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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: 1-216196698-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=216196698&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 216196698,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000307340.8",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 72,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.4106C>T",
"hgvs_p": "p.Ser1369Leu",
"transcript": "NM_206933.4",
"protein_id": "NP_996816.3",
"transcript_support_level": null,
"aa_start": 1369,
"aa_end": null,
"aa_length": 5202,
"cds_start": 4106,
"cds_end": null,
"cds_length": 15609,
"cdna_start": 4545,
"cdna_end": null,
"cdna_length": 18938,
"mane_select": "ENST00000307340.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 72,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.4106C>T",
"hgvs_p": "p.Ser1369Leu",
"transcript": "ENST00000307340.8",
"protein_id": "ENSP00000305941.3",
"transcript_support_level": 1,
"aa_start": 1369,
"aa_end": null,
"aa_length": 5202,
"cds_start": 4106,
"cds_end": null,
"cds_length": 15609,
"cdna_start": 4545,
"cdna_end": null,
"cdna_length": 18938,
"mane_select": "NM_206933.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.4106C>T",
"hgvs_p": "p.Ser1369Leu",
"transcript": "ENST00000366942.3",
"protein_id": "ENSP00000355909.3",
"transcript_support_level": 1,
"aa_start": 1369,
"aa_end": null,
"aa_length": 1546,
"cds_start": 4106,
"cds_end": null,
"cds_length": 4641,
"cdna_start": 4493,
"cdna_end": null,
"cdna_length": 6320,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 73,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.4106C>T",
"hgvs_p": "p.Ser1369Leu",
"transcript": "ENST00000674083.1",
"protein_id": "ENSP00000501296.1",
"transcript_support_level": null,
"aa_start": 1369,
"aa_end": null,
"aa_length": 5226,
"cds_start": 4106,
"cds_end": null,
"cds_length": 15681,
"cdna_start": 4545,
"cdna_end": null,
"cdna_length": 19010,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.4106C>T",
"hgvs_p": "p.Ser1369Leu",
"transcript": "NM_007123.6",
"protein_id": "NP_009054.6",
"transcript_support_level": null,
"aa_start": 1369,
"aa_end": null,
"aa_length": 1546,
"cds_start": 4106,
"cds_end": null,
"cds_length": 4641,
"cdna_start": 4545,
"cdna_end": null,
"cdna_length": 6372,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "USH2A-AS1",
"gene_hgnc_id": 40606,
"hgvs_c": "n.362+773G>A",
"hgvs_p": null,
"transcript": "ENST00000420867.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 699,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "USH2A-AS1",
"gene_hgnc_id": 40606,
"hgvs_c": "n.356+773G>A",
"hgvs_p": null,
"transcript": "ENST00000747930.1",
"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": 636,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "USH2A-AS1",
"gene_hgnc_id": 40606,
"hgvs_c": "n.213+773G>A",
"hgvs_p": null,
"transcript": "ENST00000747931.1",
"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": 609,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "USH2A-AS1",
"gene_hgnc_id": 40606,
"hgvs_c": "n.691+773G>A",
"hgvs_p": null,
"transcript": "XR_922595.4",
"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": 1028,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "USH2A-AS1",
"gene_hgnc_id": 40606,
"hgvs_c": "n.691+773G>A",
"hgvs_p": null,
"transcript": "XR_922596.4",
"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": 1000,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "USH2A-AS1",
"gene_hgnc_id": 40606,
"hgvs_c": "n.484+773G>A",
"hgvs_p": null,
"transcript": "XR_922598.1",
"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": 821,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"dbsnp": "rs201709513",
"frequency_reference_population": 0.00029445568,
"hom_count_reference_population": 0,
"allele_count_reference_population": 475,
"gnomad_exomes_af": 0.000305953,
"gnomad_genomes_af": 0.000184043,
"gnomad_exomes_ac": 447,
"gnomad_genomes_ac": 28,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11279520392417908,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.3100000023841858,
"splice_prediction_selected": "Uncertain_significance",
"splice_source_selected": "max_spliceai",
"revel_score": 0.231,
"revel_prediction": "Benign",
"alphamissense_score": 0.0733,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.23,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.744,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.31,
"spliceai_max_prediction": "Uncertain_significance",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM1,PP5",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM1",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000307340.8",
"gene_symbol": "USH2A",
"hgnc_id": 12601,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.4106C>T",
"hgvs_p": "p.Ser1369Leu"
},
{
"score": 1,
"benign_score": 0,
"pathogenic_score": 1,
"criteria": [
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000420867.1",
"gene_symbol": "USH2A-AS1",
"hgnc_id": 40606,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.362+773G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Retinal dystrophy,Retinitis pigmentosa,Retinitis pigmentosa 39,USH2A-related disorder,Usher syndrome,Usher syndrome type 2A,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:3 LP:7 US:4",
"phenotype_combined": "not specified|Retinitis pigmentosa 39|not provided|Usher syndrome type 2A;Retinitis pigmentosa 39|Usher syndrome|Retinal dystrophy|USH2A-related disorder|Retinitis pigmentosa|Usher syndrome type 2A",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}