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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: 2-87782738-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=87782738&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 87782738,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001078170.3",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD2",
"gene_hgnc_id": 32415,
"hgvs_c": "c.4286G>A",
"hgvs_p": "p.Gly1429Glu",
"transcript": "NM_001078170.3",
"protein_id": "NP_001071638.2",
"transcript_support_level": null,
"aa_start": 1429,
"aa_end": null,
"aa_length": 1756,
"cds_start": 4286,
"cds_end": null,
"cds_length": 5271,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000398146.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001078170.3"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD2",
"gene_hgnc_id": 32415,
"hgvs_c": "c.4286G>A",
"hgvs_p": "p.Gly1429Glu",
"transcript": "ENST00000398146.5",
"protein_id": "ENSP00000381214.3",
"transcript_support_level": 1,
"aa_start": 1429,
"aa_end": null,
"aa_length": 1756,
"cds_start": 4286,
"cds_end": null,
"cds_length": 5271,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001078170.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000398146.5"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD2",
"gene_hgnc_id": 32415,
"hgvs_c": "c.4283G>A",
"hgvs_p": "p.Gly1428Glu",
"transcript": "ENST00000971290.1",
"protein_id": "ENSP00000641349.1",
"transcript_support_level": null,
"aa_start": 1428,
"aa_end": null,
"aa_length": 1755,
"cds_start": 4283,
"cds_end": null,
"cds_length": 5268,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000971290.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD2",
"gene_hgnc_id": 32415,
"hgvs_c": "c.4127G>A",
"hgvs_p": "p.Gly1376Glu",
"transcript": "NM_001393613.1",
"protein_id": "NP_001380542.1",
"transcript_support_level": null,
"aa_start": 1376,
"aa_end": null,
"aa_length": 1703,
"cds_start": 4127,
"cds_end": null,
"cds_length": 5112,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001393613.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD2",
"gene_hgnc_id": 32415,
"hgvs_c": "c.4520G>A",
"hgvs_p": "p.Gly1507Glu",
"transcript": "XM_017004845.2",
"protein_id": "XP_016860334.2",
"transcript_support_level": null,
"aa_start": 1507,
"aa_end": null,
"aa_length": 1834,
"cds_start": 4520,
"cds_end": null,
"cds_length": 5505,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017004845.2"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD2",
"gene_hgnc_id": 32415,
"hgvs_c": "c.4445G>A",
"hgvs_p": "p.Gly1482Glu",
"transcript": "XM_047445734.1",
"protein_id": "XP_047301690.1",
"transcript_support_level": null,
"aa_start": 1482,
"aa_end": null,
"aa_length": 1809,
"cds_start": 4445,
"cds_end": null,
"cds_length": 5430,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445734.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD2",
"gene_hgnc_id": 32415,
"hgvs_c": "c.4286G>A",
"hgvs_p": "p.Gly1429Glu",
"transcript": "XM_047445735.1",
"protein_id": "XP_047301691.1",
"transcript_support_level": null,
"aa_start": 1429,
"aa_end": null,
"aa_length": 1679,
"cds_start": 4286,
"cds_end": null,
"cds_length": 5040,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445735.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD2",
"gene_hgnc_id": 32415,
"hgvs_c": "c.4286G>A",
"hgvs_p": "p.Gly1429Glu",
"transcript": "XM_047445736.1",
"protein_id": "XP_047301692.1",
"transcript_support_level": null,
"aa_start": 1429,
"aa_end": null,
"aa_length": 1667,
"cds_start": 4286,
"cds_end": null,
"cds_length": 5004,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445736.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD2",
"gene_hgnc_id": 32415,
"hgvs_c": "c.4286G>A",
"hgvs_p": "p.Gly1429Glu",
"transcript": "XM_047445737.1",
"protein_id": "XP_047301693.1",
"transcript_support_level": null,
"aa_start": 1429,
"aa_end": null,
"aa_length": 1653,
"cds_start": 4286,
"cds_end": null,
"cds_length": 4962,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445737.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD2",
"gene_hgnc_id": 32415,
"hgvs_c": "c.4286G>A",
"hgvs_p": "p.Gly1429Glu",
"transcript": "XM_047445738.1",
"protein_id": "XP_047301694.1",
"transcript_support_level": null,
"aa_start": 1429,
"aa_end": null,
"aa_length": 1652,
"cds_start": 4286,
"cds_end": null,
"cds_length": 4959,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047445738.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "RGPD2",
"gene_hgnc_id": 32415,
"hgvs_c": "n.4353G>A",
"hgvs_p": null,
"transcript": "XR_007081580.1",
"protein_id": null,
"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": "pseudogene",
"feature": "XR_007081580.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"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": "RGPD2",
"gene_hgnc_id": 32415,
"hgvs_c": "n.4353G>A",
"hgvs_p": null,
"transcript": "XR_007081581.1",
"protein_id": null,
"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": "pseudogene",
"feature": "XR_007081581.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RGPD2",
"gene_hgnc_id": 32415,
"hgvs_c": "n.-69G>A",
"hgvs_p": null,
"transcript": "ENST00000494592.1",
"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": "pseudogene",
"feature": "ENST00000494592.1"
}
],
"gene_symbol": "RGPD2",
"gene_hgnc_id": 32415,
"dbsnp": "rs545184978",
"frequency_reference_population": null,
"hom_count_reference_population": null,
"allele_count_reference_population": null,
"gnomad_exomes_af": 0.000172369,
"gnomad_genomes_af": 0.0000207814,
"gnomad_exomes_ac": 207,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 11,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.018387019634246826,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.125,
"revel_prediction": "Benign",
"alphamissense_score": 0.4373,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.202,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001078170.3",
"gene_symbol": "RGPD2",
"hgnc_id": 32415,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.4286G>A",
"hgvs_p": "p.Gly1429Glu"
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}