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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: 10-30313640-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=30313640&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "MTPAP",
"hgnc_id": 25532,
"hgvs_c": "c.1718G>A",
"hgvs_p": "p.Ser573Asn",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_018109.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 1,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0618,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.82,
"chr": "10",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.02773478627204895,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 582,
"aa_ref": "S",
"aa_start": 573,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5560,
"cdna_start": 1721,
"cds_end": null,
"cds_length": 1749,
"cds_start": 1718,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_018109.4",
"gene_hgnc_id": 25532,
"gene_symbol": "MTPAP",
"hgvs_c": "c.1718G>A",
"hgvs_p": "p.Ser573Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000263063.9",
"protein_coding": true,
"protein_id": "NP_060579.3",
"strand": false,
"transcript": "NM_018109.4",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 582,
"aa_ref": "S",
"aa_start": 573,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5560,
"cdna_start": 1721,
"cds_end": null,
"cds_length": 1749,
"cds_start": 1718,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000263063.9",
"gene_hgnc_id": 25532,
"gene_symbol": "MTPAP",
"hgvs_c": "c.1718G>A",
"hgvs_p": "p.Ser573Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_018109.4",
"protein_coding": true,
"protein_id": "ENSP00000263063.3",
"strand": false,
"transcript": "ENST00000263063.9",
"transcript_support_level": 1
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 599,
"aa_ref": "S",
"aa_start": 590,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2619,
"cdna_start": 1813,
"cds_end": null,
"cds_length": 1800,
"cds_start": 1769,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "ENST00000958694.1",
"gene_hgnc_id": 25532,
"gene_symbol": "MTPAP",
"hgvs_c": "c.1769G>A",
"hgvs_p": "p.Ser590Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628753.1",
"strand": false,
"transcript": "ENST00000958694.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 580,
"aa_ref": "S",
"aa_start": 571,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2552,
"cdna_start": 1738,
"cds_end": null,
"cds_length": 1743,
"cds_start": 1712,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000904049.1",
"gene_hgnc_id": 25532,
"gene_symbol": "MTPAP",
"hgvs_c": "c.1712G>A",
"hgvs_p": "p.Ser571Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574108.1",
"strand": false,
"transcript": "ENST00000904049.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 578,
"aa_ref": "S",
"aa_start": 569,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2924,
"cdna_start": 1710,
"cds_end": null,
"cds_length": 1737,
"cds_start": 1706,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000958693.1",
"gene_hgnc_id": 25532,
"gene_symbol": "MTPAP",
"hgvs_c": "c.1706G>A",
"hgvs_p": "p.Ser569Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628752.1",
"strand": false,
"transcript": "ENST00000958693.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 572,
"aa_ref": "S",
"aa_start": 563,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2565,
"cdna_start": 1751,
"cds_end": null,
"cds_length": 1719,
"cds_start": 1688,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000904048.1",
"gene_hgnc_id": 25532,
"gene_symbol": "MTPAP",
"hgvs_c": "c.1688G>A",
"hgvs_p": "p.Ser563Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000574107.1",
"strand": false,
"transcript": "ENST00000904048.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 567,
"aa_ref": "S",
"aa_start": 558,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2556,
"cdna_start": 1742,
"cds_end": null,
"cds_length": 1704,
"cds_start": 1673,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000912898.1",
"gene_hgnc_id": 25532,
"gene_symbol": "MTPAP",
"hgvs_c": "c.1673G>A",
"hgvs_p": "p.Ser558Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582957.1",
"strand": false,
"transcript": "ENST00000912898.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 559,
"aa_ref": "S",
"aa_start": 550,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2889,
"cdna_start": 1675,
"cds_end": null,
"cds_length": 1680,
"cds_start": 1649,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000958692.1",
"gene_hgnc_id": 25532,
"gene_symbol": "MTPAP",
"hgvs_c": "c.1649G>A",
"hgvs_p": "p.Ser550Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000628751.1",
"strand": false,
"transcript": "ENST00000958692.1",
"transcript_support_level": null
},
{
"aa_alt": "N",
"aa_end": null,
"aa_length": 507,
"aa_ref": "S",
"aa_start": 498,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2311,
"cdna_start": 1497,
"cds_end": null,
"cds_length": 1524,
"cds_start": 1493,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000912899.1",
"gene_hgnc_id": 25532,
"gene_symbol": "MTPAP",
"hgvs_c": "c.1493G>A",
"hgvs_p": "p.Ser498Asn",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000582958.1",
"strand": false,
"transcript": "ENST00000912899.1",
"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": 4103,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 17,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000488290.5",
"gene_hgnc_id": 25532,
"gene_symbol": "MTPAP",
"hgvs_c": "n.3473G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000488290.5",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs771523018",
"effect": "missense_variant",
"frequency_reference_population": 6.84061e-7,
"gene_hgnc_id": 25532,
"gene_symbol": "MTPAP",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 6.84061e-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": "Uncertain significance",
"phenotype_combined": "not provided",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.643,
"pos": 30313640,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.028,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.019999999552965164,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.02,
"transcript": "NM_018109.4"
}
]
}