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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: 12-123737249-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=123737249&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 123737249,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000330342.8",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.1016G>A",
"hgvs_p": "p.Arg339His",
"transcript": "NM_012463.4",
"protein_id": "NP_036595.2",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 856,
"cds_start": 1016,
"cds_end": null,
"cds_length": 2571,
"cdna_start": 1229,
"cdna_end": null,
"cdna_length": 6507,
"mane_select": "ENST00000330342.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.1016G>A",
"hgvs_p": "p.Arg339His",
"transcript": "ENST00000330342.8",
"protein_id": "ENSP00000332247.2",
"transcript_support_level": 1,
"aa_start": 339,
"aa_end": null,
"aa_length": 856,
"cds_start": 1016,
"cds_end": null,
"cds_length": 2571,
"cdna_start": 1229,
"cdna_end": null,
"cdna_length": 6507,
"mane_select": "NM_012463.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.1016G>A",
"hgvs_p": "p.Arg339His",
"transcript": "ENST00000613625.5",
"protein_id": "ENSP00000482236.1",
"transcript_support_level": 1,
"aa_start": 339,
"aa_end": null,
"aa_length": 372,
"cds_start": 1016,
"cds_end": null,
"cds_length": 1119,
"cdna_start": 1226,
"cdna_end": null,
"cdna_length": 1621,
"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": 9,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "n.1047G>A",
"hgvs_p": null,
"transcript": "ENST00000540368.6",
"protein_id": null,
"transcript_support_level": 1,
"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": 3228,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.626G>A",
"hgvs_p": "p.Arg209His",
"transcript": "ENST00000504192.2",
"protein_id": "ENSP00000443441.1",
"transcript_support_level": 5,
"aa_start": 209,
"aa_end": null,
"aa_length": 327,
"cds_start": 626,
"cds_end": null,
"cds_length": 985,
"cdna_start": 2166,
"cdna_end": null,
"cdna_length": 2525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.1016G>A",
"hgvs_p": "p.Arg339His",
"transcript": "XM_024448910.2",
"protein_id": "XP_024304678.1",
"transcript_support_level": null,
"aa_start": 339,
"aa_end": null,
"aa_length": 816,
"cds_start": 1016,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 1229,
"cdna_end": null,
"cdna_length": 6387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.503G>A",
"hgvs_p": "p.Arg168His",
"transcript": "XM_024448911.2",
"protein_id": "XP_024304679.1",
"transcript_support_level": null,
"aa_start": 168,
"aa_end": null,
"aa_length": 685,
"cds_start": 503,
"cds_end": null,
"cds_length": 2058,
"cdna_start": 604,
"cdna_end": null,
"cdna_length": 5882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.194G>A",
"hgvs_p": "p.Arg65His",
"transcript": "XM_024448912.2",
"protein_id": "XP_024304680.1",
"transcript_support_level": null,
"aa_start": 65,
"aa_end": null,
"aa_length": 582,
"cds_start": 194,
"cds_end": null,
"cds_length": 1749,
"cdna_start": 546,
"cdna_end": null,
"cdna_length": 5824,
"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": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "n.3652G>A",
"hgvs_p": null,
"transcript": "ENST00000545059.5",
"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": 4232,
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "n.*794G>A",
"hgvs_p": null,
"transcript": "ENST00000674794.1",
"protein_id": "ENSP00000502672.1",
"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": 3118,
"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": 9,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "n.1016G>A",
"hgvs_p": null,
"transcript": "ENST00000675344.1",
"protein_id": "ENSP00000501953.1",
"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": 3179,
"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": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "n.*794G>A",
"hgvs_p": null,
"transcript": "ENST00000674794.1",
"protein_id": "ENSP00000502672.1",
"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": 3118,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"dbsnp": "rs74922060",
"frequency_reference_population": 0.0066755633,
"hom_count_reference_population": 243,
"allele_count_reference_population": 10775,
"gnomad_exomes_af": 0.00502919,
"gnomad_genomes_af": 0.0224857,
"gnomad_exomes_ac": 7352,
"gnomad_genomes_ac": 3423,
"gnomad_exomes_homalt": 138,
"gnomad_genomes_homalt": 105,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0037205517292022705,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.516,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0909,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.17,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.949,
"phylop100way_prediction": "Uncertain_significance",
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000330342.8",
"gene_symbol": "ATP6V0A2",
"hgnc_id": 18481,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1016G>A",
"hgvs_p": "p.Arg339His"
}
],
"clinvar_disease": "ALG9 congenital disorder of glycosylation,Cutis laxa with osteodystrophy,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|not provided|ALG9 congenital disorder of glycosylation|Cutis laxa with osteodystrophy",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}