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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: 1-216086748-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=216086748&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 216086748,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_206933.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 72,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.4958G>A",
"hgvs_p": "p.Arg1653Gln",
"transcript": "NM_206933.4",
"protein_id": "NP_996816.3",
"transcript_support_level": null,
"aa_start": 1653,
"aa_end": null,
"aa_length": 5202,
"cds_start": 4958,
"cds_end": null,
"cds_length": 15609,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000307340.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_206933.4"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 72,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.4958G>A",
"hgvs_p": "p.Arg1653Gln",
"transcript": "ENST00000307340.8",
"protein_id": "ENSP00000305941.3",
"transcript_support_level": 1,
"aa_start": 1653,
"aa_end": null,
"aa_length": 5202,
"cds_start": 4958,
"cds_end": null,
"cds_length": 15609,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_206933.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000307340.8"
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 73,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "c.4958G>A",
"hgvs_p": "p.Arg1653Gln",
"transcript": "ENST00000674083.1",
"protein_id": "ENSP00000501296.1",
"transcript_support_level": null,
"aa_start": 1653,
"aa_end": null,
"aa_length": 5226,
"cds_start": 4958,
"cds_end": null,
"cds_length": 15681,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000674083.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A-AS2",
"gene_hgnc_id": 40605,
"hgvs_c": "n.234C>T",
"hgvs_p": null,
"transcript": "ENST00000430890.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000430890.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A-AS2",
"gene_hgnc_id": 40605,
"hgvs_c": "n.233C>T",
"hgvs_p": null,
"transcript": "ENST00000442606.1",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000442606.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A-AS2",
"gene_hgnc_id": 40605,
"hgvs_c": "n.186C>T",
"hgvs_p": null,
"transcript": "ENST00000445619.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "ENST00000445619.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A-AS2",
"gene_hgnc_id": 40605,
"hgvs_c": "n.303C>T",
"hgvs_p": null,
"transcript": "ENST00000446411.6",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000446411.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"hgvs_c": "n.200G>A",
"hgvs_p": null,
"transcript": "ENST00000481786.1",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000481786.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A-AS2",
"gene_hgnc_id": 40605,
"hgvs_c": "n.145C>T",
"hgvs_p": null,
"transcript": "ENST00000796399.1",
"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": "ENST00000796399.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A-AS2",
"gene_hgnc_id": 40605,
"hgvs_c": "n.292C>T",
"hgvs_p": null,
"transcript": "NR_125992.1",
"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": "NR_125992.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "USH2A-AS2",
"gene_hgnc_id": 40605,
"hgvs_c": "n.163C>T",
"hgvs_p": null,
"transcript": "NR_125993.1",
"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": "NR_125993.1"
}
],
"gene_symbol": "USH2A",
"gene_hgnc_id": 12601,
"dbsnp": "rs372436408",
"frequency_reference_population": 0.000042781412,
"hom_count_reference_population": 1,
"allele_count_reference_population": 69,
"gnomad_exomes_af": 0.0000438158,
"gnomad_genomes_af": 0.0000328537,
"gnomad_exomes_ac": 64,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.021223872900009155,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.18,
"revel_prediction": "Benign",
"alphamissense_score": 0.062,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.067,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM1,BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "NM_206933.4",
"gene_symbol": "USH2A",
"hgnc_id": 12601,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.4958G>A",
"hgvs_p": "p.Arg1653Gln"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000430890.5",
"gene_symbol": "USH2A-AS2",
"hgnc_id": 40605,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.234C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "not specified|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}