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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: 5-102413024-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=102413024&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PM2",
"PP3_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SLCO6A1",
"hgnc_id": 23613,
"hgvs_c": "c.1592G>C",
"hgvs_p": "p.Gly531Ala",
"inheritance_mode": "AR",
"pathogenic_score": 4,
"score": 4,
"transcript": "NM_173488.5",
"verdict": "Uncertain_significance"
}
],
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate",
"acmg_score": 4,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": 0.7367,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.21,
"chr": "5",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.9323254823684692,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 719,
"aa_ref": "G",
"aa_start": 531,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2682,
"cdna_start": 1749,
"cds_end": null,
"cds_length": 2160,
"cds_start": 1592,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_173488.5",
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"hgvs_c": "c.1592G>C",
"hgvs_p": "p.Gly531Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000506729.6",
"protein_coding": true,
"protein_id": "NP_775759.3",
"strand": false,
"transcript": "NM_173488.5",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 719,
"aa_ref": "G",
"aa_start": 531,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2682,
"cdna_start": 1749,
"cds_end": null,
"cds_length": 2160,
"cds_start": 1592,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000506729.6",
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"hgvs_c": "c.1592G>C",
"hgvs_p": "p.Gly531Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_173488.5",
"protein_coding": true,
"protein_id": "ENSP00000421339.1",
"strand": false,
"transcript": "ENST00000506729.6",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 719,
"aa_ref": "G",
"aa_start": 531,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2437,
"cdna_start": 1727,
"cds_end": null,
"cds_length": 2160,
"cds_start": 1592,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000379807.7",
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"hgvs_c": "c.1592G>C",
"hgvs_p": "p.Gly531Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000369135.3",
"strand": false,
"transcript": "ENST00000379807.7",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 657,
"aa_ref": "G",
"aa_start": 469,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2340,
"cdna_start": 1578,
"cds_end": null,
"cds_length": 1974,
"cds_start": 1406,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000389019.7",
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"hgvs_c": "c.1406G>C",
"hgvs_p": "p.Gly469Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000373671.3",
"strand": false,
"transcript": "ENST00000389019.7",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 719,
"aa_ref": "G",
"aa_start": 531,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2630,
"cdna_start": 1749,
"cds_end": null,
"cds_length": 2160,
"cds_start": 1592,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "NM_001289002.2",
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"hgvs_c": "c.1592G>C",
"hgvs_p": "p.Gly531Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001275931.1",
"strand": false,
"transcript": "NM_001289002.2",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 657,
"aa_ref": "G",
"aa_start": 469,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2496,
"cdna_start": 1563,
"cds_end": null,
"cds_length": 1974,
"cds_start": 1406,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_001289004.2",
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"hgvs_c": "c.1406G>C",
"hgvs_p": "p.Gly469Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001275933.1",
"strand": false,
"transcript": "NM_001289004.2",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 466,
"aa_ref": "G",
"aa_start": 278,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1871,
"cdna_start": 990,
"cds_end": null,
"cds_length": 1401,
"cds_start": 833,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "NM_001308014.2",
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"hgvs_c": "c.833G>C",
"hgvs_p": "p.Gly278Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001294943.1",
"strand": false,
"transcript": "NM_001308014.2",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 466,
"aa_ref": "G",
"aa_start": 278,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1611,
"cdna_start": 902,
"cds_end": null,
"cds_length": 1401,
"cds_start": 833,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000513675.1",
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"hgvs_c": "c.833G>C",
"hgvs_p": "p.Gly278Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000421990.1",
"strand": false,
"transcript": "ENST00000513675.1",
"transcript_support_level": 2
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 719,
"aa_ref": "G",
"aa_start": 531,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2514,
"cdna_start": 1749,
"cds_end": null,
"cds_length": 2160,
"cds_start": 1592,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_005271874.4",
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"hgvs_c": "c.1592G>C",
"hgvs_p": "p.Gly531Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_005271931.1",
"strand": false,
"transcript": "XM_005271874.4",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 684,
"aa_ref": "G",
"aa_start": 496,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2577,
"cdna_start": 1644,
"cds_end": null,
"cds_length": 2055,
"cds_start": 1487,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_011543147.3",
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"hgvs_c": "c.1487G>C",
"hgvs_p": "p.Gly496Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011541449.1",
"strand": false,
"transcript": "XM_011543147.3",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 657,
"aa_ref": "G",
"aa_start": 469,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2444,
"cdna_start": 1563,
"cds_end": null,
"cds_length": 1974,
"cds_start": 1406,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_047416703.1",
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"hgvs_c": "c.1406G>C",
"hgvs_p": "p.Gly469Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047272659.1",
"strand": false,
"transcript": "XM_047416703.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 640,
"aa_ref": "G",
"aa_start": 452,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2445,
"cdna_start": 1512,
"cds_end": null,
"cds_length": 1923,
"cds_start": 1355,
"consequences": [
"missense_variant"
],
"exon_count": 14,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "XM_011543148.3",
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"hgvs_c": "c.1355G>C",
"hgvs_p": "p.Gly452Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011541450.1",
"strand": false,
"transcript": "XM_011543148.3",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 476,
"aa_ref": "G",
"aa_start": 288,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1846,
"cdna_start": 913,
"cds_end": null,
"cds_length": 1431,
"cds_start": 863,
"consequences": [
"missense_variant"
],
"exon_count": 13,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "XM_011543150.2",
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"hgvs_c": "c.863G>C",
"hgvs_p": "p.Gly288Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011541452.1",
"strand": false,
"transcript": "XM_011543150.2",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": null,
"effect": "missense_variant",
"frequency_reference_population": 7.1883284e-7,
"gene_hgnc_id": 23613,
"gene_symbol": "SLCO6A1",
"gnomad_exomes_ac": 1,
"gnomad_exomes_af": 7.18833e-7,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.245,
"pos": 102413024,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.215,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_173488.5"
}
]
}