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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: 2-189563874-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=189563874&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 1,
"criteria": [
"BP4"
],
"effects": [
"missense_variant"
],
"gene_symbol": "SLC40A1",
"hgnc_id": 10909,
"hgvs_c": "c.1112G>A",
"hgvs_p": "p.Arg371Gln",
"inheritance_mode": "AD,AR",
"pathogenic_score": 0,
"score": -1,
"transcript": "NM_014585.6",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_score": -1,
"allele_count_reference_population": 80,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.095,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Uncertain_significance",
"bayesdelnoaf_score": 0,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Hemochromatosis type 4,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3 O:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.34136223793029785,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 571,
"aa_ref": "R",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3330,
"cdna_start": 1438,
"cds_end": null,
"cds_length": 1716,
"cds_start": 1112,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_014585.6",
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"hgvs_c": "c.1112G>A",
"hgvs_p": "p.Arg371Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000261024.7",
"protein_coding": true,
"protein_id": "NP_055400.1",
"strand": false,
"transcript": "NM_014585.6",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 571,
"aa_ref": "R",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3330,
"cdna_start": 1438,
"cds_end": null,
"cds_length": 1716,
"cds_start": 1112,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000261024.7",
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"hgvs_c": "c.1112G>A",
"hgvs_p": "p.Arg371Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_014585.6",
"protein_coding": true,
"protein_id": "ENSP00000261024.3",
"strand": false,
"transcript": "ENST00000261024.7",
"transcript_support_level": 1
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 571,
"aa_ref": "R",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3235,
"cdna_start": 1346,
"cds_end": null,
"cds_length": 1716,
"cds_start": 1112,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000852923.1",
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"hgvs_c": "c.1112G>A",
"hgvs_p": "p.Arg371Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522982.1",
"strand": false,
"transcript": "ENST00000852923.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 571,
"aa_ref": "R",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3158,
"cdna_start": 1269,
"cds_end": null,
"cds_length": 1716,
"cds_start": 1112,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000852924.1",
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"hgvs_c": "c.1112G>A",
"hgvs_p": "p.Arg371Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522983.1",
"strand": false,
"transcript": "ENST00000852924.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 571,
"aa_ref": "R",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3184,
"cdna_start": 1295,
"cds_end": null,
"cds_length": 1716,
"cds_start": 1112,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000852925.1",
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"hgvs_c": "c.1112G>A",
"hgvs_p": "p.Arg371Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522984.1",
"strand": false,
"transcript": "ENST00000852925.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 571,
"aa_ref": "R",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2073,
"cdna_start": 1369,
"cds_end": null,
"cds_length": 1716,
"cds_start": 1112,
"consequences": [
"missense_variant"
],
"exon_count": 10,
"exon_rank": 9,
"exon_rank_end": null,
"feature": "ENST00000852926.1",
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"hgvs_c": "c.1112G>A",
"hgvs_p": "p.Arg371Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522985.1",
"strand": false,
"transcript": "ENST00000852926.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 571,
"aa_ref": "R",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3204,
"cdna_start": 1312,
"cds_end": null,
"cds_length": 1716,
"cds_start": 1112,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000852927.1",
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"hgvs_c": "c.1112G>A",
"hgvs_p": "p.Arg371Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522986.1",
"strand": false,
"transcript": "ENST00000852927.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 571,
"aa_ref": "R",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2570,
"cdna_start": 1332,
"cds_end": null,
"cds_length": 1716,
"cds_start": 1112,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000852928.1",
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"hgvs_c": "c.1112G>A",
"hgvs_p": "p.Arg371Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522987.1",
"strand": false,
"transcript": "ENST00000852928.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 571,
"aa_ref": "R",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3216,
"cdna_start": 1328,
"cds_end": null,
"cds_length": 1716,
"cds_start": 1112,
"consequences": [
"missense_variant"
],
"exon_count": 9,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000972158.1",
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"hgvs_c": "c.1112G>A",
"hgvs_p": "p.Arg371Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000642217.1",
"strand": false,
"transcript": "ENST00000972158.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 571,
"aa_ref": "R",
"aa_start": 371,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3391,
"cdna_start": 1447,
"cds_end": null,
"cds_length": 1716,
"cds_start": 1112,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000972159.1",
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"hgvs_c": "c.1112G>A",
"hgvs_p": "p.Arg371Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000642218.1",
"strand": false,
"transcript": "ENST00000972159.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 569,
"aa_ref": "R",
"aa_start": 369,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3320,
"cdna_start": 1430,
"cds_end": null,
"cds_length": 1710,
"cds_start": 1106,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000972160.1",
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"hgvs_c": "c.1106G>A",
"hgvs_p": "p.Arg369Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000642219.1",
"strand": false,
"transcript": "ENST00000972160.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 479,
"aa_ref": "R",
"aa_start": 279,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3052,
"cdna_start": 1162,
"cds_end": null,
"cds_length": 1440,
"cds_start": 836,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "ENST00000852929.1",
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"hgvs_c": "c.836G>A",
"hgvs_p": "p.Arg279Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000522988.1",
"strand": false,
"transcript": "ENST00000852929.1",
"transcript_support_level": null
},
{
"aa_alt": "Q",
"aa_end": null,
"aa_length": 531,
"aa_ref": "R",
"aa_start": 331,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3077,
"cdna_start": 1185,
"cds_end": null,
"cds_length": 1596,
"cds_start": 992,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "XM_047444066.1",
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"hgvs_c": "c.992G>A",
"hgvs_p": "p.Arg331Gln",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047300022.1",
"strand": false,
"transcript": "XM_047444066.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs387907378",
"effect": "missense_variant",
"frequency_reference_population": 0.000049564696,
"gene_hgnc_id": 10909,
"gene_symbol": "SLC40A1",
"gnomad_exomes_ac": 77,
"gnomad_exomes_af": 0.0000526717,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197153,
"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": "Uncertain significance",
"phenotype_combined": "not provided|Hemochromatosis type 4",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.025,
"pos": 189563874,
"ref": "C",
"revel_prediction": "Uncertain_significance",
"revel_score": 0.464,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.009999999776482582,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.01,
"transcript": "NM_014585.6"
}
]
}