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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: 5-180313818-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=180313818&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 180313818,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_005110.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFPT2",
"gene_hgnc_id": 4242,
"hgvs_c": "c.1420G>T",
"hgvs_p": "p.Ala474Ser",
"transcript": "NM_005110.4",
"protein_id": "NP_005101.1",
"transcript_support_level": null,
"aa_start": 474,
"aa_end": null,
"aa_length": 682,
"cds_start": 1420,
"cds_end": null,
"cds_length": 2049,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000253778.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_005110.4"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFPT2",
"gene_hgnc_id": 4242,
"hgvs_c": "c.1420G>T",
"hgvs_p": "p.Ala474Ser",
"transcript": "ENST00000253778.13",
"protein_id": "ENSP00000253778.8",
"transcript_support_level": 1,
"aa_start": 474,
"aa_end": null,
"aa_length": 682,
"cds_start": 1420,
"cds_end": null,
"cds_length": 2049,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_005110.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000253778.13"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFPT2",
"gene_hgnc_id": 4242,
"hgvs_c": "c.1483G>T",
"hgvs_p": "p.Ala495Ser",
"transcript": "ENST00000889627.1",
"protein_id": "ENSP00000559686.1",
"transcript_support_level": null,
"aa_start": 495,
"aa_end": null,
"aa_length": 703,
"cds_start": 1483,
"cds_end": null,
"cds_length": 2112,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889627.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFPT2",
"gene_hgnc_id": 4242,
"hgvs_c": "c.1417G>T",
"hgvs_p": "p.Ala473Ser",
"transcript": "ENST00000920229.1",
"protein_id": "ENSP00000590288.1",
"transcript_support_level": null,
"aa_start": 473,
"aa_end": null,
"aa_length": 681,
"cds_start": 1417,
"cds_end": null,
"cds_length": 2046,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920229.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFPT2",
"gene_hgnc_id": 4242,
"hgvs_c": "c.1312G>T",
"hgvs_p": "p.Ala438Ser",
"transcript": "ENST00000920227.1",
"protein_id": "ENSP00000590286.1",
"transcript_support_level": null,
"aa_start": 438,
"aa_end": null,
"aa_length": 646,
"cds_start": 1312,
"cds_end": null,
"cds_length": 1941,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920227.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFPT2",
"gene_hgnc_id": 4242,
"hgvs_c": "c.1420G>T",
"hgvs_p": "p.Ala474Ser",
"transcript": "ENST00000889625.1",
"protein_id": "ENSP00000559684.1",
"transcript_support_level": null,
"aa_start": 474,
"aa_end": null,
"aa_length": 628,
"cds_start": 1420,
"cds_end": null,
"cds_length": 1887,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889625.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFPT2",
"gene_hgnc_id": 4242,
"hgvs_c": "c.1417G>T",
"hgvs_p": "p.Ala473Ser",
"transcript": "ENST00000953748.1",
"protein_id": "ENSP00000623807.1",
"transcript_support_level": null,
"aa_start": 473,
"aa_end": null,
"aa_length": 627,
"cds_start": 1417,
"cds_end": null,
"cds_length": 1884,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953748.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFPT2",
"gene_hgnc_id": 4242,
"hgvs_c": "c.1420G>T",
"hgvs_p": "p.Ala474Ser",
"transcript": "ENST00000889626.1",
"protein_id": "ENSP00000559685.1",
"transcript_support_level": null,
"aa_start": 474,
"aa_end": null,
"aa_length": 626,
"cds_start": 1420,
"cds_end": null,
"cds_length": 1881,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000889626.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFPT2",
"gene_hgnc_id": 4242,
"hgvs_c": "c.1195G>T",
"hgvs_p": "p.Ala399Ser",
"transcript": "ENST00000920228.1",
"protein_id": "ENSP00000590287.1",
"transcript_support_level": null,
"aa_start": 399,
"aa_end": null,
"aa_length": 607,
"cds_start": 1195,
"cds_end": null,
"cds_length": 1824,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920228.1"
},
{
"aa_ref": "A",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GFPT2",
"gene_hgnc_id": 4242,
"hgvs_c": "c.1420G>T",
"hgvs_p": "p.Ala474Ser",
"transcript": "ENST00000920226.1",
"protein_id": "ENSP00000590285.1",
"transcript_support_level": null,
"aa_start": 474,
"aa_end": null,
"aa_length": 572,
"cds_start": 1420,
"cds_end": null,
"cds_length": 1719,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920226.1"
},
{
"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": 17,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "GFPT2",
"gene_hgnc_id": 4242,
"hgvs_c": "c.1273+2523G>T",
"hgvs_p": null,
"transcript": "ENST00000920230.1",
"protein_id": "ENSP00000590289.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 591,
"cds_start": null,
"cds_end": null,
"cds_length": 1776,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000920230.1"
},
{
"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": 17,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "GFPT2",
"gene_hgnc_id": 4242,
"hgvs_c": "c.1153-1274G>T",
"hgvs_p": null,
"transcript": "ENST00000953747.1",
"protein_id": "ENSP00000623806.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 589,
"cds_start": null,
"cds_end": null,
"cds_length": 1770,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000953747.1"
},
{
"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": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000297119",
"gene_hgnc_id": null,
"hgvs_c": "n.-100C>A",
"hgvs_p": null,
"transcript": "ENST00000745608.1",
"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": "ENST00000745608.1"
}
],
"gene_symbol": "GFPT2",
"gene_hgnc_id": 4242,
"dbsnp": "rs1443773342",
"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": 0.9687657356262207,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.624,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.8098,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.1,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.608,
"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": 6,
"acmg_classification": "Likely_pathogenic",
"acmg_criteria": "PM2,PP3_Strong",
"acmg_by_gene": [
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "NM_005110.4",
"gene_symbol": "GFPT2",
"hgnc_id": 4242,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1420G>T",
"hgvs_p": "p.Ala474Ser"
},
{
"score": 6,
"benign_score": 0,
"pathogenic_score": 6,
"criteria": [
"PM2",
"PP3_Strong"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000745608.1",
"gene_symbol": "ENSG00000297119",
"hgnc_id": null,
"effects": [
"upstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.-100C>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}