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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: 5-179550787-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=179550787&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 179550787,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_025158.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY1",
"gene_hgnc_id": 19760,
"hgvs_c": "c.218C>T",
"hgvs_p": "p.Ala73Val",
"transcript": "NM_025158.5",
"protein_id": "NP_079434.3",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 708,
"cds_start": 218,
"cds_end": null,
"cds_length": 2127,
"cdna_start": 234,
"cdna_end": null,
"cdna_length": 2636,
"mane_select": "ENST00000319449.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY1",
"gene_hgnc_id": 19760,
"hgvs_c": "c.218C>T",
"hgvs_p": "p.Ala73Val",
"transcript": "ENST00000319449.9",
"protein_id": "ENSP00000325594.4",
"transcript_support_level": 1,
"aa_start": 73,
"aa_end": null,
"aa_length": 708,
"cds_start": 218,
"cds_end": null,
"cds_length": 2127,
"cdna_start": 234,
"cdna_end": null,
"cdna_length": 2636,
"mane_select": "NM_025158.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY1",
"gene_hgnc_id": 19760,
"hgvs_c": "c.218C>T",
"hgvs_p": "p.Ala73Val",
"transcript": "XM_006714921.4",
"protein_id": "XP_006714984.2",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 686,
"cds_start": 218,
"cds_end": null,
"cds_length": 2061,
"cdna_start": 234,
"cdna_end": null,
"cdna_length": 2570,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY1",
"gene_hgnc_id": 19760,
"hgvs_c": "c.218C>T",
"hgvs_p": "p.Ala73Val",
"transcript": "XM_047417780.1",
"protein_id": "XP_047273736.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 412,
"cds_start": 218,
"cds_end": null,
"cds_length": 1239,
"cdna_start": 234,
"cdna_end": null,
"cdna_length": 1279,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY1",
"gene_hgnc_id": 19760,
"hgvs_c": "c.218C>T",
"hgvs_p": "p.Ala73Val",
"transcript": "XM_047417781.1",
"protein_id": "XP_047273737.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 390,
"cds_start": 218,
"cds_end": null,
"cds_length": 1173,
"cdna_start": 234,
"cdna_end": null,
"cdna_length": 1213,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY1",
"gene_hgnc_id": 19760,
"hgvs_c": "n.234C>T",
"hgvs_p": null,
"transcript": "XR_245276.4",
"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": 2817,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY1",
"gene_hgnc_id": 19760,
"hgvs_c": "n.234C>T",
"hgvs_p": null,
"transcript": "XR_245277.4",
"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": 2763,
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "LOC128966623",
"gene_hgnc_id": null,
"hgvs_c": "n.783+26072C>T",
"hgvs_p": null,
"transcript": "NR_185480.1",
"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": 2036,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY1",
"gene_hgnc_id": 19760,
"hgvs_c": "n.-50C>T",
"hgvs_p": null,
"transcript": "ENST00000393448.6",
"protein_id": "ENSP00000377094.2",
"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": 2320,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RUFY1",
"gene_hgnc_id": 19760,
"hgvs_c": "c.-53C>T",
"hgvs_p": null,
"transcript": "ENST00000502984.5",
"protein_id": "ENSP00000425533.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 217,
"cds_start": -4,
"cds_end": null,
"cds_length": 656,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 658,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "RUFY1",
"gene_hgnc_id": 19760,
"dbsnp": "rs1761788224",
"frequency_reference_population": 8.3070694e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 8.30707e-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": 0.796840250492096,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.132,
"revel_prediction": "Benign",
"alphamissense_score": 0.594,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.913,
"phylop100way_prediction": "Uncertain_significance",
"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": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_025158.5",
"gene_symbol": "RUFY1",
"hgnc_id": 19760,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.218C>T",
"hgvs_p": "p.Ala73Val"
},
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NR_185480.1",
"gene_symbol": "LOC128966623",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.783+26072C>T",
"hgvs_p": null
}
],
"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
}