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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-84119953-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=84119953&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 84119953,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_014496.5",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr",
"transcript": "NM_014496.5",
"protein_id": "NP_055311.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 745,
"cds_start": 721,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000262752.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_014496.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr",
"transcript": "ENST00000262752.5",
"protein_id": "ENSP00000262752.2",
"transcript_support_level": 1,
"aa_start": 241,
"aa_end": null,
"aa_length": 745,
"cds_start": 721,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_014496.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000262752.5"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr",
"transcript": "NM_001330512.1",
"protein_id": "NP_001317441.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 745,
"cds_start": 721,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001330512.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr",
"transcript": "ENST00000620340.4",
"protein_id": "ENSP00000483896.1",
"transcript_support_level": 5,
"aa_start": 241,
"aa_end": null,
"aa_length": 745,
"cds_start": 721,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000620340.4"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr",
"transcript": "ENST00000911420.1",
"protein_id": "ENSP00000581479.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 732,
"cds_start": 721,
"cds_end": null,
"cds_length": 2199,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911420.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr",
"transcript": "ENST00000911418.1",
"protein_id": "ENSP00000581477.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 698,
"cds_start": 721,
"cds_end": null,
"cds_length": 2097,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911418.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.772G>A",
"hgvs_p": "p.Ala258Thr",
"transcript": "XM_017029423.2",
"protein_id": "XP_016884912.1",
"transcript_support_level": null,
"aa_start": 258,
"aa_end": null,
"aa_length": 762,
"cds_start": 772,
"cds_end": null,
"cds_length": 2289,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029423.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.772G>A",
"hgvs_p": "p.Ala258Thr",
"transcript": "XM_017029424.2",
"protein_id": "XP_016884913.1",
"transcript_support_level": null,
"aa_start": 258,
"aa_end": null,
"aa_length": 762,
"cds_start": 772,
"cds_end": null,
"cds_length": 2289,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029424.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.772G>A",
"hgvs_p": "p.Ala258Thr",
"transcript": "XM_017029425.2",
"protein_id": "XP_016884914.1",
"transcript_support_level": null,
"aa_start": 258,
"aa_end": null,
"aa_length": 762,
"cds_start": 772,
"cds_end": null,
"cds_length": 2289,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029425.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr",
"transcript": "XM_011530917.3",
"protein_id": "XP_011529219.1",
"transcript_support_level": null,
"aa_start": 241,
"aa_end": null,
"aa_length": 745,
"cds_start": 721,
"cds_end": null,
"cds_length": 2238,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011530917.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Ala209Thr",
"transcript": "XM_047441996.1",
"protein_id": "XP_047297952.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 713,
"cds_start": 625,
"cds_end": null,
"cds_length": 2142,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441996.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.625G>A",
"hgvs_p": "p.Ala209Thr",
"transcript": "XM_047441997.1",
"protein_id": "XP_047297953.1",
"transcript_support_level": null,
"aa_start": 209,
"aa_end": null,
"aa_length": 713,
"cds_start": 625,
"cds_end": null,
"cds_length": 2142,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047441997.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.412G>A",
"hgvs_p": "p.Ala138Thr",
"transcript": "XM_011530919.3",
"protein_id": "XP_011529221.1",
"transcript_support_level": null,
"aa_start": 138,
"aa_end": null,
"aa_length": 642,
"cds_start": 412,
"cds_end": null,
"cds_length": 1929,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011530919.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.358G>A",
"hgvs_p": "p.Ala120Thr",
"transcript": "XM_011530920.3",
"protein_id": "XP_011529222.1",
"transcript_support_level": null,
"aa_start": 120,
"aa_end": null,
"aa_length": 624,
"cds_start": 358,
"cds_end": null,
"cds_length": 1875,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011530920.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"hgvs_c": "c.502-12228G>A",
"hgvs_p": null,
"transcript": "ENST00000911419.1",
"protein_id": "ENSP00000581478.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 576,
"cds_start": null,
"cds_end": null,
"cds_length": 1731,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000911419.1"
}
],
"gene_symbol": "RPS6KA6",
"gene_hgnc_id": 10435,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9671808481216431,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.762,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9962,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.31,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.729,
"phylop100way_prediction": "Pathogenic",
"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": 5,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Strong,BP6",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 1,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong",
"BP6"
],
"verdict": "Uncertain_significance",
"transcript": "NM_014496.5",
"gene_symbol": "RPS6KA6",
"hgnc_id": 10435,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.721G>A",
"hgvs_p": "p.Ala241Thr"
}
],
"clinvar_disease": "EBV-positive nodal T- and NK-cell lymphoma",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "EBV-positive nodal T- and NK-cell lymphoma",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}