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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: 1-158656669-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=158656669&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 158656669,
"ref": "A",
"alt": "C",
"effect": "intron_variant",
"transcript": "ENST00000643759.2",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.2806-13T>G",
"hgvs_p": null,
"transcript": "NM_003126.4",
"protein_id": "NP_003117.2",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2419,
"cds_start": -4,
"cds_end": null,
"cds_length": 7260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8018,
"mane_select": "ENST00000643759.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.2806-13T>G",
"hgvs_p": null,
"transcript": "ENST00000643759.2",
"protein_id": "ENSP00000495214.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2419,
"cds_start": -4,
"cds_end": null,
"cds_length": 7260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8018,
"mane_select": "NM_003126.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "n.406-13T>G",
"hgvs_p": null,
"transcript": "ENST00000647256.1",
"protein_id": null,
"transcript_support_level": null,
"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": 431,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": 20,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.2806-13T>G",
"hgvs_p": null,
"transcript": "XM_011509916.3",
"protein_id": "XP_011508218.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2419,
"cds_start": -4,
"cds_end": null,
"cds_length": 7260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7901,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.2806-13T>G",
"hgvs_p": null,
"transcript": "XM_011509917.4",
"protein_id": "XP_011508219.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2413,
"cds_start": -4,
"cds_end": null,
"cds_length": 7242,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 8000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.2485-13T>G",
"hgvs_p": null,
"transcript": "XM_047428883.1",
"protein_id": "XP_047284839.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2312,
"cds_start": -4,
"cds_end": null,
"cds_length": 6939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7855,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 44,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.2806-13T>G",
"hgvs_p": null,
"transcript": "XM_011509918.4",
"protein_id": "XP_011508220.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2041,
"cds_start": -4,
"cds_end": null,
"cds_length": 6126,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6419,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 37,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.2806-13T>G",
"hgvs_p": null,
"transcript": "XM_011509919.4",
"protein_id": "XP_011508221.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1695,
"cds_start": -4,
"cds_end": null,
"cds_length": 5088,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5386,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.2806-13T>G",
"hgvs_p": null,
"transcript": "XM_047428888.1",
"protein_id": "XP_047284844.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1474,
"cds_start": -4,
"cds_end": null,
"cds_length": 4425,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4710,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 41,
"intron_rank": 19,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "n.3004-13T>G",
"hgvs_p": null,
"transcript": "XR_921911.4",
"protein_id": null,
"transcript_support_level": null,
"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": 5927,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"dbsnp": "rs757147440",
"frequency_reference_population": 0.0000031204013,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000206866,
"gnomad_genomes_af": 0.0000131453,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5400000214576721,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.8899999856948853,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.632,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.89,
"spliceai_max_prediction": "Pathogenic",
"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": "PM2,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000643759.2",
"gene_symbol": "SPTA1",
"hgnc_id": 11272,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.2806-13T>G",
"hgvs_p": null
}
],
"clinvar_disease": " hereditary,Pyropoikilocytosis,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Pyropoikilocytosis, hereditary|not provided",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}