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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: 2-70963289-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=70963289&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 70963289,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000234396.10",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V1B1",
"gene_hgnc_id": 853,
"hgvs_c": "c.1037C>G",
"hgvs_p": "p.Pro346Arg",
"transcript": "NM_001692.4",
"protein_id": "NP_001683.2",
"transcript_support_level": null,
"aa_start": 346,
"aa_end": null,
"aa_length": 513,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1542,
"cdna_start": 1092,
"cdna_end": null,
"cdna_length": 1907,
"mane_select": "ENST00000234396.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V1B1",
"gene_hgnc_id": 853,
"hgvs_c": "c.1037C>G",
"hgvs_p": "p.Pro346Arg",
"transcript": "ENST00000234396.10",
"protein_id": "ENSP00000234396.4",
"transcript_support_level": 1,
"aa_start": 346,
"aa_end": null,
"aa_length": 513,
"cds_start": 1037,
"cds_end": null,
"cds_length": 1542,
"cdna_start": 1092,
"cdna_end": null,
"cdna_length": 1907,
"mane_select": "NM_001692.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258881",
"gene_hgnc_id": null,
"hgvs_c": "c.476-20856G>C",
"hgvs_p": null,
"transcript": "ENST00000606025.5",
"protein_id": "ENSP00000475641.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 197,
"cds_start": -4,
"cds_end": null,
"cds_length": 594,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4170,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V1B1",
"gene_hgnc_id": 853,
"hgvs_c": "c.1157C>G",
"hgvs_p": "p.Pro386Arg",
"transcript": "XM_011532907.3",
"protein_id": "XP_011531209.1",
"transcript_support_level": null,
"aa_start": 386,
"aa_end": null,
"aa_length": 553,
"cds_start": 1157,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 1325,
"cdna_end": null,
"cdna_length": 2140,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAX2",
"gene_hgnc_id": 12661,
"hgvs_c": "n.*925C>G",
"hgvs_p": null,
"transcript": "ENST00000646783.1",
"protein_id": "ENSP00000495231.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1200,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAX2",
"gene_hgnc_id": 12661,
"hgvs_c": "n.*925C>G",
"hgvs_p": null,
"transcript": "ENST00000646783.1",
"protein_id": "ENSP00000495231.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1200,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "ATP6V1B1",
"gene_hgnc_id": 853,
"hgvs_c": "c.1009+28C>G",
"hgvs_p": null,
"transcript": "ENST00000412314.5",
"protein_id": "ENSP00000388353.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 496,
"cds_start": -4,
"cds_end": null,
"cds_length": 1491,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1805,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "VAX2",
"gene_hgnc_id": 12661,
"hgvs_c": "n.*837-283C>G",
"hgvs_p": null,
"transcript": "ENST00000432367.6",
"protein_id": "ENSP00000405114.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1847,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000258881",
"gene_hgnc_id": null,
"hgvs_c": "n.142-14914G>C",
"hgvs_p": null,
"transcript": "ENST00000453130.1",
"protein_id": "ENSP00000475757.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 423,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP6V1B1",
"gene_hgnc_id": 853,
"dbsnp": "rs781838938",
"frequency_reference_population": 0.00001549613,
"hom_count_reference_population": 0,
"allele_count_reference_population": 25,
"gnomad_exomes_af": 0.0000143724,
"gnomad_genomes_af": 0.0000262857,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9853020906448364,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.962,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9962,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 7.864,
"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": 14,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM2,PP3_Strong,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000234396.10",
"gene_symbol": "ATP6V1B1",
"hgnc_id": 853,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1037C>G",
"hgvs_p": "p.Pro346Arg"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000606025.5",
"gene_symbol": "ENSG00000258881",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.476-20856G>C",
"hgvs_p": null
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000646783.1",
"gene_symbol": "VAX2",
"hgnc_id": 12661,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*925C>G",
"hgvs_p": null
}
],
"clinvar_disease": "Distal renal tubular acidosis,Renal tubular acidosis with progressive nerve deafness,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:6",
"phenotype_combined": "not provided|Renal tubular acidosis with progressive nerve deafness|Distal renal tubular acidosis",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}