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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: 1-243304716-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=243304716&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 243304716,
"ref": "A",
"alt": "T",
"effect": "stop_gained",
"transcript": "ENST00000366541.8",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.679A>T",
"hgvs_p": "p.Lys227*",
"transcript": "NM_006642.5",
"protein_id": "NP_006633.1",
"transcript_support_level": null,
"aa_start": 227,
"aa_end": null,
"aa_length": 713,
"cds_start": 679,
"cds_end": null,
"cds_length": 2142,
"cdna_start": 812,
"cdna_end": null,
"cdna_length": 2581,
"mane_select": "ENST00000366541.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.679A>T",
"hgvs_p": "p.Lys227*",
"transcript": "ENST00000366541.8",
"protein_id": "ENSP00000355499.3",
"transcript_support_level": 1,
"aa_start": 227,
"aa_end": null,
"aa_length": 713,
"cds_start": 679,
"cds_end": null,
"cds_length": 2142,
"cdna_start": 812,
"cdna_end": null,
"cdna_length": 2581,
"mane_select": "NM_006642.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.19A>T",
"hgvs_p": "p.Lys7*",
"transcript": "ENST00000435549.1",
"protein_id": "ENSP00000410200.1",
"transcript_support_level": 1,
"aa_start": 7,
"aa_end": null,
"aa_length": 414,
"cds_start": 19,
"cds_end": null,
"cds_length": 1245,
"cdna_start": 19,
"cdna_end": null,
"cdna_length": 1551,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.775A>T",
"hgvs_p": "p.Lys259*",
"transcript": "NM_001350248.2",
"protein_id": "NP_001337177.1",
"transcript_support_level": null,
"aa_start": 259,
"aa_end": null,
"aa_length": 745,
"cds_start": 775,
"cds_end": null,
"cds_length": 2238,
"cdna_start": 908,
"cdna_end": null,
"cdna_length": 2677,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.385A>T",
"hgvs_p": "p.Lys129*",
"transcript": "NM_001350249.2",
"protein_id": "NP_001337178.1",
"transcript_support_level": null,
"aa_start": 129,
"aa_end": null,
"aa_length": 615,
"cds_start": 385,
"cds_end": null,
"cds_length": 1848,
"cdna_start": 825,
"cdna_end": null,
"cdna_length": 2594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.271A>T",
"hgvs_p": "p.Lys91*",
"transcript": "ENST00000476722.6",
"protein_id": "ENSP00000473868.1",
"transcript_support_level": 3,
"aa_start": 91,
"aa_end": null,
"aa_length": 154,
"cds_start": 271,
"cds_end": null,
"cds_length": 465,
"cdna_start": 273,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "n.412A>T",
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "n.106A>T",
"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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.-434A>T",
"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": [
"5_prime_UTR_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.-322A>T",
"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": [
"5_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"hgvs_c": "c.-599A>T",
"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
}
],
"gene_symbol": "SDCCAG8",
"gene_hgnc_id": 10671,
"dbsnp": "rs267607031",
"frequency_reference_population": 0.000010359178,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.0000107732,
"gnomad_genomes_af": 0.00000657142,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4000000059604645,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.4000000059604645,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.044,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.4,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"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": "ENST00000366541.8",
"gene_symbol": "SDCCAG8",
"hgnc_id": 10671,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.679A>T",
"hgvs_p": "p.Lys227*"
}
],
"clinvar_disease": "Bardet-Biedl syndrome 16,Senior-Loken syndrome 7",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"phenotype_combined": "Bardet-Biedl syndrome 16|Bardet-Biedl syndrome 16;Senior-Loken syndrome 7",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}