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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: 1-216200071-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=216200071&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 216200071,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000307340.8",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 72,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.3367T>C",
"hgvs_p": "p.Tyr1123His",
"transcript": "NM_206933.4",
"protein_id": "NP_996816.3",
"transcript_support_level": null,
"aa_start": 1123,
"aa_end": null,
"aa_length": 5202,
"cds_start": 3367,
"cds_end": null,
"cds_length": 15609,
"cdna_start": 3806,
"cdna_end": null,
"cdna_length": 18938,
"mane_select": "ENST00000307340.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 72,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.3367T>C",
"hgvs_p": "p.Tyr1123His",
"transcript": "ENST00000307340.8",
"protein_id": "ENSP00000305941.3",
"transcript_support_level": 1,
"aa_start": 1123,
"aa_end": null,
"aa_length": 5202,
"cds_start": 3367,
"cds_end": null,
"cds_length": 15609,
"cdna_start": 3806,
"cdna_end": null,
"cdna_length": 18938,
"mane_select": "NM_206933.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.3367T>C",
"hgvs_p": "p.Tyr1123His",
"transcript": "ENST00000366942.3",
"protein_id": "ENSP00000355909.3",
"transcript_support_level": 1,
"aa_start": 1123,
"aa_end": null,
"aa_length": 1546,
"cds_start": 3367,
"cds_end": null,
"cds_length": 4641,
"cdna_start": 3754,
"cdna_end": null,
"cdna_length": 6320,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 73,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.3367T>C",
"hgvs_p": "p.Tyr1123His",
"transcript": "ENST00000674083.1",
"protein_id": "ENSP00000501296.1",
"transcript_support_level": null,
"aa_start": 1123,
"aa_end": null,
"aa_length": 5226,
"cds_start": 3367,
"cds_end": null,
"cds_length": 15681,
"cdna_start": 3806,
"cdna_end": null,
"cdna_length": 19010,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.3367T>C",
"hgvs_p": "p.Tyr1123His",
"transcript": "NM_007123.6",
"protein_id": "NP_009054.6",
"transcript_support_level": null,
"aa_start": 1123,
"aa_end": null,
"aa_length": 1546,
"cds_start": 3367,
"cds_end": null,
"cds_length": 4641,
"cdna_start": 3806,
"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.363-3959A>G",
"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+4146A>G",
"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+4146A>G",
"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.692-3959A>G",
"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+4146A>G",
"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.485-3959A>G",
"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": "rs794729204",
"frequency_reference_population": 0.000021689635,
"hom_count_reference_population": 0,
"allele_count_reference_population": 35,
"gnomad_exomes_af": 0.0000225771,
"gnomad_genomes_af": 0.0000131565,
"gnomad_exomes_ac": 33,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9478366374969482,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.672,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8054,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.39,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.645,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM5,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM5",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000307340.8",
"gene_symbol": "USH2A",
"hgnc_id": 12601,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.3367T>C",
"hgvs_p": "p.Tyr1123His"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000420867.1",
"gene_symbol": "USH2A-AS1",
"hgnc_id": 40606,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.363-3959A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Usher syndrome,not provided",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "not provided|Usher syndrome",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}