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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: 12-116723068-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=116723068&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 116723068,
"ref": "G",
"alt": "T",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "NM_024738.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRING1",
"gene_hgnc_id": 26128,
"hgvs_c": "c.267C>A",
"hgvs_p": "p.Leu89Leu",
"transcript": "NM_024738.4",
"protein_id": "NP_079014.1",
"transcript_support_level": null,
"aa_start": 89,
"aa_end": null,
"aa_length": 205,
"cds_start": 267,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000261318.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_024738.4"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRING1",
"gene_hgnc_id": 26128,
"hgvs_c": "c.267C>A",
"hgvs_p": "p.Leu89Leu",
"transcript": "ENST00000261318.5",
"protein_id": "ENSP00000261318.3",
"transcript_support_level": 1,
"aa_start": 89,
"aa_end": null,
"aa_length": 205,
"cds_start": 267,
"cds_end": null,
"cds_length": 618,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_024738.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000261318.5"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPRING1",
"gene_hgnc_id": 26128,
"hgvs_c": "n.112-2621C>A",
"hgvs_p": null,
"transcript": "ENST00000547630.1",
"protein_id": "ENSP00000446478.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000547630.1"
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SPRING1",
"gene_hgnc_id": 26128,
"hgvs_c": "c.270C>A",
"hgvs_p": "p.Leu90Leu",
"transcript": "XM_024449189.2",
"protein_id": "XP_024304957.1",
"transcript_support_level": null,
"aa_start": 90,
"aa_end": null,
"aa_length": 206,
"cds_start": 270,
"cds_end": null,
"cds_length": 621,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_024449189.2"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPRING1",
"gene_hgnc_id": 26128,
"hgvs_c": "c.179-2621C>A",
"hgvs_p": null,
"transcript": "NM_001353623.2",
"protein_id": "NP_001340552.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 175,
"cds_start": null,
"cds_end": null,
"cds_length": 528,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001353623.2"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPRING1",
"gene_hgnc_id": 26128,
"hgvs_c": "c.112-3192C>A",
"hgvs_p": null,
"transcript": "NM_001353624.2",
"protein_id": "NP_001340553.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 102,
"cds_start": null,
"cds_end": null,
"cds_length": 309,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001353624.2"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPRING1",
"gene_hgnc_id": 26128,
"hgvs_c": "c.112-5175C>A",
"hgvs_p": null,
"transcript": "NM_001353625.2",
"protein_id": "NP_001340554.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 64,
"cds_start": null,
"cds_end": null,
"cds_length": 195,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001353625.2"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "SPRING1",
"gene_hgnc_id": 26128,
"hgvs_c": "c.46-5175C>A",
"hgvs_p": null,
"transcript": "ENST00000547606.1",
"protein_id": "ENSP00000447722.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 42,
"cds_start": null,
"cds_end": null,
"cds_length": 129,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000547606.1"
}
],
"gene_symbol": "SPRING1",
"gene_hgnc_id": 26128,
"dbsnp": "rs118149811",
"frequency_reference_population": 0.012765934,
"hom_count_reference_population": 179,
"allele_count_reference_population": 20583,
"gnomad_exomes_af": 0.0130865,
"gnomad_genomes_af": 0.00969389,
"gnomad_exomes_ac": 19106,
"gnomad_genomes_ac": 1477,
"gnomad_exomes_homalt": 167,
"gnomad_genomes_homalt": 12,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6700000166893005,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.09799999743700027,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.924,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.000115565010984769,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_024738.4",
"gene_symbol": "SPRING1",
"hgnc_id": 26128,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.267C>A",
"hgvs_p": "p.Leu89Leu"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}