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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-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=153694445&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 21,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"gene_symbol": "SLC6A8",
"hgnc_id": 11055,
"hgvs_c": "c.1494C>T",
"hgvs_p": "p.Tyr498Tyr",
"inheritance_mode": "XL",
"pathogenic_score": 0,
"score": -21,
"transcript": "NM_005629.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_score": -21,
"allele_count_reference_population": 4324,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.72,
"chr": "X",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": "Creatine transporter deficiency,Inborn genetic diseases,Intellectual disability,SLC6A8-related disorder,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:8",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7200000286102295,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "Y",
"aa_end": null,
"aa_length": 635,
"aa_ref": "Y",
"aa_start": 498,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3931,
"cdna_start": 2143,
"cds_end": null,
"cds_length": 1908,
"cds_start": 1494,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_005629.4",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1494C>T",
"hgvs_p": "p.Tyr498Tyr",
"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": "Y",
"aa_end": null,
"aa_length": 635,
"aa_ref": "Y",
"aa_start": 498,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3931,
"cdna_start": 2143,
"cds_end": null,
"cds_length": 1908,
"cds_start": 1494,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000253122.10",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1494C>T",
"hgvs_p": "p.Tyr498Tyr",
"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": "Y",
"aa_end": null,
"aa_length": 634,
"aa_ref": "Y",
"aa_start": 498,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3920,
"cdna_start": 2141,
"cds_end": null,
"cds_length": 1905,
"cds_start": 1494,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000955775.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1494C>T",
"hgvs_p": "p.Tyr498Tyr",
"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": "Y",
"aa_end": null,
"aa_length": 632,
"aa_ref": "Y",
"aa_start": 495,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3924,
"cdna_start": 2133,
"cds_end": null,
"cds_length": 1899,
"cds_start": 1485,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000922630.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1485C>T",
"hgvs_p": "p.Tyr495Tyr",
"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": "Y",
"aa_end": null,
"aa_length": 625,
"aa_ref": "Y",
"aa_start": 488,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3901,
"cdna_start": 2113,
"cds_end": null,
"cds_length": 1878,
"cds_start": 1464,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001142805.2",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1464C>T",
"hgvs_p": "p.Tyr488Tyr",
"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": "Y",
"aa_end": null,
"aa_length": 619,
"aa_ref": "Y",
"aa_start": 482,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3879,
"cdna_start": 2091,
"cds_end": null,
"cds_length": 1860,
"cds_start": 1446,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000922632.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1446C>T",
"hgvs_p": "p.Tyr482Tyr",
"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": "Y",
"aa_end": null,
"aa_length": 598,
"aa_ref": "Y",
"aa_start": 461,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2638,
"cdna_start": 2031,
"cds_end": null,
"cds_length": 1797,
"cds_start": 1383,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000922633.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1383C>T",
"hgvs_p": "p.Tyr461Tyr",
"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": "Y",
"aa_end": null,
"aa_length": 589,
"aa_ref": "Y",
"aa_start": 452,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3792,
"cdna_start": 2004,
"cds_end": null,
"cds_length": 1770,
"cds_start": 1356,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000922631.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1356C>T",
"hgvs_p": "p.Tyr452Tyr",
"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": "Y",
"aa_end": null,
"aa_length": 582,
"aa_ref": "Y",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2460,
"cdna_start": 1855,
"cds_end": null,
"cds_length": 1749,
"cds_start": 1335,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 12,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000955776.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1335C>T",
"hgvs_p": "p.Tyr445Tyr",
"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": "Y",
"aa_end": null,
"aa_length": 520,
"aa_ref": "Y",
"aa_start": 383,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3114,
"cdna_start": 1321,
"cds_end": null,
"cds_length": 1563,
"cds_start": 1149,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "NM_001142806.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1149C>T",
"hgvs_p": "p.Tyr383Tyr",
"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": "Y",
"aa_end": null,
"aa_length": 520,
"aa_ref": "Y",
"aa_start": 383,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1892,
"cdna_start": 1365,
"cds_end": null,
"cds_length": 1563,
"cds_start": 1149,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 13,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000430077.6",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.1149C>T",
"hgvs_p": "p.Tyr383Tyr",
"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": "Y",
"aa_end": null,
"aa_length": 155,
"aa_ref": "Y",
"aa_start": 141,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 468,
"cdna_start": 423,
"cds_end": null,
"cds_length": 468,
"cds_start": 423,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000413787.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.423C>T",
"hgvs_p": "p.Tyr141Tyr",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000400463.1",
"strand": true,
"transcript": "ENST00000413787.1",
"transcript_support_level": 5
},
{
"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": 4,
"exon_rank_end": null,
"feature": "ENST00000485324.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "n.1715C>T",
"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
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 172,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 523,
"cdna_start": null,
"cds_end": null,
"cds_length": 521,
"cds_start": null,
"consequences": [
"downstream_gene_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000442457.1",
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"hgvs_c": "c.*25C>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000403682.1",
"strand": true,
"transcript": "ENST00000442457.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Benign",
"dbscsnv_ada_score": 0.000342695257275124,
"dbsnp": "rs143916832",
"effect": "splice_region_variant,synonymous_variant",
"frequency_reference_population": 0.0035963594,
"gene_hgnc_id": 11055,
"gene_symbol": "SLC6A8",
"gnomad_exomes_ac": 4048,
"gnomad_exomes_af": 0.00371132,
"gnomad_exomes_homalt": 7,
"gnomad_genomes_ac": 276,
"gnomad_genomes_af": 0.00247287,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1350,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "not provided|not specified|Creatine transporter deficiency|Inborn genetic diseases|SLC6A8-related disorder|Intellectual disability",
"phylop100way_prediction": "Benign",
"phylop100way_score": -2.531,
"pos": 153694445,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.057999998331069946,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.14,
"transcript": "NM_005629.4"
}
]
}