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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: X-16841722-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=16841722&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 16841722,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_018360.3",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXLNG",
"gene_hgnc_id": 18578,
"hgvs_c": "c.1543C>T",
"hgvs_p": "p.Pro515Ser",
"transcript": "NM_018360.3",
"protein_id": "NP_060830.2",
"transcript_support_level": null,
"aa_start": 515,
"aa_end": null,
"aa_length": 528,
"cds_start": 1543,
"cds_end": null,
"cds_length": 1587,
"cdna_start": 1565,
"cdna_end": null,
"cdna_length": 4362,
"mane_select": "ENST00000380122.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXLNG",
"gene_hgnc_id": 18578,
"hgvs_c": "c.1543C>T",
"hgvs_p": "p.Pro515Ser",
"transcript": "ENST00000380122.10",
"protein_id": "ENSP00000369465.5",
"transcript_support_level": 1,
"aa_start": 515,
"aa_end": null,
"aa_length": 528,
"cds_start": 1543,
"cds_end": null,
"cds_length": 1587,
"cdna_start": 1565,
"cdna_end": null,
"cdna_length": 4362,
"mane_select": "NM_018360.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXLNG",
"gene_hgnc_id": 18578,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Pro383Ser",
"transcript": "ENST00000398155.4",
"protein_id": "ENSP00000381222.4",
"transcript_support_level": 1,
"aa_start": 383,
"aa_end": null,
"aa_length": 396,
"cds_start": 1147,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1203,
"cdna_end": null,
"cdna_length": 3998,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXLNG",
"gene_hgnc_id": 18578,
"hgvs_c": "c.1147C>T",
"hgvs_p": "p.Pro383Ser",
"transcript": "NM_001168683.2",
"protein_id": "NP_001162154.1",
"transcript_support_level": null,
"aa_start": 383,
"aa_end": null,
"aa_length": 396,
"cds_start": 1147,
"cds_end": null,
"cds_length": 1191,
"cdna_start": 1169,
"cdna_end": null,
"cdna_length": 3966,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXLNG",
"gene_hgnc_id": 18578,
"hgvs_c": "c.1426C>T",
"hgvs_p": "p.Pro476Ser",
"transcript": "XM_024452400.2",
"protein_id": "XP_024308168.1",
"transcript_support_level": null,
"aa_start": 476,
"aa_end": null,
"aa_length": 489,
"cds_start": 1426,
"cds_end": null,
"cds_length": 1470,
"cdna_start": 1459,
"cdna_end": null,
"cdna_length": 4256,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXLNG",
"gene_hgnc_id": 18578,
"hgvs_c": "c.928C>T",
"hgvs_p": "p.Pro310Ser",
"transcript": "XM_017029631.2",
"protein_id": "XP_016885120.1",
"transcript_support_level": null,
"aa_start": 310,
"aa_end": null,
"aa_length": 323,
"cds_start": 928,
"cds_end": null,
"cds_length": 972,
"cdna_start": 1577,
"cdna_end": null,
"cdna_length": 4374,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TXLNG",
"gene_hgnc_id": 18578,
"hgvs_c": "n.434C>T",
"hgvs_p": null,
"transcript": "ENST00000485153.1",
"protein_id": null,
"transcript_support_level": 3,
"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": 3231,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "RBBP7",
"gene_hgnc_id": 9890,
"hgvs_c": "c.*8-2332G>A",
"hgvs_p": null,
"transcript": "ENST00000425696.5",
"protein_id": "ENSP00000415747.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 85,
"cds_start": -4,
"cds_end": null,
"cds_length": 258,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 373,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TXLNG",
"gene_hgnc_id": 18578,
"dbsnp": "rs745481556",
"frequency_reference_population": 0.00004049627,
"hom_count_reference_population": 22,
"allele_count_reference_population": 49,
"gnomad_exomes_af": 0.0000428063,
"gnomad_genomes_af": 0.0000178541,
"gnomad_exomes_ac": 47,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06371456384658813,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.05,
"revel_prediction": "Benign",
"alphamissense_score": 0.0664,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.77,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.467,
"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": -8,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BS2",
"acmg_by_gene": [
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_018360.3",
"gene_symbol": "TXLNG",
"hgnc_id": 18578,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1543C>T",
"hgvs_p": "p.Pro515Ser"
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000425696.5",
"gene_symbol": "RBBP7",
"hgnc_id": 9890,
"effects": [
"intron_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.*8-2332G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}