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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: 3-98800650-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=98800650&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"missense_variant"
],
"gene_symbol": "DCBLD2",
"hgnc_id": 24627,
"hgvs_c": "c.1787G>T",
"hgvs_p": "p.Arg596Leu",
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "NM_080927.4",
"verdict": "Uncertain_significance"
},
{
"benign_score": 0,
"criteria": [
"PM2"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ST3GAL6",
"hgnc_id": 18080,
"hgvs_c": "c.*32-899C>A",
"hgvs_p": null,
"inheritance_mode": "AR",
"pathogenic_score": 2,
"score": 2,
"transcript": "ENST00000881500.1",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_score": 2,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.1368,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.12,
"chr": "3",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Uncertain_significance",
"computational_score_selected": 0.5363917350769043,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 775,
"aa_ref": "R",
"aa_start": 596,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6128,
"cdna_start": 2156,
"cds_end": null,
"cds_length": 2328,
"cds_start": 1787,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "NM_080927.4",
"gene_hgnc_id": 24627,
"gene_symbol": "DCBLD2",
"hgvs_c": "c.1787G>T",
"hgvs_p": "p.Arg596Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000326840.11",
"protein_coding": true,
"protein_id": "NP_563615.3",
"strand": false,
"transcript": "NM_080927.4",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 775,
"aa_ref": "R",
"aa_start": 596,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 6128,
"cdna_start": 2156,
"cds_end": null,
"cds_length": 2328,
"cds_start": 1787,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000326840.11",
"gene_hgnc_id": 24627,
"gene_symbol": "DCBLD2",
"hgvs_c": "c.1787G>T",
"hgvs_p": "p.Arg596Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_080927.4",
"protein_coding": true,
"protein_id": "ENSP00000321573.6",
"strand": false,
"transcript": "ENST00000326840.11",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 789,
"aa_ref": "R",
"aa_start": 610,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3959,
"cdna_start": 1829,
"cds_end": null,
"cds_length": 2370,
"cds_start": 1829,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000326857.9",
"gene_hgnc_id": 24627,
"gene_symbol": "DCBLD2",
"hgvs_c": "c.1829G>T",
"hgvs_p": "p.Arg610Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000321646.9",
"strand": false,
"transcript": "ENST00000326857.9",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 729,
"aa_ref": "R",
"aa_start": 550,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3625,
"cdna_start": 2000,
"cds_end": null,
"cds_length": 2190,
"cds_start": 1649,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000946562.1",
"gene_hgnc_id": 24627,
"gene_symbol": "DCBLD2",
"hgvs_c": "c.1649G>T",
"hgvs_p": "p.Arg550Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000616621.1",
"strand": false,
"transcript": "ENST00000946562.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 706,
"aa_ref": "R",
"aa_start": 527,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5872,
"cdna_start": 1949,
"cds_end": null,
"cds_length": 2121,
"cds_start": 1580,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000926049.1",
"gene_hgnc_id": 24627,
"gene_symbol": "DCBLD2",
"hgvs_c": "c.1580G>T",
"hgvs_p": "p.Arg527Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596108.1",
"strand": false,
"transcript": "ENST00000926049.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 699,
"aa_ref": "R",
"aa_start": 520,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5907,
"cdna_start": 1961,
"cds_end": null,
"cds_length": 2100,
"cds_start": 1559,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "ENST00000881287.1",
"gene_hgnc_id": 24627,
"gene_symbol": "DCBLD2",
"hgvs_c": "c.1559G>T",
"hgvs_p": "p.Arg520Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551346.1",
"strand": false,
"transcript": "ENST00000881287.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 653,
"aa_ref": "R",
"aa_start": 474,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5770,
"cdna_start": 1824,
"cds_end": null,
"cds_length": 1962,
"cds_start": 1421,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 13,
"exon_rank_end": null,
"feature": "ENST00000926048.1",
"gene_hgnc_id": 24627,
"gene_symbol": "DCBLD2",
"hgvs_c": "c.1421G>T",
"hgvs_p": "p.Arg474Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596107.1",
"strand": false,
"transcript": "ENST00000926048.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 630,
"aa_ref": "R",
"aa_start": 451,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5631,
"cdna_start": 1685,
"cds_end": null,
"cds_length": 1893,
"cds_start": 1352,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000926050.1",
"gene_hgnc_id": 24627,
"gene_symbol": "DCBLD2",
"hgvs_c": "c.1352G>T",
"hgvs_p": "p.Arg451Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000596109.1",
"strand": false,
"transcript": "ENST00000926050.1",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 699,
"aa_ref": "R",
"aa_start": 520,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5900,
"cdna_start": 1928,
"cds_end": null,
"cds_length": 2100,
"cds_start": 1559,
"consequences": [
"missense_variant"
],
"exon_count": 15,
"exon_rank": 14,
"exon_rank_end": null,
"feature": "XM_011512419.3",
"gene_hgnc_id": 24627,
"gene_symbol": "DCBLD2",
"hgvs_c": "c.1559G>T",
"hgvs_p": "p.Arg520Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011510721.1",
"strand": false,
"transcript": "XM_011512419.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 669,
"aa_ref": "R",
"aa_start": 490,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 16328,
"cdna_start": 12356,
"cds_end": null,
"cds_length": 2010,
"cds_start": 1469,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "XM_024453348.2",
"gene_hgnc_id": 24627,
"gene_symbol": "DCBLD2",
"hgvs_c": "c.1469G>T",
"hgvs_p": "p.Arg490Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024309116.1",
"strand": false,
"transcript": "XM_024453348.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 331,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2463,
"cdna_start": null,
"cds_end": null,
"cds_length": 996,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000881500.1",
"gene_hgnc_id": 18080,
"gene_symbol": "ST3GAL6",
"hgvs_c": "c.*32-899C>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000551559.1",
"strand": true,
"transcript": "ENST00000881500.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 331,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1561,
"cdna_start": null,
"cds_end": null,
"cds_length": 996,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 11,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000946763.1",
"gene_hgnc_id": 18080,
"gene_symbol": "ST3GAL6",
"hgvs_c": "c.*31+6858C>A",
"hgvs_p": null,
"intron_rank": 10,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000616822.1",
"strand": true,
"transcript": "ENST00000946763.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 516,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000496736.1",
"gene_hgnc_id": 24627,
"gene_symbol": "DCBLD2",
"hgvs_c": "n.439G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000496736.1",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 659,
"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": "ENST00000491912.1",
"gene_hgnc_id": 18080,
"gene_symbol": "ST3GAL6",
"hgvs_c": "n.254-772C>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": "ENST00000491912.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs199755908",
"effect": "missense_variant",
"frequency_reference_population": 0.000006573066,
"gene_hgnc_id": 24627,
"gene_symbol": "DCBLD2",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000657307,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.4,
"pos": 98800650,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.143,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_080927.4"
}
]
}