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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: X-134498657-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=134498657&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 134498657,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "NM_000194.3",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.582C>T",
"hgvs_p": "p.Asp194Asp",
"transcript": "NM_000194.3",
"protein_id": "NP_000185.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 218,
"cds_start": 582,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000298556.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_000194.3"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.582C>T",
"hgvs_p": "p.Asp194Asp",
"transcript": "ENST00000298556.8",
"protein_id": "ENSP00000298556.7",
"transcript_support_level": 1,
"aa_start": 194,
"aa_end": null,
"aa_length": 218,
"cds_start": 582,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_000194.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000298556.8"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.627C>T",
"hgvs_p": "p.Asp209Asp",
"transcript": "ENST00000969780.1",
"protein_id": "ENSP00000639839.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 233,
"cds_start": 627,
"cds_end": null,
"cds_length": 702,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969780.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.618C>T",
"hgvs_p": "p.Asp206Asp",
"transcript": "ENST00000969779.1",
"protein_id": "ENSP00000639838.1",
"transcript_support_level": null,
"aa_start": 206,
"aa_end": null,
"aa_length": 230,
"cds_start": 618,
"cds_end": null,
"cds_length": 693,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969779.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.573C>T",
"hgvs_p": "p.Asp191Asp",
"transcript": "ENST00000916520.1",
"protein_id": "ENSP00000586579.1",
"transcript_support_level": null,
"aa_start": 191,
"aa_end": null,
"aa_length": 215,
"cds_start": 573,
"cds_end": null,
"cds_length": 648,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916520.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.564C>T",
"hgvs_p": "p.Asp188Asp",
"transcript": "ENST00000916519.1",
"protein_id": "ENSP00000586578.1",
"transcript_support_level": null,
"aa_start": 188,
"aa_end": null,
"aa_length": 212,
"cds_start": 564,
"cds_end": null,
"cds_length": 639,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000916519.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.516C>T",
"hgvs_p": "p.Asp172Asp",
"transcript": "ENST00000969781.1",
"protein_id": "ENSP00000639840.1",
"transcript_support_level": null,
"aa_start": 172,
"aa_end": null,
"aa_length": 196,
"cds_start": 516,
"cds_end": null,
"cds_length": 591,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000969781.1"
},
{
"aa_ref": "D",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.291C>T",
"hgvs_p": "p.Asp97Asp",
"transcript": "ENST00000883913.1",
"protein_id": "ENSP00000553972.1",
"transcript_support_level": null,
"aa_start": 97,
"aa_end": null,
"aa_length": 121,
"cds_start": 291,
"cds_end": null,
"cds_length": 366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883913.1"
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "c.319-1373C>T",
"hgvs_p": null,
"transcript": "ENST00000883914.1",
"protein_id": "ENSP00000553973.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 121,
"cds_start": null,
"cds_end": null,
"cds_length": 366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000883914.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "n.540C>T",
"hgvs_p": null,
"transcript": "ENST00000475720.1",
"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": "ENST00000475720.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"hgvs_c": "n.*16C>T",
"hgvs_p": null,
"transcript": "ENST00000462974.5",
"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": "ENST00000462974.5"
}
],
"gene_symbol": "HPRT1",
"gene_hgnc_id": 5157,
"dbsnp": "rs137852504",
"frequency_reference_population": 9.427292e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 9.42729e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.3400000035762787,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.79,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP7",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 3,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "NM_000194.3",
"gene_symbol": "HPRT1",
"hgnc_id": 5157,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.582C>T",
"hgvs_p": "p.Asp194Asp"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}