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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: 10-30316175-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=30316175&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 30316175,
"ref": "A",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_018109.4",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.1255T>A",
"hgvs_p": "p.Cys419Ser",
"transcript": "NM_018109.4",
"protein_id": "NP_060579.3",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 582,
"cds_start": 1255,
"cds_end": null,
"cds_length": 1749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000263063.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_018109.4"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.1255T>A",
"hgvs_p": "p.Cys419Ser",
"transcript": "ENST00000263063.9",
"protein_id": "ENSP00000263063.3",
"transcript_support_level": 1,
"aa_start": 419,
"aa_end": null,
"aa_length": 582,
"cds_start": 1255,
"cds_end": null,
"cds_length": 1749,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_018109.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000263063.9"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.1306T>A",
"hgvs_p": "p.Cys436Ser",
"transcript": "ENST00000958694.1",
"protein_id": "ENSP00000628753.1",
"transcript_support_level": null,
"aa_start": 436,
"aa_end": null,
"aa_length": 599,
"cds_start": 1306,
"cds_end": null,
"cds_length": 1800,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958694.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.1249T>A",
"hgvs_p": "p.Cys417Ser",
"transcript": "ENST00000904049.1",
"protein_id": "ENSP00000574108.1",
"transcript_support_level": null,
"aa_start": 417,
"aa_end": null,
"aa_length": 580,
"cds_start": 1249,
"cds_end": null,
"cds_length": 1743,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904049.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.1243T>A",
"hgvs_p": "p.Cys415Ser",
"transcript": "ENST00000958693.1",
"protein_id": "ENSP00000628752.1",
"transcript_support_level": null,
"aa_start": 415,
"aa_end": null,
"aa_length": 578,
"cds_start": 1243,
"cds_end": null,
"cds_length": 1737,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958693.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.1225T>A",
"hgvs_p": "p.Cys409Ser",
"transcript": "ENST00000904048.1",
"protein_id": "ENSP00000574107.1",
"transcript_support_level": null,
"aa_start": 409,
"aa_end": null,
"aa_length": 572,
"cds_start": 1225,
"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": "ENST00000904048.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.1255T>A",
"hgvs_p": "p.Cys419Ser",
"transcript": "ENST00000912898.1",
"protein_id": "ENSP00000582957.1",
"transcript_support_level": null,
"aa_start": 419,
"aa_end": null,
"aa_length": 567,
"cds_start": 1255,
"cds_end": null,
"cds_length": 1704,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912898.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.1186T>A",
"hgvs_p": "p.Cys396Ser",
"transcript": "ENST00000958692.1",
"protein_id": "ENSP00000628751.1",
"transcript_support_level": null,
"aa_start": 396,
"aa_end": null,
"aa_length": 559,
"cds_start": 1186,
"cds_end": null,
"cds_length": 1680,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000958692.1"
},
{
"aa_ref": "C",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.1030T>A",
"hgvs_p": "p.Cys344Ser",
"transcript": "ENST00000912899.1",
"protein_id": "ENSP00000582958.1",
"transcript_support_level": null,
"aa_start": 344,
"aa_end": null,
"aa_length": 507,
"cds_start": 1030,
"cds_end": null,
"cds_length": 1524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000912899.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "n.3010T>A",
"hgvs_p": null,
"transcript": "ENST00000488290.5",
"protein_id": null,
"transcript_support_level": 2,
"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": "ENST00000488290.5"
}
],
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"dbsnp": "rs17857517",
"frequency_reference_population": 0.0000034205623,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000342056,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8168424367904663,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.553,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.628,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.2,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.114,
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_018109.4",
"gene_symbol": "MTPAP",
"hgnc_id": 25532,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1255T>A",
"hgvs_p": "p.Cys419Ser"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}