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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: 19-55078089-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=55078089&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 55078089,
"ref": "C",
"alt": "T",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000201647.11",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Pro7Ser",
"transcript": "NM_133180.3",
"protein_id": "NP_573441.2",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 723,
"cds_start": 19,
"cds_end": null,
"cds_length": 2172,
"cdna_start": 107,
"cdna_end": null,
"cdna_length": 2569,
"mane_select": "ENST00000201647.11",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Pro7Ser",
"transcript": "ENST00000201647.11",
"protein_id": "ENSP00000201647.5",
"transcript_support_level": 1,
"aa_start": 7,
"aa_end": null,
"aa_length": 723,
"cds_start": 19,
"cds_end": null,
"cds_length": 2172,
"cdna_start": 107,
"cdna_end": null,
"cdna_length": 2569,
"mane_select": "NM_133180.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"hgvs_c": "n.-37C>T",
"hgvs_p": null,
"transcript": "ENST00000587786.5",
"protein_id": "ENSP00000465830.1",
"transcript_support_level": 1,
"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": 2343,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"hgvs_c": "n.123C>T",
"hgvs_p": null,
"transcript": "ENST00000592824.5",
"protein_id": null,
"transcript_support_level": 1,
"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": 1708,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"hgvs_c": "n.-37C>T",
"hgvs_p": null,
"transcript": "ENST00000587786.5",
"protein_id": "ENSP00000465830.1",
"transcript_support_level": 1,
"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": 2343,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Pro7Ser",
"transcript": "XM_005259020.3",
"protein_id": "XP_005259077.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 755,
"cds_start": 19,
"cds_end": null,
"cds_length": 2268,
"cdna_start": 107,
"cdna_end": null,
"cdna_length": 2665,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Pro7Ser",
"transcript": "XM_047439021.1",
"protein_id": "XP_047294977.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 755,
"cds_start": 19,
"cds_end": null,
"cds_length": 2268,
"cdna_start": 65,
"cdna_end": null,
"cdna_length": 2623,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Pro7Ser",
"transcript": "XM_047439022.1",
"protein_id": "XP_047294978.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 723,
"cds_start": 19,
"cds_end": null,
"cds_length": 2172,
"cdna_start": 595,
"cdna_end": null,
"cdna_length": 3057,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Pro7Ser",
"transcript": "XM_011527051.4",
"protein_id": "XP_011525353.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 474,
"cds_start": 19,
"cds_end": null,
"cds_length": 1425,
"cdna_start": 107,
"cdna_end": null,
"cdna_length": 1609,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Pro7Ser",
"transcript": "XM_011527052.4",
"protein_id": "XP_011525354.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 466,
"cds_start": 19,
"cds_end": null,
"cds_length": 1401,
"cdna_start": 107,
"cdna_end": null,
"cdna_length": 1949,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"hgvs_c": "n.88C>T",
"hgvs_p": null,
"transcript": "ENST00000591219.5",
"protein_id": null,
"transcript_support_level": 2,
"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": 596,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"hgvs_c": "c.-75-1601C>T",
"hgvs_p": null,
"transcript": "ENST00000540810.5",
"protein_id": "ENSP00000437541.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 659,
"cds_start": -4,
"cds_end": null,
"cds_length": 1980,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2360,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"hgvs_c": "c.64-1601C>T",
"hgvs_p": null,
"transcript": "ENST00000586329.5",
"protein_id": "ENSP00000466828.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 548,
"cds_start": -4,
"cds_end": null,
"cds_length": 1647,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2130,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EPS8L1",
"gene_hgnc_id": 21295,
"dbsnp": "rs370970115",
"frequency_reference_population": 0.00020263487,
"hom_count_reference_population": 1,
"allele_count_reference_population": 327,
"gnomad_exomes_af": 0.000216881,
"gnomad_genomes_af": 0.000065741,
"gnomad_exomes_ac": 317,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.19709661602973938,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.024000000208616257,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.136,
"revel_prediction": "Benign",
"alphamissense_score": 0.092,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.48,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.625,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.07,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0045675133160013,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000201647.11",
"gene_symbol": "EPS8L1",
"hgnc_id": 21295,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.19C>T",
"hgvs_p": "p.Pro7Ser"
}
],
"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
}