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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: 5-151505584-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=151505584&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 151505584,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001447.3",
"consequences": [
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.13031G>A",
"hgvs_p": "p.Cys4344Tyr",
"transcript": "NM_001447.3",
"protein_id": "NP_001438.1",
"transcript_support_level": null,
"aa_start": 4344,
"aa_end": null,
"aa_length": 4349,
"cds_start": 13031,
"cds_end": null,
"cds_length": 13050,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000261800.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001447.3"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.13031G>A",
"hgvs_p": "p.Cys4344Tyr",
"transcript": "ENST00000261800.6",
"protein_id": "ENSP00000261800.5",
"transcript_support_level": 1,
"aa_start": 4344,
"aa_end": null,
"aa_length": 4349,
"cds_start": 13031,
"cds_end": null,
"cds_length": 13050,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001447.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000261800.6"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.3347G>A",
"hgvs_p": "p.Cys1116Tyr",
"transcript": "ENST00000520200.5",
"protein_id": "ENSP00000429678.1",
"transcript_support_level": 1,
"aa_start": 1116,
"aa_end": null,
"aa_length": 1121,
"cds_start": 3347,
"cds_end": null,
"cds_length": 3366,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000520200.5"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.13031G>A",
"hgvs_p": "p.Cys4344Tyr",
"transcript": "XM_011537600.3",
"protein_id": "XP_011535902.1",
"transcript_support_level": null,
"aa_start": 4344,
"aa_end": null,
"aa_length": 4349,
"cds_start": 13031,
"cds_end": null,
"cds_length": 13050,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011537600.3"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.13031G>A",
"hgvs_p": "p.Cys4344Tyr",
"transcript": "XM_011537603.2",
"protein_id": "XP_011535905.1",
"transcript_support_level": null,
"aa_start": 4344,
"aa_end": null,
"aa_length": 4349,
"cds_start": 13031,
"cds_end": null,
"cds_length": 13050,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011537603.2"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 26,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.13031G>A",
"hgvs_p": "p.Cys4344Tyr",
"transcript": "XM_017009224.2",
"protein_id": "XP_016864713.1",
"transcript_support_level": null,
"aa_start": 4344,
"aa_end": null,
"aa_length": 4349,
"cds_start": 13031,
"cds_end": null,
"cds_length": 13050,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009224.2"
},
{
"aa_ref": "C",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"hgvs_c": "c.13031G>A",
"hgvs_p": "p.Cys4344Tyr",
"transcript": "XM_017009225.2",
"protein_id": "XP_016864714.1",
"transcript_support_level": null,
"aa_start": 4344,
"aa_end": null,
"aa_length": 4349,
"cds_start": 13031,
"cds_end": null,
"cds_length": 13050,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009225.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "SLC36A1",
"gene_hgnc_id": 18761,
"hgvs_c": "c.1252+26095C>T",
"hgvs_p": null,
"transcript": "XM_047416925.1",
"protein_id": "XP_047272881.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 449,
"cds_start": null,
"cds_end": null,
"cds_length": 1350,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047416925.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "SLC36A1",
"gene_hgnc_id": 18761,
"hgvs_c": "c.1252+26095C>T",
"hgvs_p": null,
"transcript": "XM_011537595.3",
"protein_id": "XP_011535897.3",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 447,
"cds_start": null,
"cds_end": null,
"cds_length": 1344,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011537595.3"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "SLC36A1",
"gene_hgnc_id": 18761,
"hgvs_c": "c.1159+26095C>T",
"hgvs_p": null,
"transcript": "XM_017009217.2",
"protein_id": "XP_016864706.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 418,
"cds_start": null,
"cds_end": null,
"cds_length": 1257,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017009217.2"
}
],
"gene_symbol": "FAT2",
"gene_hgnc_id": 3596,
"dbsnp": "rs776323616",
"frequency_reference_population": 0.00016293324,
"hom_count_reference_population": 3,
"allele_count_reference_population": 263,
"gnomad_exomes_af": 0.000173072,
"gnomad_genomes_af": 0.0000656418,
"gnomad_exomes_ac": 253,
"gnomad_genomes_ac": 10,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.14208382368087769,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.581,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9291,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.17,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 4.436,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001447.3",
"gene_symbol": "FAT2",
"hgnc_id": 3596,
"effects": [
"missense_variant"
],
"inheritance_mode": "Unknown,AD",
"hgvs_c": "c.13031G>A",
"hgvs_p": "p.Cys4344Tyr"
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "XM_047416925.1",
"gene_symbol": "SLC36A1",
"hgnc_id": 18761,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1252+26095C>T",
"hgvs_p": null
}
],
"clinvar_disease": "FAT2-related disorder,not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided|FAT2-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}