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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: 2-70958060-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=70958060&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 70958060,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000234396.10",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V1B1",
"gene_hgnc_id": 853,
"hgvs_c": "c.189G>A",
"hgvs_p": "p.Ala63Ala",
"transcript": "NM_001692.4",
"protein_id": "NP_001683.2",
"transcript_support_level": null,
"aa_start": 63,
"aa_end": null,
"aa_length": 513,
"cds_start": 189,
"cds_end": null,
"cds_length": 1542,
"cdna_start": 244,
"cdna_end": null,
"cdna_length": 1907,
"mane_select": "ENST00000234396.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V1B1",
"gene_hgnc_id": 853,
"hgvs_c": "c.189G>A",
"hgvs_p": "p.Ala63Ala",
"transcript": "ENST00000234396.10",
"protein_id": "ENSP00000234396.4",
"transcript_support_level": 1,
"aa_start": 63,
"aa_end": null,
"aa_length": 513,
"cds_start": 189,
"cds_end": null,
"cds_length": 1542,
"cdna_start": 244,
"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.476-15627C>T",
"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": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V1B1",
"gene_hgnc_id": 853,
"hgvs_c": "c.189G>A",
"hgvs_p": "p.Ala63Ala",
"transcript": "ENST00000412314.5",
"protein_id": "ENSP00000388353.1",
"transcript_support_level": 5,
"aa_start": 63,
"aa_end": null,
"aa_length": 496,
"cds_start": 189,
"cds_end": null,
"cds_length": 1491,
"cdna_start": 223,
"cdna_end": null,
"cdna_length": 1805,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V1B1",
"gene_hgnc_id": 853,
"hgvs_c": "c.189G>A",
"hgvs_p": "p.Ala63Ala",
"transcript": "ENST00000454446.6",
"protein_id": "ENSP00000408361.2",
"transcript_support_level": 5,
"aa_start": 63,
"aa_end": null,
"aa_length": 309,
"cds_start": 189,
"cds_end": null,
"cds_length": 930,
"cdna_start": 243,
"cdna_end": null,
"cdna_length": 984,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V1B1",
"gene_hgnc_id": 853,
"hgvs_c": "c.309G>A",
"hgvs_p": "p.Ala103Ala",
"transcript": "XM_011532907.3",
"protein_id": "XP_011531209.1",
"transcript_support_level": null,
"aa_start": 103,
"aa_end": null,
"aa_length": 553,
"cds_start": 309,
"cds_end": null,
"cds_length": 1662,
"cdna_start": 477,
"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": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V1B1",
"gene_hgnc_id": 853,
"hgvs_c": "n.355G>A",
"hgvs_p": null,
"transcript": "ENST00000432098.2",
"protein_id": null,
"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": 853,
"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": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAX2",
"gene_hgnc_id": 12661,
"hgvs_c": "n.*116G>A",
"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": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V1B1",
"gene_hgnc_id": 853,
"hgvs_c": "n.290G>A",
"hgvs_p": null,
"transcript": "ENST00000463380.1",
"protein_id": null,
"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": 574,
"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": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAX2",
"gene_hgnc_id": 12661,
"hgvs_c": "n.*77G>A",
"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": 5,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAX2",
"gene_hgnc_id": 12661,
"hgvs_c": "n.*116G>A",
"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": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VAX2",
"gene_hgnc_id": 12661,
"hgvs_c": "n.*77G>A",
"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": 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.142-9685C>T",
"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": "rs376581983",
"frequency_reference_population": 0.000068157795,
"hom_count_reference_population": 0,
"allele_count_reference_population": 110,
"gnomad_exomes_af": 0.0000704643,
"gnomad_genomes_af": 0.0000460018,
"gnomad_exomes_ac": 103,
"gnomad_genomes_ac": 7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6600000262260437,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.66,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -4.452,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP6,BP7",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 6,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000234396.10",
"gene_symbol": "ATP6V1B1",
"hgnc_id": 853,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.189G>A",
"hgvs_p": "p.Ala63Ala"
},
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000606025.5",
"gene_symbol": "ENSG00000258881",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.476-15627C>T",
"hgvs_p": null
},
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000646783.1",
"gene_symbol": "VAX2",
"hgnc_id": 12661,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.*77G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Renal tubular acidosis with progressive nerve deafness,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:2",
"phenotype_combined": "not specified|Renal tubular acidosis with progressive nerve deafness|not provided",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}