cds_end": null,
"cds_length": 1860,
"cds_start": 1826,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000922632.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1826G>A",
"hgvs_p": "p.Ser609Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592691.1",
"strand": true,
"transcript": "ENST00000922632.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 598,
"aa_ref": "S",
"aa_start": 588,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2638,
"cdna_start": 2411,
"cds_end": null,
"cds_length": 1797,
"cds_start": 1763,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000922633.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1763G>A",
"hgvs_p": "p.Ser588Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592692.1",
"strand": true,
"transcript": "ENST00000922633.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 589,
"aa_ref": "S",
"aa_start": 579,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3792,
"cdna_start": 2384,
"cds_end": null,
"cds_length": 1770,
"cds_start": 1736,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000922631.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1736G>A",
"hgvs_p": "p.Ser579Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592690.1",
"strand": true,
"transcript": "ENST00000922631.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 582,
"aa_ref": "S",
"aa_start": 572,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2460,
"cdna_start": 2235,
"cds_end": null,
"cds_length": 1749,
"cds_start": 1715,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000955776.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1715G>A",
"hgvs_p": "p.Ser572Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000625835.1",
"strand": true,
"transcript": "ENST00000955776.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 520,
"aa_ref": "S",
"aa_start": 510,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3114,
"cdna_start": 1701,
"cds_end": null,
"cds_length": 1563,
"cds_start": 1529,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "NM_001142806.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1529G>A",
"hgvs_p": "p.Ser510Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001136278.1",
"strand": true,
"transcript": "NM_001142806.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 520,
"aa_ref": "S",
"aa_start": 510,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1892,
"cdna_start": 1745,
"cds_end": null,
"cds_length": 1563,
"cds_start": 1529,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000430077.6",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1529G>A",
"hgvs_p": "p.Ser510Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000403041.2",
"strand": true,
"transcript": "ENST00000430077.6",
"transcript_support_level": 2
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 2401,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000485324.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "n.2181G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000485324.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1181103233",
"effect": "missense_variant",
"frequency_reference_population": 0.000050378974,
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"gnomad_exomes_ac": 58,
"gnomad_exomes_af": 0.0000537359,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 2,
"gnomad_genomes_af": 0.0000179178,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 22,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not provided|Creatine deficiency syndrome 1|Creatine transporter deficiency",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.182,
"pos": 153695180,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.156,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005629.4"
}
]
}