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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: 12-64743245-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=12&pos=64743245&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "12",
"pos": 64743245,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "ENST00000258145.8",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNS",
"gene_hgnc_id": 4422,
"hgvs_c": "c.688G>A",
"hgvs_p": "p.Ala230Thr",
"transcript": "NM_002076.4",
"protein_id": "NP_002067.1",
"transcript_support_level": null,
"aa_start": 230,
"aa_end": null,
"aa_length": 552,
"cds_start": 688,
"cds_end": null,
"cds_length": 1659,
"cdna_start": 818,
"cdna_end": null,
"cdna_length": 5081,
"mane_select": "ENST00000258145.8",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNS",
"gene_hgnc_id": 4422,
"hgvs_c": "c.688G>A",
"hgvs_p": "p.Ala230Thr",
"transcript": "ENST00000258145.8",
"protein_id": "ENSP00000258145.3",
"transcript_support_level": 1,
"aa_start": 230,
"aa_end": null,
"aa_length": 552,
"cds_start": 688,
"cds_end": null,
"cds_length": 1659,
"cdna_start": 818,
"cdna_end": null,
"cdna_length": 5081,
"mane_select": "NM_002076.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNS",
"gene_hgnc_id": 4422,
"hgvs_c": "c.520G>A",
"hgvs_p": "p.Ala174Thr",
"transcript": "ENST00000418919.6",
"protein_id": "ENSP00000413130.2",
"transcript_support_level": 1,
"aa_start": 174,
"aa_end": null,
"aa_length": 496,
"cds_start": 520,
"cds_end": null,
"cds_length": 1491,
"cdna_start": 610,
"cdna_end": null,
"cdna_length": 4877,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNS",
"gene_hgnc_id": 4422,
"hgvs_c": "c.784G>A",
"hgvs_p": "p.Ala262Thr",
"transcript": "ENST00000543646.5",
"protein_id": "ENSP00000438497.1",
"transcript_support_level": 2,
"aa_start": 262,
"aa_end": null,
"aa_length": 584,
"cds_start": 784,
"cds_end": null,
"cds_length": 1755,
"cdna_start": 914,
"cdna_end": null,
"cdna_length": 2164,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNS",
"gene_hgnc_id": 4422,
"hgvs_c": "c.628G>A",
"hgvs_p": "p.Ala210Thr",
"transcript": "ENST00000542058.5",
"protein_id": "ENSP00000444819.1",
"transcript_support_level": 2,
"aa_start": 210,
"aa_end": null,
"aa_length": 532,
"cds_start": 628,
"cds_end": null,
"cds_length": 1599,
"cdna_start": 783,
"cdna_end": null,
"cdna_length": 2020,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNS",
"gene_hgnc_id": 4422,
"hgvs_c": "c.145G>A",
"hgvs_p": "p.Ala49Thr",
"transcript": "ENST00000540196.5",
"protein_id": "ENSP00000437782.1",
"transcript_support_level": 5,
"aa_start": 49,
"aa_end": null,
"aa_length": 301,
"cds_start": 145,
"cds_end": null,
"cds_length": 906,
"cdna_start": 146,
"cdna_end": null,
"cdna_length": 907,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNS",
"gene_hgnc_id": 4422,
"hgvs_c": "c.460G>A",
"hgvs_p": "p.Ala154Thr",
"transcript": "ENST00000545273.1",
"protein_id": "ENSP00000445055.1",
"transcript_support_level": 5,
"aa_start": 154,
"aa_end": null,
"aa_length": 246,
"cds_start": 460,
"cds_end": null,
"cds_length": 743,
"cdna_start": 623,
"cdna_end": null,
"cdna_length": 906,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNS",
"gene_hgnc_id": 4422,
"hgvs_c": "n.743G>A",
"hgvs_p": null,
"transcript": "ENST00000541781.5",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1846,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "GNS",
"gene_hgnc_id": 4422,
"dbsnp": "rs140270805",
"frequency_reference_population": 0.000024813095,
"hom_count_reference_population": 0,
"allele_count_reference_population": 40,
"gnomad_exomes_af": 0.0000239736,
"gnomad_genomes_af": 0.0000328709,
"gnomad_exomes_ac": 35,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.47228068113327026,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.635,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3003,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.05,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.263,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000258145.8",
"gene_symbol": "GNS",
"hgnc_id": 4422,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.688G>A",
"hgvs_p": "p.Ala230Thr"
}
],
"clinvar_disease": " MPS-III-D,Mucopolysaccharidosis,Sanfilippo syndrome",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Mucopolysaccharidosis, MPS-III-D|Sanfilippo syndrome",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}