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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: 4-107614337-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=107614337&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3"
],
"effects": [
"missense_variant"
],
"gene_symbol": "PAPSS1",
"hgnc_id": 8603,
"hgvs_c": "c.1787G>C",
"hgvs_p": "p.Arg596Pro",
"inheritance_mode": "AR",
"pathogenic_score": 3,
"score": 3,
"transcript": "NM_005443.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_score": 3,
"allele_count_reference_population": 1,
"alphamissense_prediction": "Pathogenic",
"alphamissense_score": 0.9834,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": -0.04,
"chr": "4",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.8043808937072754,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 624,
"aa_ref": "R",
"aa_start": 596,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2513,
"cdna_start": 1842,
"cds_end": null,
"cds_length": 1875,
"cds_start": 1787,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_005443.5",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "c.1787G>C",
"hgvs_p": "p.Arg596Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000265174.5",
"protein_coding": true,
"protein_id": "NP_005434.4",
"strand": false,
"transcript": "NM_005443.5",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 624,
"aa_ref": "R",
"aa_start": 596,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2513,
"cdna_start": 1842,
"cds_end": null,
"cds_length": 1875,
"cds_start": 1787,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000265174.5",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "c.1787G>C",
"hgvs_p": "p.Arg596Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_005443.5",
"protein_coding": true,
"protein_id": "ENSP00000265174.4",
"strand": false,
"transcript": "ENST00000265174.5",
"transcript_support_level": 1
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 647,
"aa_ref": "R",
"aa_start": 619,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2573,
"cdna_start": 1902,
"cds_end": null,
"cds_length": 1944,
"cds_start": 1856,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000873396.1",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "c.1856G>C",
"hgvs_p": "p.Arg619Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000543455.1",
"strand": false,
"transcript": "ENST00000873396.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 623,
"aa_ref": "R",
"aa_start": 595,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2516,
"cdna_start": 1848,
"cds_end": null,
"cds_length": 1872,
"cds_start": 1784,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000970503.1",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "c.1784G>C",
"hgvs_p": "p.Arg595Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000640562.1",
"strand": false,
"transcript": "ENST00000970503.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 622,
"aa_ref": "R",
"aa_start": 594,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2525,
"cdna_start": 1854,
"cds_end": null,
"cds_length": 1869,
"cds_start": 1781,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000931561.1",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "c.1781G>C",
"hgvs_p": "p.Arg594Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601620.1",
"strand": false,
"transcript": "ENST00000931561.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 621,
"aa_ref": "R",
"aa_start": 593,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2551,
"cdna_start": 1880,
"cds_end": null,
"cds_length": 1866,
"cds_start": 1778,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000931560.1",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "c.1778G>C",
"hgvs_p": "p.Arg593Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601619.1",
"strand": false,
"transcript": "ENST00000931560.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 620,
"aa_ref": "R",
"aa_start": 592,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2271,
"cdna_start": 1836,
"cds_end": null,
"cds_length": 1863,
"cds_start": 1775,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000970505.1",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "c.1775G>C",
"hgvs_p": "p.Arg592Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000640564.1",
"strand": false,
"transcript": "ENST00000970505.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 606,
"aa_ref": "R",
"aa_start": 578,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2261,
"cdna_start": 1764,
"cds_end": null,
"cds_length": 1821,
"cds_start": 1733,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000970504.1",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "c.1733G>C",
"hgvs_p": "p.Arg578Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000640563.1",
"strand": false,
"transcript": "ENST00000970504.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 473,
"aa_ref": "R",
"aa_start": 445,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2220,
"cdna_start": 1550,
"cds_end": null,
"cds_length": 1422,
"cds_start": 1334,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000931559.1",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "c.1334G>C",
"hgvs_p": "p.Arg445Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601618.1",
"strand": false,
"transcript": "ENST00000931559.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 413,
"aa_ref": "R",
"aa_start": 385,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1869,
"cdna_start": 1200,
"cds_end": null,
"cds_length": 1242,
"cds_start": 1154,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000931563.1",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "c.1154G>C",
"hgvs_p": "p.Arg385Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601622.1",
"strand": false,
"transcript": "ENST00000931563.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 345,
"aa_ref": "R",
"aa_start": 317,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1690,
"cdna_start": 1019,
"cds_end": null,
"cds_length": 1038,
"cds_start": 950,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000931562.1",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "c.950G>C",
"hgvs_p": "p.Arg317Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000601621.1",
"strand": false,
"transcript": "ENST00000931562.1",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 603,
"aa_ref": "R",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2482,
"cdna_start": 1811,
"cds_end": null,
"cds_length": 1812,
"cds_start": 1724,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_011532400.3",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "c.1724G>C",
"hgvs_p": "p.Arg575Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530702.1",
"strand": false,
"transcript": "XM_011532400.3",
"transcript_support_level": null
},
{
"aa_alt": "P",
"aa_end": null,
"aa_length": 603,
"aa_ref": "R",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2512,
"cdna_start": 1841,
"cds_end": null,
"cds_length": 1812,
"cds_start": 1724,
"consequences": [
"missense_variant"
],
"exon_count": 12,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "XM_011532401.2",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "c.1724G>C",
"hgvs_p": "p.Arg575Pro",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011530703.1",
"strand": false,
"transcript": "XM_011532401.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 296,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000514815.1",
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"hgvs_c": "n.174+17294G>C",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000514815.1",
"transcript_support_level": 5
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs370009530",
"effect": "missense_variant",
"frequency_reference_population": 6.8415363e-7,
"gene_hgnc_id": 8603,
"gene_symbol": "PAPSS1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84154e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 4.574,
"pos": 107614337,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.412,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_005443.5"
}
]
}