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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-132628318-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=132628318&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "HS6ST2",
"hgnc_id": 19133,
"hgvs_c": "c.1843C>T",
"hgvs_p": "p.Arg615Trp",
"inheritance_mode": "Unknown,XL",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_001077188.2",
"verdict": "Likely_benign"
},
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000296977",
"hgnc_id": null,
"hgvs_c": "n.352-5485G>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -6,
"transcript": "ENST00000743982.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS2",
"acmg_score": -6,
"allele_count_reference_population": 31,
"alphamissense_prediction": null,
"alphamissense_score": 0.1121,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.49,
"chr": "X",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.07105851173400879,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 645,
"aa_ref": "R",
"aa_start": 615,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4173,
"cdna_start": 1870,
"cds_end": null,
"cds_length": 1938,
"cds_start": 1843,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "NM_001394073.1",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1843C>T",
"hgvs_p": "p.Arg615Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000370833.7",
"protein_coding": true,
"protein_id": "NP_001381002.1",
"strand": false,
"transcript": "NM_001394073.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 645,
"aa_ref": "R",
"aa_start": 615,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4173,
"cdna_start": 1870,
"cds_end": null,
"cds_length": 1938,
"cds_start": 1843,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000370833.7",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1843C>T",
"hgvs_p": "p.Arg615Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001394073.1",
"protein_coding": true,
"protein_id": "ENSP00000359870.3",
"strand": false,
"transcript": "ENST00000370833.7",
"transcript_support_level": 5
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 499,
"aa_ref": "R",
"aa_start": 469,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3775,
"cdna_start": 1485,
"cds_end": null,
"cds_length": 1500,
"cds_start": 1405,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000406696.5",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1405C>T",
"hgvs_p": "p.Arg469Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000384013.5",
"strand": false,
"transcript": "ENST00000406696.5",
"transcript_support_level": 1
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 645,
"aa_ref": "R",
"aa_start": 615,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4537,
"cdna_start": 2234,
"cds_end": null,
"cds_length": 1938,
"cds_start": 1843,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001077188.2",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1843C>T",
"hgvs_p": "p.Arg615Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001070656.1",
"strand": false,
"transcript": "NM_001077188.2",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 645,
"aa_ref": "R",
"aa_start": 615,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2607,
"cdna_start": 2259,
"cds_end": null,
"cds_length": 1938,
"cds_start": 1843,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000521489.5",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1843C>T",
"hgvs_p": "p.Arg615Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000429473.1",
"strand": false,
"transcript": "ENST00000521489.5",
"transcript_support_level": 5
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 605,
"aa_ref": "R",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4053,
"cdna_start": 1750,
"cds_end": null,
"cds_length": 1818,
"cds_start": 1723,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001394074.1",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1723C>T",
"hgvs_p": "p.Arg575Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001381003.1",
"strand": false,
"transcript": "NM_001394074.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 605,
"aa_ref": "R",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4417,
"cdna_start": 2114,
"cds_end": null,
"cds_length": 1818,
"cds_start": 1723,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_147175.4",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1723C>T",
"hgvs_p": "p.Arg575Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_671704.3",
"strand": false,
"transcript": "NM_147175.4",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 605,
"aa_ref": "R",
"aa_start": 575,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4441,
"cdna_start": 2139,
"cds_end": null,
"cds_length": 1818,
"cds_start": 1723,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000370836.6",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1723C>T",
"hgvs_p": "p.Arg575Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000359873.2",
"strand": false,
"transcript": "ENST00000370836.6",
"transcript_support_level": 2
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 499,
"aa_ref": "R",
"aa_start": 469,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3808,
"cdna_start": 1518,
"cds_end": null,
"cds_length": 1500,
"cds_start": 1405,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000640529.2",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1405C>T",
"hgvs_p": "p.Arg469Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000491722.2",
"strand": false,
"transcript": "ENST00000640529.2",
"transcript_support_level": 5
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 616,
"aa_ref": "R",
"aa_start": 586,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4450,
"cdna_start": 2147,
"cds_end": null,
"cds_length": 1851,
"cds_start": 1756,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_047442618.1",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1756C>T",
"hgvs_p": "p.Arg586Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047298574.1",
"strand": false,
"transcript": "XM_047442618.1",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 499,
"aa_ref": "R",
"aa_start": 469,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3783,
"cdna_start": 1480,
"cds_end": null,
"cds_length": 1500,
"cds_start": 1405,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_011531406.2",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1405C>T",
"hgvs_p": "p.Arg469Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011529708.1",
"strand": false,
"transcript": "XM_011531406.2",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 499,
"aa_ref": "R",
"aa_start": 469,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3734,
"cdna_start": 1431,
"cds_end": null,
"cds_length": 1500,
"cds_start": 1405,
"consequences": [
"missense_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_017029945.2",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1405C>T",
"hgvs_p": "p.Arg469Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016885434.1",
"strand": false,
"transcript": "XM_017029945.2",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 470,
"aa_ref": "R",
"aa_start": 440,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3700,
"cdna_start": 1397,
"cds_end": null,
"cds_length": 1413,
"cds_start": 1318,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "XM_017029946.2",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1318C>T",
"hgvs_p": "p.Arg440Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016885435.1",
"strand": false,
"transcript": "XM_017029946.2",
"transcript_support_level": null
},
{
"aa_alt": "W",
"aa_end": null,
"aa_length": 459,
"aa_ref": "R",
"aa_start": 429,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3697,
"cdna_start": 1394,
"cds_end": null,
"cds_length": 1380,
"cds_start": 1285,
"consequences": [
"missense_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047442619.1",
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"hgvs_c": "c.1285C>T",
"hgvs_p": "p.Arg429Trp",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047298575.1",
"strand": false,
"transcript": "XM_047442619.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 827,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000743982.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000296977",
"hgvs_c": "n.352-5485G>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000743982.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs374128505",
"effect": "missense_variant",
"frequency_reference_population": 0.000026589609,
"gene_hgnc_id": 19133,
"gene_symbol": "HS6ST2",
"gnomad_exomes_ac": 28,
"gnomad_exomes_af": 0.0000265427,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000270351,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 8,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 0.368,
"pos": 132628318,
"ref": "G",
"revel_prediction": "Benign",
"revel_score": 0.134,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001077188.2"
}
]
}