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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: 5-177090530-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=177090530&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 177090530,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_213647.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"transcript": "NM_213647.3",
"protein_id": "NP_998812.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 802,
"cds_start": 232,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 448,
"cdna_end": null,
"cdna_length": 3093,
"mane_select": "ENST00000292408.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"transcript": "ENST00000292408.9",
"protein_id": "ENSP00000292408.4",
"transcript_support_level": 1,
"aa_start": 78,
"aa_end": null,
"aa_length": 802,
"cds_start": 232,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 448,
"cdna_end": null,
"cdna_length": 3093,
"mane_select": "NM_213647.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"transcript": "ENST00000502906.5",
"protein_id": "ENSP00000424960.1",
"transcript_support_level": 1,
"aa_start": 78,
"aa_end": null,
"aa_length": 802,
"cds_start": 232,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 405,
"cdna_end": null,
"cdna_length": 2638,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"transcript": "ENST00000393637.5",
"protein_id": "ENSP00000377254.1",
"transcript_support_level": 1,
"aa_start": 78,
"aa_end": null,
"aa_length": 762,
"cds_start": 232,
"cds_end": null,
"cds_length": 2289,
"cdna_start": 268,
"cdna_end": null,
"cdna_length": 2418,
"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": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "n.237C>T",
"hgvs_p": null,
"transcript": "ENST00000426612.5",
"protein_id": null,
"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": 712,
"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": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "n.*96C>T",
"hgvs_p": null,
"transcript": "ENST00000430285.5",
"protein_id": "ENSP00000395164.1",
"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": 713,
"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": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "n.232C>T",
"hgvs_p": null,
"transcript": "ENST00000509511.5",
"protein_id": null,
"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": 1341,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "n.*96C>T",
"hgvs_p": null,
"transcript": "ENST00000430285.5",
"protein_id": "ENSP00000395164.1",
"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": 713,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"transcript": "NM_001354984.2",
"protein_id": "NP_001341913.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 802,
"cds_start": 232,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 389,
"cdna_end": null,
"cdna_length": 3034,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"transcript": "NM_002011.5",
"protein_id": "NP_002002.3",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 802,
"cds_start": 232,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 404,
"cdna_end": null,
"cdna_length": 3049,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"transcript": "NM_022963.3",
"protein_id": "NP_075252.2",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 762,
"cds_start": 232,
"cds_end": null,
"cds_length": 2289,
"cdna_start": 285,
"cdna_end": null,
"cdna_length": 2808,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"transcript": "NM_001291980.2",
"protein_id": "NP_001278909.1",
"transcript_support_level": null,
"aa_start": 78,
"aa_end": null,
"aa_length": 734,
"cds_start": 232,
"cds_end": null,
"cds_length": 2205,
"cdna_start": 404,
"cdna_end": null,
"cdna_length": 2845,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"transcript": "ENST00000393648.6",
"protein_id": "ENSP00000377259.2",
"transcript_support_level": 2,
"aa_start": 78,
"aa_end": null,
"aa_length": 734,
"cds_start": 232,
"cds_end": null,
"cds_length": 2205,
"cdna_start": 414,
"cdna_end": null,
"cdna_length": 2733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"transcript": "ENST00000503708.5",
"protein_id": "ENSP00000424905.1",
"transcript_support_level": 4,
"aa_start": 78,
"aa_end": null,
"aa_length": 200,
"cds_start": 232,
"cds_end": null,
"cds_length": 603,
"cdna_start": 399,
"cdna_end": null,
"cdna_length": 770,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"transcript": "ENST00000514472.1",
"protein_id": "ENSP00000426492.1",
"transcript_support_level": 4,
"aa_start": 78,
"aa_end": null,
"aa_length": 113,
"cds_start": 232,
"cds_end": null,
"cds_length": 343,
"cdna_start": 441,
"cdna_end": null,
"cdna_length": 552,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"transcript": "ENST00000513166.1",
"protein_id": "ENSP00000422889.1",
"transcript_support_level": 4,
"aa_start": 78,
"aa_end": null,
"aa_length": 107,
"cds_start": 232,
"cds_end": null,
"cds_length": 324,
"cdna_start": 502,
"cdna_end": null,
"cdna_length": 594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys",
"transcript": "ENST00000510911.5",
"protein_id": "ENSP00000427222.1",
"transcript_support_level": 4,
"aa_start": 78,
"aa_end": null,
"aa_length": 86,
"cds_start": 232,
"cds_end": null,
"cds_length": 262,
"cdna_start": 679,
"cdna_end": null,
"cdna_length": 709,
"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": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"hgvs_c": "n.443C>T",
"hgvs_p": null,
"transcript": "ENST00000507708.1",
"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": 476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "FGFR4",
"gene_hgnc_id": 3691,
"dbsnp": "rs1784326239",
"frequency_reference_population": 7.1248314e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 7.12483e-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": 0.8834813833236694,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.87,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.6098,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.28,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 3.413,
"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": 4,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_by_gene": [
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP3_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_213647.3",
"gene_symbol": "FGFR4",
"hgnc_id": 3691,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.232C>T",
"hgvs_p": "p.Arg78Cys"
}
],
"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
}