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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: 12-123754482-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=123754482&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 123754482,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000330342.8",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.2238C>T",
"hgvs_p": "p.Cys746Cys",
"transcript": "NM_012463.4",
"protein_id": "NP_036595.2",
"transcript_support_level": null,
"aa_start": 746,
"aa_end": null,
"aa_length": 856,
"cds_start": 2238,
"cds_end": null,
"cds_length": 2571,
"cdna_start": 2451,
"cdna_end": null,
"cdna_length": 6507,
"mane_select": "ENST00000330342.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.2238C>T",
"hgvs_p": "p.Cys746Cys",
"transcript": "ENST00000330342.8",
"protein_id": "ENSP00000332247.2",
"transcript_support_level": 1,
"aa_start": 746,
"aa_end": null,
"aa_length": 856,
"cds_start": 2238,
"cds_end": null,
"cds_length": 2571,
"cdna_start": 2451,
"cdna_end": null,
"cdna_length": 6507,
"mane_select": "NM_012463.4",
"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": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "n.2269C>T",
"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": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.84C>T",
"hgvs_p": "p.Cys28Cys",
"transcript": "ENST00000544833.1",
"protein_id": "ENSP00000441143.1",
"transcript_support_level": 2,
"aa_start": 28,
"aa_end": null,
"aa_length": 138,
"cds_start": 84,
"cds_end": null,
"cds_length": 417,
"cdna_start": 492,
"cdna_end": null,
"cdna_length": 1013,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.78C>T",
"hgvs_p": "p.Cys26Cys",
"transcript": "ENST00000534943.5",
"protein_id": "ENSP00000443726.1",
"transcript_support_level": 2,
"aa_start": 26,
"aa_end": null,
"aa_length": 130,
"cds_start": 78,
"cds_end": null,
"cds_length": 394,
"cdna_start": 1417,
"cdna_end": null,
"cdna_length": 1733,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.2118C>T",
"hgvs_p": "p.Cys706Cys",
"transcript": "XM_024448910.2",
"protein_id": "XP_024304678.1",
"transcript_support_level": null,
"aa_start": 706,
"aa_end": null,
"aa_length": 816,
"cds_start": 2118,
"cds_end": null,
"cds_length": 2451,
"cdna_start": 2331,
"cdna_end": null,
"cdna_length": 6387,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.1725C>T",
"hgvs_p": "p.Cys575Cys",
"transcript": "XM_024448911.2",
"protein_id": "XP_024304679.1",
"transcript_support_level": null,
"aa_start": 575,
"aa_end": null,
"aa_length": 685,
"cds_start": 1725,
"cds_end": null,
"cds_length": 2058,
"cdna_start": 1826,
"cdna_end": null,
"cdna_length": 5882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "C",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "c.1416C>T",
"hgvs_p": "p.Cys472Cys",
"transcript": "XM_024448912.2",
"protein_id": "XP_024304680.1",
"transcript_support_level": null,
"aa_start": 472,
"aa_end": null,
"aa_length": 582,
"cds_start": 1416,
"cds_end": null,
"cds_length": 1749,
"cdna_start": 1768,
"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": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000280300",
"gene_hgnc_id": null,
"hgvs_c": "n.313G>A",
"hgvs_p": null,
"transcript": "ENST00000623681.1",
"protein_id": null,
"transcript_support_level": 6,
"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": 549,
"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": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "n.*2016C>T",
"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": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "n.*1259C>T",
"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": 14,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "n.*2016C>T",
"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": [
"3_prime_UTR_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"hgvs_c": "n.*1259C>T",
"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
}
],
"gene_symbol": "ATP6V0A2",
"gene_hgnc_id": 18481,
"dbsnp": "rs138886791",
"frequency_reference_population": 0.0016906626,
"hom_count_reference_population": 5,
"allele_count_reference_population": 2729,
"gnomad_exomes_af": 0.00171153,
"gnomad_genomes_af": 0.00149034,
"gnomad_exomes_ac": 2502,
"gnomad_genomes_ac": 227,
"gnomad_exomes_homalt": 5,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.36000001430511475,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.36,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 3.195,
"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": -12,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -12,
"benign_score": 12,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000330342.8",
"gene_symbol": "ATP6V0A2",
"hgnc_id": 18481,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2238C>T",
"hgvs_p": "p.Cys746Cys"
},
{
"score": -7,
"benign_score": 7,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000623681.1",
"gene_symbol": "ENSG00000280300",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.313G>A",
"hgvs_p": null
}
],
"clinvar_disease": "ALG9 congenital disorder of glycosylation,ATP6V0A2-related disorder,Cutis laxa with osteodystrophy,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 LB:4 B:2",
"phenotype_combined": "not specified|not provided|Cutis laxa with osteodystrophy|ALG9 congenital disorder of glycosylation|ATP6V0A2-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}