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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: 10-30340435-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=10&pos=30340435&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "10",
"pos": 30340435,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_018109.4",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Val116Ile",
"transcript": "NM_018109.4",
"protein_id": "NP_060579.3",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 582,
"cds_start": 346,
"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": "V",
"aa_alt": "I",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Val116Ile",
"transcript": "ENST00000263063.9",
"protein_id": "ENSP00000263063.3",
"transcript_support_level": 1,
"aa_start": 116,
"aa_end": null,
"aa_length": 582,
"cds_start": 346,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.397G>A",
"hgvs_p": "p.Val133Ile",
"transcript": "ENST00000958694.1",
"protein_id": "ENSP00000628753.1",
"transcript_support_level": null,
"aa_start": 133,
"aa_end": null,
"aa_length": 599,
"cds_start": 397,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Val116Ile",
"transcript": "ENST00000904049.1",
"protein_id": "ENSP00000574108.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 580,
"cds_start": 346,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Val116Ile",
"transcript": "ENST00000958693.1",
"protein_id": "ENSP00000628752.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 578,
"cds_start": 346,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Val116Ile",
"transcript": "ENST00000904048.1",
"protein_id": "ENSP00000574107.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 572,
"cds_start": 346,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Val116Ile",
"transcript": "ENST00000912898.1",
"protein_id": "ENSP00000582957.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 567,
"cds_start": 346,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Val116Ile",
"transcript": "ENST00000958692.1",
"protein_id": "ENSP00000628751.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 559,
"cds_start": 346,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Val116Ile",
"transcript": "ENST00000912899.1",
"protein_id": "ENSP00000582958.1",
"transcript_support_level": null,
"aa_start": 116,
"aa_end": null,
"aa_length": 507,
"cds_start": 346,
"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": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.151G>A",
"hgvs_p": "p.Val51Ile",
"transcript": "ENST00000417581.1",
"protein_id": "ENSP00000404392.1",
"transcript_support_level": 5,
"aa_start": 51,
"aa_end": null,
"aa_length": 218,
"cds_start": 151,
"cds_end": null,
"cds_length": 657,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000417581.1"
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "c.232G>A",
"hgvs_p": "p.Val78Ile",
"transcript": "ENST00000421701.1",
"protein_id": "ENSP00000394118.1",
"transcript_support_level": 2,
"aa_start": 78,
"aa_end": null,
"aa_length": 150,
"cds_start": 232,
"cds_end": null,
"cds_length": 453,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000421701.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MTPAP",
"gene_hgnc_id": 25532,
"hgvs_c": "n.2101G>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": "rs560622337",
"frequency_reference_population": 0.00009109139,
"hom_count_reference_population": 0,
"allele_count_reference_population": 147,
"gnomad_exomes_af": 0.0000916773,
"gnomad_genomes_af": 0.0000854611,
"gnomad_exomes_ac": 134,
"gnomad_genomes_ac": 13,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.14870458841323853,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.046,
"revel_prediction": "Benign",
"alphamissense_score": 0.0971,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.357,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_018109.4",
"gene_symbol": "MTPAP",
"hgnc_id": 25532,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.346G>A",
"hgvs_p": "p.Val116Ile"
}
],
"clinvar_disease": "Inborn genetic diseases,Spastic ataxia 4,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:4",
"phenotype_combined": "Spastic ataxia 4|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}