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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: 2-107871445-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=107871445&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 107871445,
"ref": "A",
"alt": "G",
"effect": "synonymous_variant",
"transcript": "ENST00000408999.4",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD4",
"gene_hgnc_id": 32417,
"hgvs_c": "c.3441A>G",
"hgvs_p": "p.Leu1147Leu",
"transcript": "NM_182588.3",
"protein_id": "NP_872394.2",
"transcript_support_level": null,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1758,
"cds_start": 3441,
"cds_end": null,
"cds_length": 5277,
"cdna_start": 3563,
"cdna_end": null,
"cdna_length": 7212,
"mane_select": "ENST00000408999.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD4",
"gene_hgnc_id": 32417,
"hgvs_c": "c.3441A>G",
"hgvs_p": "p.Leu1147Leu",
"transcript": "ENST00000408999.4",
"protein_id": "ENSP00000386810.4",
"transcript_support_level": 1,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1758,
"cds_start": 3441,
"cds_end": null,
"cds_length": 5277,
"cdna_start": 3563,
"cdna_end": null,
"cdna_length": 7212,
"mane_select": "NM_182588.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD4",
"gene_hgnc_id": 32417,
"hgvs_c": "c.3441A>G",
"hgvs_p": "p.Leu1147Leu",
"transcript": "XM_011511017.4",
"protein_id": "XP_011509319.1",
"transcript_support_level": null,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1703,
"cds_start": 3441,
"cds_end": null,
"cds_length": 5112,
"cdna_start": 3563,
"cdna_end": null,
"cdna_length": 5347,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD4",
"gene_hgnc_id": 32417,
"hgvs_c": "c.3441A>G",
"hgvs_p": "p.Leu1147Leu",
"transcript": "XM_011511018.4",
"protein_id": "XP_011509320.1",
"transcript_support_level": null,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1687,
"cds_start": 3441,
"cds_end": null,
"cds_length": 5064,
"cdna_start": 3563,
"cdna_end": null,
"cdna_length": 5248,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD4",
"gene_hgnc_id": 32417,
"hgvs_c": "c.3441A>G",
"hgvs_p": "p.Leu1147Leu",
"transcript": "XM_011511019.4",
"protein_id": "XP_011509321.1",
"transcript_support_level": null,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1661,
"cds_start": 3441,
"cds_end": null,
"cds_length": 4986,
"cdna_start": 3563,
"cdna_end": null,
"cdna_length": 5170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD4",
"gene_hgnc_id": 32417,
"hgvs_c": "c.3441A>G",
"hgvs_p": "p.Leu1147Leu",
"transcript": "XM_011511020.4",
"protein_id": "XP_011509322.1",
"transcript_support_level": null,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1660,
"cds_start": 3441,
"cds_end": null,
"cds_length": 4983,
"cdna_start": 3563,
"cdna_end": null,
"cdna_length": 5250,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD4",
"gene_hgnc_id": 32417,
"hgvs_c": "n.3563A>G",
"hgvs_p": null,
"transcript": "XR_007073111.1",
"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": 5345,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD4",
"gene_hgnc_id": 32417,
"hgvs_c": "n.3563A>G",
"hgvs_p": null,
"transcript": "XR_922911.4",
"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": 5347,
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "LOC124906057",
"gene_hgnc_id": null,
"hgvs_c": "n.217-22812T>C",
"hgvs_p": null,
"transcript": "XR_007087170.1",
"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": 612,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RGPD4",
"gene_hgnc_id": 32417,
"dbsnp": "rs832358",
"frequency_reference_population": null,
"hom_count_reference_population": null,
"allele_count_reference_population": null,
"gnomad_exomes_af": 0.480058,
"gnomad_genomes_af": 0.205785,
"gnomad_exomes_ac": 426449,
"gnomad_genomes_ac": 6702,
"gnomad_exomes_homalt": 207130,
"gnomad_genomes_homalt": 1825,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7099999785423279,
"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": -0.71,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.078,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7"
],
"verdict": "Benign",
"transcript": "ENST00000408999.4",
"gene_symbol": "RGPD4",
"hgnc_id": 32417,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3441A>G",
"hgvs_p": "p.Leu1147Leu"
},
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong"
],
"verdict": "Benign",
"transcript": "XR_007087170.1",
"gene_symbol": "LOC124906057",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.217-22812T>C",
"hgvs_p": null
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}