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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: 1-158612856-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=158612856&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 158612856,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_003126.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.7095A>G",
"hgvs_p": "p.Ala2365Ala",
"transcript": "NM_003126.4",
"protein_id": "NP_003117.2",
"transcript_support_level": null,
"aa_start": 2365,
"aa_end": null,
"aa_length": 2419,
"cds_start": 7095,
"cds_end": null,
"cds_length": 7260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000643759.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003126.4"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.7095A>G",
"hgvs_p": "p.Ala2365Ala",
"transcript": "ENST00000643759.2",
"protein_id": "ENSP00000495214.1",
"transcript_support_level": null,
"aa_start": 2365,
"aa_end": null,
"aa_length": 2419,
"cds_start": 7095,
"cds_end": null,
"cds_length": 7260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003126.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000643759.2"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 52,
"exon_rank_end": null,
"exon_count": 53,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.7095A>G",
"hgvs_p": "p.Ala2365Ala",
"transcript": "XM_011509916.3",
"protein_id": "XP_011508218.1",
"transcript_support_level": null,
"aa_start": 2365,
"aa_end": null,
"aa_length": 2419,
"cds_start": 7095,
"cds_end": null,
"cds_length": 7260,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011509916.3"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 50,
"exon_rank_end": null,
"exon_count": 51,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.7077A>G",
"hgvs_p": "p.Ala2359Ala",
"transcript": "XM_011509917.4",
"protein_id": "XP_011508219.1",
"transcript_support_level": null,
"aa_start": 2359,
"aa_end": null,
"aa_length": 2413,
"cds_start": 7077,
"cds_end": null,
"cds_length": 7242,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011509917.4"
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 51,
"exon_rank_end": null,
"exon_count": 52,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "c.6774A>G",
"hgvs_p": "p.Ala2258Ala",
"transcript": "XM_047428883.1",
"protein_id": "XP_047284839.1",
"transcript_support_level": null,
"aa_start": 2258,
"aa_end": null,
"aa_length": 2312,
"cds_start": 6774,
"cds_end": null,
"cds_length": 6939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047428883.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "n.536A>G",
"hgvs_p": null,
"transcript": "ENST00000481212.5",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000481212.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"hgvs_c": "n.527A>G",
"hgvs_p": null,
"transcript": "ENST00000498708.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000498708.1"
}
],
"gene_symbol": "SPTA1",
"gene_hgnc_id": 11272,
"dbsnp": "rs2251969",
"frequency_reference_population": 0.5418983,
"hom_count_reference_population": 238993,
"allele_count_reference_population": 874250,
"gnomad_exomes_af": 0.544028,
"gnomad_genomes_af": 0.521425,
"gnomad_exomes_ac": 795007,
"gnomad_genomes_ac": 79243,
"gnomad_exomes_homalt": 217919,
"gnomad_genomes_homalt": 21074,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7300000190734863,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.73,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.734,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_003126.4",
"gene_symbol": "SPTA1",
"hgnc_id": 11272,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.7095A>G",
"hgvs_p": "p.Ala2365Ala"
}
],
"clinvar_disease": " hereditary,Elliptocytosis 2,Hereditary spherocytosis type 3,Pyropoikilocytosis,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:11",
"phenotype_combined": "not specified|Hereditary spherocytosis type 3|Pyropoikilocytosis, hereditary|Elliptocytosis 2|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}