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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: 2-173910145-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=173910145&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 173910145,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "NM_003111.5",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SP3",
"gene_hgnc_id": 11208,
"hgvs_c": "c.2142A>G",
"hgvs_p": "p.Thr714Thr",
"transcript": "NM_003111.5",
"protein_id": "NP_003102.1",
"transcript_support_level": null,
"aa_start": 714,
"aa_end": null,
"aa_length": 781,
"cds_start": 2142,
"cds_end": null,
"cds_length": 2346,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000310015.12",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003111.5"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SP3",
"gene_hgnc_id": 11208,
"hgvs_c": "c.2142A>G",
"hgvs_p": "p.Thr714Thr",
"transcript": "ENST00000310015.12",
"protein_id": "ENSP00000310301.6",
"transcript_support_level": 1,
"aa_start": 714,
"aa_end": null,
"aa_length": 781,
"cds_start": 2142,
"cds_end": null,
"cds_length": 2346,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003111.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000310015.12"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SP3",
"gene_hgnc_id": 11208,
"hgvs_c": "c.2010A>G",
"hgvs_p": "p.Thr670Thr",
"transcript": "ENST00000416195.1",
"protein_id": "ENSP00000413665.1",
"transcript_support_level": 1,
"aa_start": 670,
"aa_end": null,
"aa_length": 737,
"cds_start": 2010,
"cds_end": null,
"cds_length": 2214,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000416195.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SP3",
"gene_hgnc_id": 11208,
"hgvs_c": "c.1938A>G",
"hgvs_p": "p.Thr646Thr",
"transcript": "ENST00000418194.7",
"protein_id": "ENSP00000406140.3",
"transcript_support_level": 1,
"aa_start": 646,
"aa_end": null,
"aa_length": 713,
"cds_start": 1938,
"cds_end": null,
"cds_length": 2142,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000418194.7"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "SP3",
"gene_hgnc_id": 11208,
"hgvs_c": "n.3876A>G",
"hgvs_p": null,
"transcript": "ENST00000465379.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000465379.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SP3",
"gene_hgnc_id": 11208,
"hgvs_c": "c.2133A>G",
"hgvs_p": "p.Thr711Thr",
"transcript": "NM_001172712.1",
"protein_id": "NP_001166183.1",
"transcript_support_level": null,
"aa_start": 711,
"aa_end": null,
"aa_length": 778,
"cds_start": 2133,
"cds_end": null,
"cds_length": 2337,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001172712.1"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SP3",
"gene_hgnc_id": 11208,
"hgvs_c": "c.1980A>G",
"hgvs_p": "p.Thr660Thr",
"transcript": "ENST00000652005.2",
"protein_id": "ENSP00000498392.2",
"transcript_support_level": null,
"aa_start": 660,
"aa_end": null,
"aa_length": 727,
"cds_start": 1980,
"cds_end": null,
"cds_length": 2184,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000652005.2"
},
{
"aa_ref": "T",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SP3",
"gene_hgnc_id": 11208,
"hgvs_c": "c.1938A>G",
"hgvs_p": "p.Thr646Thr",
"transcript": "NM_001017371.5",
"protein_id": "NP_001017371.3",
"transcript_support_level": null,
"aa_start": 646,
"aa_end": null,
"aa_length": 713,
"cds_start": 1938,
"cds_end": null,
"cds_length": 2142,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001017371.5"
},
{
"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": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "SP3",
"gene_hgnc_id": 11208,
"hgvs_c": "n.1843+20A>G",
"hgvs_p": null,
"transcript": "ENST00000650743.1",
"protein_id": "ENSP00000498794.1",
"transcript_support_level": null,
"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": "nonsense_mediated_decay",
"feature": "ENST00000650743.1"
},
{
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "SP3",
"gene_hgnc_id": 11208,
"hgvs_c": "n.388+2925A>G",
"hgvs_p": null,
"transcript": "ENST00000651846.1",
"protein_id": "ENSP00000499057.1",
"transcript_support_level": null,
"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": "nonsense_mediated_decay",
"feature": "ENST00000651846.1"
}
],
"gene_symbol": "SP3",
"gene_hgnc_id": 11208,
"dbsnp": "rs7561583",
"frequency_reference_population": 0.00006010695,
"hom_count_reference_population": 0,
"allele_count_reference_population": 97,
"gnomad_exomes_af": 0.0000629458,
"gnomad_genomes_af": 0.0000328481,
"gnomad_exomes_ac": 92,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.13300000131130219,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.133,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.51,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.865,
"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": -7,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP7,BS2",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_003111.5",
"gene_symbol": "SP3",
"hgnc_id": 11208,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.2142A>G",
"hgvs_p": "p.Thr714Thr"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}