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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: 11-68688012-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=68688012&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PVS1_Strong",
"BS2"
],
"effects": [
"splice_acceptor_variant",
"intron_variant"
],
"gene_symbol": "GAL",
"hgnc_id": 4114,
"hgvs_c": "c.137-2A>G",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 4,
"score": 0,
"transcript": "NM_015973.5",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PP3_Moderate"
],
"effects": [
"intron_variant"
],
"gene_symbol": "LOC107984343",
"hgnc_id": null,
"hgvs_c": "n.68-9T>C",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": 2,
"transcript": "XR_001748281.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PVS1_Strong,BS2",
"acmg_score": 0,
"allele_count_reference_population": 15,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.26,
"chr": "11",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Familial temporal lobe epilepsy 8",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.25999999046325684,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 123,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 749,
"cdna_start": null,
"cds_end": null,
"cds_length": 372,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_015973.5",
"gene_hgnc_id": 4114,
"gene_symbol": "GAL",
"hgvs_c": "c.137-2A>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000265643.4",
"protein_coding": true,
"protein_id": "NP_057057.2",
"strand": true,
"transcript": "NM_015973.5",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 123,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 749,
"cdna_start": null,
"cds_end": null,
"cds_length": 372,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000265643.4",
"gene_hgnc_id": 4114,
"gene_symbol": "GAL",
"hgvs_c": "c.137-2A>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015973.5",
"protein_coding": true,
"protein_id": "ENSP00000265643.3",
"strand": true,
"transcript": "ENST00000265643.4",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 189,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 944,
"cdna_start": null,
"cds_end": null,
"cds_length": 570,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 7,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000933457.1",
"gene_hgnc_id": 4114,
"gene_symbol": "GAL",
"hgvs_c": "c.335-2A>G",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603516.1",
"strand": true,
"transcript": "ENST00000933457.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 141,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 830,
"cdna_start": null,
"cds_end": null,
"cds_length": 426,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000933456.1",
"gene_hgnc_id": 4114,
"gene_symbol": "GAL",
"hgvs_c": "c.137-2A>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603515.1",
"strand": true,
"transcript": "ENST00000933456.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 123,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 768,
"cdna_start": null,
"cds_end": null,
"cds_length": 372,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000933453.1",
"gene_hgnc_id": 4114,
"gene_symbol": "GAL",
"hgvs_c": "c.137-2A>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603512.1",
"strand": true,
"transcript": "ENST00000933453.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 123,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 970,
"cdna_start": null,
"cds_end": null,
"cds_length": 372,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000933455.1",
"gene_hgnc_id": 4114,
"gene_symbol": "GAL",
"hgvs_c": "c.137-2A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603514.1",
"strand": true,
"transcript": "ENST00000933455.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 121,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 736,
"cdna_start": null,
"cds_end": null,
"cds_length": 366,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000933458.1",
"gene_hgnc_id": 4114,
"gene_symbol": "GAL",
"hgvs_c": "c.137-2A>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603517.1",
"strand": true,
"transcript": "ENST00000933458.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 97,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 738,
"cdna_start": null,
"cds_end": null,
"cds_length": 294,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000933454.1",
"gene_hgnc_id": 4114,
"gene_symbol": "GAL",
"hgvs_c": "c.137-2A>G",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603513.1",
"strand": true,
"transcript": "ENST00000933454.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 97,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 494,
"cdna_start": null,
"cds_end": null,
"cds_length": 294,
"cds_start": null,
"consequences": [
"splice_acceptor_variant",
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000933459.1",
"gene_hgnc_id": 4114,
"gene_symbol": "GAL",
"hgvs_c": "c.137-2A>G",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000603518.1",
"strand": true,
"transcript": "ENST00000933459.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 314,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XR_001748281.1",
"gene_hgnc_id": null,
"gene_symbol": "LOC107984343",
"hgvs_c": "n.68-9T>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_001748281.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999919326924268,
"dbsnp": "rs762777313",
"effect": "splice_acceptor_variant,intron_variant",
"frequency_reference_population": 0.000009359066,
"gene_hgnc_id": 4114,
"gene_symbol": "GAL",
"gnomad_exomes_ac": 3,
"gnomad_exomes_af": 0.00000206824,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 12,
"gnomad_genomes_af": 0.0000788374,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Familial temporal lobe epilepsy 8",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.615,
"pos": 68688012,
"ref": "A",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.8059999942779541,
"splice_source_selected": "dbscSNV1_RF",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 1,
"transcript": "NM_015973.5"
}
]
}