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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: 1-9245143-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=9245143&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 9245143,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_004285.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.209C>T",
"hgvs_p": "p.Pro70Leu",
"transcript": "NM_004285.4",
"protein_id": "NP_004276.2",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 791,
"cds_start": 209,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 512,
"cdna_end": null,
"cdna_length": 9147,
"mane_select": "ENST00000377403.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.209C>T",
"hgvs_p": "p.Pro70Leu",
"transcript": "ENST00000377403.7",
"protein_id": "ENSP00000366620.2",
"transcript_support_level": 1,
"aa_start": 70,
"aa_end": null,
"aa_length": 791,
"cds_start": 209,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 512,
"cdna_end": null,
"cdna_length": 9147,
"mane_select": "NM_004285.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.242C>T",
"hgvs_p": "p.Pro81Leu",
"transcript": "ENST00000602477.1",
"protein_id": "ENSP00000473348.1",
"transcript_support_level": 1,
"aa_start": 81,
"aa_end": null,
"aa_length": 802,
"cds_start": 242,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 394,
"cdna_end": null,
"cdna_length": 5590,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.242C>T",
"hgvs_p": "p.Pro81Leu",
"transcript": "NM_001282587.2",
"protein_id": "NP_001269516.1",
"transcript_support_level": null,
"aa_start": 81,
"aa_end": null,
"aa_length": 802,
"cds_start": 242,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 391,
"cdna_end": null,
"cdna_length": 9026,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.242C>T",
"hgvs_p": "p.Pro81Leu",
"transcript": "XM_047435002.1",
"protein_id": "XP_047290958.1",
"transcript_support_level": null,
"aa_start": 81,
"aa_end": null,
"aa_length": 802,
"cds_start": 242,
"cds_end": null,
"cds_length": 2409,
"cdna_start": 716,
"cdna_end": null,
"cdna_length": 9351,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.236C>T",
"hgvs_p": "p.Pro79Leu",
"transcript": "XM_005263540.6",
"protein_id": "XP_005263597.1",
"transcript_support_level": null,
"aa_start": 79,
"aa_end": null,
"aa_length": 800,
"cds_start": 236,
"cds_end": null,
"cds_length": 2403,
"cdna_start": 367,
"cdna_end": null,
"cdna_length": 9002,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.230C>T",
"hgvs_p": "p.Pro77Leu",
"transcript": "XM_047435003.1",
"protein_id": "XP_047290959.1",
"transcript_support_level": null,
"aa_start": 77,
"aa_end": null,
"aa_length": 798,
"cds_start": 230,
"cds_end": null,
"cds_length": 2397,
"cdna_start": 361,
"cdna_end": null,
"cdna_length": 8996,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.209C>T",
"hgvs_p": "p.Pro70Leu",
"transcript": "XM_006711052.5",
"protein_id": "XP_006711115.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 791,
"cds_start": 209,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 504,
"cdna_end": null,
"cdna_length": 9139,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.209C>T",
"hgvs_p": "p.Pro70Leu",
"transcript": "XM_017002865.3",
"protein_id": "XP_016858354.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 791,
"cds_start": 209,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 383,
"cdna_end": null,
"cdna_length": 9018,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"hgvs_c": "c.209C>T",
"hgvs_p": "p.Pro70Leu",
"transcript": "XM_047435005.1",
"protein_id": "XP_047290961.1",
"transcript_support_level": null,
"aa_start": 70,
"aa_end": null,
"aa_length": 791,
"cds_start": 209,
"cds_end": null,
"cds_length": 2376,
"cdna_start": 381,
"cdna_end": null,
"cdna_length": 9016,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "H6PD",
"gene_hgnc_id": 4795,
"dbsnp": "rs1165969718",
"frequency_reference_population": 0.000016108008,
"hom_count_reference_population": 0,
"allele_count_reference_population": 26,
"gnomad_exomes_af": 0.0000171012,
"gnomad_genomes_af": 0.00000656953,
"gnomad_exomes_ac": 25,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11213591694831848,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.387,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0761,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.18,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.46,
"phylop100way_prediction": "Benign",
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_004285.4",
"gene_symbol": "H6PD",
"hgnc_id": 4795,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.209C>T",
"hgvs_p": "p.Pro70Leu"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}