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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-132628419-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=132628419&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 132628419,
"ref": "G",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001077188.2",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1742C>A",
"hgvs_p": "p.Pro581Gln",
"transcript": "NM_001394073.1",
"protein_id": "NP_001381002.1",
"transcript_support_level": null,
"aa_start": 581,
"aa_end": null,
"aa_length": 645,
"cds_start": 1742,
"cds_end": null,
"cds_length": 1938,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000370833.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394073.1"
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1742C>A",
"hgvs_p": "p.Pro581Gln",
"transcript": "ENST00000370833.7",
"protein_id": "ENSP00000359870.3",
"transcript_support_level": 5,
"aa_start": 581,
"aa_end": null,
"aa_length": 645,
"cds_start": 1742,
"cds_end": null,
"cds_length": 1938,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001394073.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370833.7"
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1304C>A",
"hgvs_p": "p.Pro435Gln",
"transcript": "ENST00000406696.5",
"protein_id": "ENSP00000384013.5",
"transcript_support_level": 1,
"aa_start": 435,
"aa_end": null,
"aa_length": 499,
"cds_start": 1304,
"cds_end": null,
"cds_length": 1500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000406696.5"
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1742C>A",
"hgvs_p": "p.Pro581Gln",
"transcript": "NM_001077188.2",
"protein_id": "NP_001070656.1",
"transcript_support_level": null,
"aa_start": 581,
"aa_end": null,
"aa_length": 645,
"cds_start": 1742,
"cds_end": null,
"cds_length": 1938,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001077188.2"
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1742C>A",
"hgvs_p": "p.Pro581Gln",
"transcript": "ENST00000521489.5",
"protein_id": "ENSP00000429473.1",
"transcript_support_level": 5,
"aa_start": 581,
"aa_end": null,
"aa_length": 645,
"cds_start": 1742,
"cds_end": null,
"cds_length": 1938,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000521489.5"
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1622C>A",
"hgvs_p": "p.Pro541Gln",
"transcript": "NM_001394074.1",
"protein_id": "NP_001381003.1",
"transcript_support_level": null,
"aa_start": 541,
"aa_end": null,
"aa_length": 605,
"cds_start": 1622,
"cds_end": null,
"cds_length": 1818,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001394074.1"
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1622C>A",
"hgvs_p": "p.Pro541Gln",
"transcript": "NM_147175.4",
"protein_id": "NP_671704.3",
"transcript_support_level": null,
"aa_start": 541,
"aa_end": null,
"aa_length": 605,
"cds_start": 1622,
"cds_end": null,
"cds_length": 1818,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_147175.4"
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1622C>A",
"hgvs_p": "p.Pro541Gln",
"transcript": "ENST00000370836.6",
"protein_id": "ENSP00000359873.2",
"transcript_support_level": 2,
"aa_start": 541,
"aa_end": null,
"aa_length": 605,
"cds_start": 1622,
"cds_end": null,
"cds_length": 1818,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370836.6"
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1304C>A",
"hgvs_p": "p.Pro435Gln",
"transcript": "ENST00000640529.2",
"protein_id": "ENSP00000491722.2",
"transcript_support_level": 5,
"aa_start": 435,
"aa_end": null,
"aa_length": 499,
"cds_start": 1304,
"cds_end": null,
"cds_length": 1500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000640529.2"
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1655C>A",
"hgvs_p": "p.Pro552Gln",
"transcript": "XM_047442618.1",
"protein_id": "XP_047298574.1",
"transcript_support_level": null,
"aa_start": 552,
"aa_end": null,
"aa_length": 616,
"cds_start": 1655,
"cds_end": null,
"cds_length": 1851,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442618.1"
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1304C>A",
"hgvs_p": "p.Pro435Gln",
"transcript": "XM_011531406.2",
"protein_id": "XP_011529708.1",
"transcript_support_level": null,
"aa_start": 435,
"aa_end": null,
"aa_length": 499,
"cds_start": 1304,
"cds_end": null,
"cds_length": 1500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011531406.2"
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1304C>A",
"hgvs_p": "p.Pro435Gln",
"transcript": "XM_017029945.2",
"protein_id": "XP_016885434.1",
"transcript_support_level": null,
"aa_start": 435,
"aa_end": null,
"aa_length": 499,
"cds_start": 1304,
"cds_end": null,
"cds_length": 1500,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029945.2"
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1217C>A",
"hgvs_p": "p.Pro406Gln",
"transcript": "XM_017029946.2",
"protein_id": "XP_016885435.1",
"transcript_support_level": null,
"aa_start": 406,
"aa_end": null,
"aa_length": 470,
"cds_start": 1217,
"cds_end": null,
"cds_length": 1413,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017029946.2"
},
{
"aa_ref": "P",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"hgvs_c": "c.1184C>A",
"hgvs_p": "p.Pro395Gln",
"transcript": "XM_047442619.1",
"protein_id": "XP_047298575.1",
"transcript_support_level": null,
"aa_start": 395,
"aa_end": null,
"aa_length": 459,
"cds_start": 1184,
"cds_end": null,
"cds_length": 1380,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047442619.1"
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000296977",
"gene_hgnc_id": null,
"hgvs_c": "n.352-5384G>T",
"hgvs_p": null,
"transcript": "ENST00000743982.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000743982.1"
}
],
"gene_symbol": "HS6ST2",
"gene_hgnc_id": 19133,
"dbsnp": "rs367714566",
"frequency_reference_population": 0.00001081269,
"hom_count_reference_population": 3,
"allele_count_reference_population": 13,
"gnomad_exomes_af": 0.0000027488,
"gnomad_genomes_af": 0.0000901681,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.05521202087402344,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.187,
"revel_prediction": "Benign",
"alphamissense_score": 0.0635,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.62,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.991,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001077188.2",
"gene_symbol": "HS6ST2",
"hgnc_id": 19133,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,XL",
"hgvs_c": "c.1742C>A",
"hgvs_p": "p.Pro581Gln"
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000743982.1",
"gene_symbol": "ENSG00000296977",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.352-5384G>T",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}