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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: 5-151343594-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=151343594&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 151343594,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000335244.9",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A2",
"gene_hgnc_id": 18762,
"hgvs_c": "c.260G>T",
"hgvs_p": "p.Gly87Val",
"transcript": "NM_181776.3",
"protein_id": "NP_861441.2",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 483,
"cds_start": 260,
"cds_end": null,
"cds_length": 1452,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 3396,
"mane_select": "ENST00000335244.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A2",
"gene_hgnc_id": 18762,
"hgvs_c": "c.260G>T",
"hgvs_p": "p.Gly87Val",
"transcript": "ENST00000335244.9",
"protein_id": "ENSP00000334223.4",
"transcript_support_level": 1,
"aa_start": 87,
"aa_end": null,
"aa_length": 483,
"cds_start": 260,
"cds_end": null,
"cds_length": 1452,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 3396,
"mane_select": "NM_181776.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A2",
"gene_hgnc_id": 18762,
"hgvs_c": "c.260G>T",
"hgvs_p": "p.Gly87Val",
"transcript": "ENST00000521967.1",
"protein_id": "ENSP00000430535.1",
"transcript_support_level": 1,
"aa_start": 87,
"aa_end": null,
"aa_length": 395,
"cds_start": 260,
"cds_end": null,
"cds_length": 1188,
"cdna_start": 390,
"cdna_end": null,
"cdna_length": 1471,
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A2",
"gene_hgnc_id": 18762,
"hgvs_c": "n.260G>T",
"hgvs_p": null,
"transcript": "ENST00000518280.5",
"protein_id": "ENSP00000428453.1",
"transcript_support_level": 1,
"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": 2059,
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A2",
"gene_hgnc_id": 18762,
"hgvs_c": "n.260G>T",
"hgvs_p": null,
"transcript": "ENST00000518617.5",
"protein_id": "ENSP00000430149.1",
"transcript_support_level": 1,
"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": 2156,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A2",
"gene_hgnc_id": 18762,
"hgvs_c": "c.260G>T",
"hgvs_p": "p.Gly87Val",
"transcript": "XM_005268377.5",
"protein_id": "XP_005268434.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 393,
"cds_start": 260,
"cds_end": null,
"cds_length": 1182,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 1561,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "G",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A2",
"gene_hgnc_id": 18762,
"hgvs_c": "c.260G>T",
"hgvs_p": "p.Gly87Val",
"transcript": "XM_017009083.3",
"protein_id": "XP_016864572.1",
"transcript_support_level": null,
"aa_start": 87,
"aa_end": null,
"aa_length": 310,
"cds_start": 260,
"cds_end": null,
"cds_length": 933,
"cdna_start": 359,
"cdna_end": null,
"cdna_length": 1039,
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC36A2",
"gene_hgnc_id": 18762,
"hgvs_c": "n.356G>T",
"hgvs_p": null,
"transcript": "ENST00000522829.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 1068,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000297368",
"gene_hgnc_id": null,
"hgvs_c": "n.532-997C>A",
"hgvs_p": null,
"transcript": "ENST00000747508.1",
"protein_id": null,
"transcript_support_level": null,
"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": 934,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SLC36A2",
"gene_hgnc_id": 18762,
"dbsnp": "rs77010315",
"frequency_reference_population": 0.01052269,
"hom_count_reference_population": 119,
"allele_count_reference_population": 16982,
"gnomad_exomes_af": 0.0107242,
"gnomad_genomes_af": 0.00858589,
"gnomad_exomes_ac": 15676,
"gnomad_genomes_ac": 1306,
"gnomad_exomes_homalt": 105,
"gnomad_genomes_homalt": 14,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.01255345344543457,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.432,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7122,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.29,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.177,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0,
"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": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000335244.9",
"gene_symbol": "SLC36A2",
"hgnc_id": 18762,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,SD",
"hgvs_c": "c.260G>T",
"hgvs_p": "p.Gly87Val"
},
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000747508.1",
"gene_symbol": "ENSG00000297368",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.532-997C>A",
"hgvs_p": null
}
],
"clinvar_disease": "Hyperglycinuria,Iminoglycinuria,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 B:3",
"phenotype_combined": "Hyperglycinuria|not provided|Iminoglycinuria|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}