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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: 1-243293087-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=243293087&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 243293087,
"ref": "T",
"alt": "G",
"effect": "splice_region_variant,intron_variant",
"transcript": "ENST00000366541.8",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.547-4T>G",
"hgvs_p": null,
"transcript": "NM_006642.5",
"protein_id": "NP_006633.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 713,
"cds_start": -4,
"cds_end": null,
"cds_length": 2142,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2581,
"mane_select": "ENST00000366541.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.547-4T>G",
"hgvs_p": null,
"transcript": "ENST00000366541.8",
"protein_id": "ENSP00000355499.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 713,
"cds_start": -4,
"cds_end": null,
"cds_length": 2142,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2581,
"mane_select": "NM_006642.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.15+6690T>G",
"hgvs_p": null,
"transcript": "ENST00000435549.1",
"protein_id": "ENSP00000410200.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 414,
"cds_start": -4,
"cds_end": null,
"cds_length": 1245,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.547-4T>G",
"hgvs_p": null,
"transcript": "NM_001350248.2",
"protein_id": "NP_001337177.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 745,
"cds_start": -4,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.253-4T>G",
"hgvs_p": null,
"transcript": "NM_001350249.2",
"protein_id": "NP_001337178.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 615,
"cds_start": -4,
"cds_end": null,
"cds_length": 1848,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.-566-4T>G",
"hgvs_p": null,
"transcript": "NM_001350246.2",
"protein_id": "NP_001337175.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 412,
"cds_start": -4,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2790,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.-454-4T>G",
"hgvs_p": null,
"transcript": "NM_001350247.2",
"protein_id": "NP_001337176.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 412,
"cds_start": -4,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2678,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.-827-4T>G",
"hgvs_p": null,
"transcript": "NM_001350251.2",
"protein_id": "NP_001337180.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 412,
"cds_start": -4,
"cds_end": null,
"cds_length": 1239,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.43-4T>G",
"hgvs_p": null,
"transcript": "ENST00000476722.6",
"protein_id": "ENSP00000473868.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 154,
"cds_start": -4,
"cds_end": null,
"cds_length": 465,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1871,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "n.280-4T>G",
"hgvs_p": null,
"transcript": "ENST00000482234.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 549,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "n.-31T>G",
"hgvs_p": null,
"transcript": "ENST00000496361.1",
"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": 947,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"dbsnp": "rs12080579",
"frequency_reference_population": 0.00008239641,
"hom_count_reference_population": 0,
"allele_count_reference_population": 133,
"gnomad_exomes_af": 0.0000451494,
"gnomad_genomes_af": 0.000439823,
"gnomad_exomes_ac": 66,
"gnomad_genomes_ac": 67,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.47999998927116394,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.12600000202655792,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.627,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.09,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0135670790628007,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1"
],
"verdict": "Benign",
"transcript": "ENST00000366541.8",
"gene_symbol": "SDCCAG8",
"hgnc_id": 10671,
"effects": [
"splice_region_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.547-4T>G",
"hgvs_p": null
}
],
"clinvar_disease": "Bardet-Biedl syndrome 16,Senior-Loken syndrome 7,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "not specified|Bardet-Biedl syndrome 16;Senior-Loken syndrome 7",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}