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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: X-132708467-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=132708467&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 132708467,
"ref": "T",
"alt": "C",
"effect": "synonymous_variant",
"transcript": "ENST00000370833.7",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.975A>G",
"hgvs_p": "p.Ala325Ala",
"transcript": "NM_001394073.1",
"protein_id": "NP_001381002.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 645,
"cds_start": 975,
"cds_end": null,
"cds_length": 1938,
"cdna_start": 1002,
"cdna_end": null,
"cdna_length": 4173,
"mane_select": "ENST00000370833.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.975A>G",
"hgvs_p": "p.Ala325Ala",
"transcript": "ENST00000370833.7",
"protein_id": "ENSP00000359870.3",
"transcript_support_level": 5,
"aa_start": 325,
"aa_end": null,
"aa_length": 645,
"cds_start": 975,
"cds_end": null,
"cds_length": 1938,
"cdna_start": 1002,
"cdna_end": null,
"cdna_length": 4173,
"mane_select": "NM_001394073.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.537A>G",
"hgvs_p": "p.Ala179Ala",
"transcript": "ENST00000406696.5",
"protein_id": "ENSP00000384013.5",
"transcript_support_level": 1,
"aa_start": 179,
"aa_end": null,
"aa_length": 499,
"cds_start": 537,
"cds_end": null,
"cds_length": 1500,
"cdna_start": 617,
"cdna_end": null,
"cdna_length": 3775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.975A>G",
"hgvs_p": "p.Ala325Ala",
"transcript": "NM_001077188.2",
"protein_id": "NP_001070656.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 645,
"cds_start": 975,
"cds_end": null,
"cds_length": 1938,
"cdna_start": 1366,
"cdna_end": null,
"cdna_length": 4537,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.975A>G",
"hgvs_p": "p.Ala325Ala",
"transcript": "ENST00000521489.5",
"protein_id": "ENSP00000429473.1",
"transcript_support_level": 5,
"aa_start": 325,
"aa_end": null,
"aa_length": 645,
"cds_start": 975,
"cds_end": null,
"cds_length": 1938,
"cdna_start": 1391,
"cdna_end": null,
"cdna_length": 2607,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.537A>G",
"hgvs_p": "p.Ala179Ala",
"transcript": "ENST00000640529.2",
"protein_id": "ENSP00000491722.2",
"transcript_support_level": 5,
"aa_start": 179,
"aa_end": null,
"aa_length": 499,
"cds_start": 537,
"cds_end": null,
"cds_length": 1500,
"cdna_start": 650,
"cdna_end": null,
"cdna_length": 3808,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.975A>G",
"hgvs_p": "p.Ala325Ala",
"transcript": "XM_047442618.1",
"protein_id": "XP_047298574.1",
"transcript_support_level": null,
"aa_start": 325,
"aa_end": null,
"aa_length": 616,
"cds_start": 975,
"cds_end": null,
"cds_length": 1851,
"cdna_start": 1366,
"cdna_end": null,
"cdna_length": 4450,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.537A>G",
"hgvs_p": "p.Ala179Ala",
"transcript": "XM_011531406.2",
"protein_id": "XP_011529708.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 499,
"cds_start": 537,
"cds_end": null,
"cds_length": 1500,
"cdna_start": 612,
"cdna_end": null,
"cdna_length": 3783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.537A>G",
"hgvs_p": "p.Ala179Ala",
"transcript": "XM_017029945.2",
"protein_id": "XP_016885434.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 499,
"cds_start": 537,
"cds_end": null,
"cds_length": 1500,
"cdna_start": 563,
"cdna_end": null,
"cdna_length": 3734,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.537A>G",
"hgvs_p": "p.Ala179Ala",
"transcript": "XM_017029946.2",
"protein_id": "XP_016885435.1",
"transcript_support_level": null,
"aa_start": 179,
"aa_end": null,
"aa_length": 470,
"cds_start": 537,
"cds_end": null,
"cds_length": 1413,
"cdna_start": 616,
"cdna_end": null,
"cdna_length": 3700,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.948-79374A>G",
"hgvs_p": null,
"transcript": "NM_001394074.1",
"protein_id": "NP_001381003.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 605,
"cds_start": -4,
"cds_end": null,
"cds_length": 1818,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4053,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.948-79374A>G",
"hgvs_p": null,
"transcript": "NM_147175.4",
"protein_id": "NP_671704.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 605,
"cds_start": -4,
"cds_end": null,
"cds_length": 1818,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4417,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.948-79374A>G",
"hgvs_p": null,
"transcript": "ENST00000370836.6",
"protein_id": "ENSP00000359873.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 605,
"cds_start": -4,
"cds_end": null,
"cds_length": 1818,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.510-79374A>G",
"hgvs_p": null,
"transcript": "XM_047442619.1",
"protein_id": "XP_047298575.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 459,
"cds_start": -4,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3697,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"dbsnp": "rs143752287",
"frequency_reference_population": 0.0019011907,
"hom_count_reference_population": 610,
"allele_count_reference_population": 2239,
"gnomad_exomes_af": 0.00106745,
"gnomad_genomes_af": 0.00994063,
"gnomad_exomes_ac": 1139,
"gnomad_genomes_ac": 1100,
"gnomad_exomes_homalt": 15,
"gnomad_genomes_homalt": 16,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.800000011920929,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.8,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.209,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BS1,BS2",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000370833.7",
"gene_symbol": "HS6ST2",
"hgnc_id": 19133,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "Unknown,XL",
"hgvs_c": "c.975A>G",
"hgvs_p": "p.Ala325Ala"
}
],
"clinvar_disease": "Paganini-Miozzo syndrome,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:2",
"phenotype_combined": "Paganini-Miozzo syndrome|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}