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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-106034380-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=106034380&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 106034380,
"ref": "C",
"alt": "T",
"effect": "stop_gained,splice_region_variant",
"transcript": "ENST00000372563.2",
"consequences": [
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINA7",
"gene_hgnc_id": 11583,
"hgvs_c": "c.899G>A",
"hgvs_p": "p.Trp300*",
"transcript": "NM_000354.6",
"protein_id": "NP_000345.2",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 415,
"cds_start": 899,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 946,
"cdna_end": null,
"cdna_length": 2360,
"mane_select": "ENST00000372563.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINA7",
"gene_hgnc_id": 11583,
"hgvs_c": "c.899G>A",
"hgvs_p": "p.Trp300*",
"transcript": "ENST00000372563.2",
"protein_id": "ENSP00000361644.1",
"transcript_support_level": 5,
"aa_start": 300,
"aa_end": null,
"aa_length": 415,
"cds_start": 899,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 946,
"cdna_end": null,
"cdna_length": 2360,
"mane_select": "NM_000354.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINA7",
"gene_hgnc_id": 11583,
"hgvs_c": "c.899G>A",
"hgvs_p": "p.Trp300*",
"transcript": "ENST00000327674.8",
"protein_id": "ENSP00000329374.4",
"transcript_support_level": 1,
"aa_start": 300,
"aa_end": null,
"aa_length": 415,
"cds_start": 899,
"cds_end": null,
"cds_length": 1248,
"cdna_start": 1235,
"cdna_end": null,
"cdna_length": 2642,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINA7",
"gene_hgnc_id": 11583,
"hgvs_c": "c.899G>A",
"hgvs_p": "p.Trp300*",
"transcript": "XM_006724683.3",
"protein_id": "XP_006724746.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 425,
"cds_start": 899,
"cds_end": null,
"cds_length": 1278,
"cdna_start": 946,
"cdna_end": null,
"cdna_length": 1395,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "W",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained",
"splice_region_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINA7",
"gene_hgnc_id": 11583,
"hgvs_c": "c.899G>A",
"hgvs_p": "p.Trp300*",
"transcript": "XM_005262180.5",
"protein_id": "XP_005262237.1",
"transcript_support_level": null,
"aa_start": 300,
"aa_end": null,
"aa_length": 371,
"cds_start": 899,
"cds_end": null,
"cds_length": 1116,
"cdna_start": 946,
"cdna_end": null,
"cdna_length": 1426,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SERPINA7",
"gene_hgnc_id": 11583,
"hgvs_c": "n.172G>A",
"hgvs_p": null,
"transcript": "ENST00000487487.1",
"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": 395,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SERPINA7",
"gene_hgnc_id": 11583,
"dbsnp": "rs121909496",
"frequency_reference_population": 0.000012844154,
"hom_count_reference_population": 5,
"allele_count_reference_population": 14,
"gnomad_exomes_af": 0.0000128442,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 14,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4699999988079071,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.6899999976158142,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.47,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": -1.394,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.69,
"spliceai_max_prediction": "Pathogenic",
"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": "Likely_pathogenic",
"acmg_criteria": "PVS1,PP3,BS2_Supporting",
"acmg_by_gene": [
{
"score": 8,
"benign_score": 1,
"pathogenic_score": 9,
"criteria": [
"PVS1",
"PP3",
"BS2_Supporting"
],
"verdict": "Likely_pathogenic",
"transcript": "ENST00000372563.2",
"gene_symbol": "SERPINA7",
"hgnc_id": 11583,
"effects": [
"stop_gained",
"splice_region_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.899G>A",
"hgvs_p": "p.Trp300*"
}
],
"clinvar_disease": "Thyroxine-binding globulin quantitative trait locus",
"clinvar_classification": "association",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Thyroxine-binding globulin quantitative trait locus",
"pathogenicity_classification_combined": "association",
"custom_annotations": null
}
],
"message": null
}