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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-151404917-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=151404917&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 151404917,
"ref": "C",
"alt": "T",
"effect": "splice_region_variant,synonymous_variant",
"transcript": "NM_001363810.1",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VMA21",
"gene_hgnc_id": 22082,
"hgvs_c": "c.165C>T",
"hgvs_p": "p.Gly55Gly",
"transcript": "NM_001017980.4",
"protein_id": "NP_001017980.1",
"transcript_support_level": null,
"aa_start": 55,
"aa_end": null,
"aa_length": 101,
"cds_start": 165,
"cds_end": null,
"cds_length": 306,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000330374.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001017980.4"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VMA21",
"gene_hgnc_id": 22082,
"hgvs_c": "c.165C>T",
"hgvs_p": "p.Gly55Gly",
"transcript": "ENST00000330374.7",
"protein_id": "ENSP00000333255.6",
"transcript_support_level": 1,
"aa_start": 55,
"aa_end": null,
"aa_length": 101,
"cds_start": 165,
"cds_end": null,
"cds_length": 306,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001017980.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000330374.7"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VMA21",
"gene_hgnc_id": 22082,
"hgvs_c": "c.330C>T",
"hgvs_p": "p.Gly110Gly",
"transcript": "NM_001363810.1",
"protein_id": "NP_001350739.1",
"transcript_support_level": null,
"aa_start": 110,
"aa_end": null,
"aa_length": 156,
"cds_start": 330,
"cds_end": null,
"cds_length": 471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001363810.1"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VMA21",
"gene_hgnc_id": 22082,
"hgvs_c": "c.330C>T",
"hgvs_p": "p.Gly110Gly",
"transcript": "ENST00000370361.5",
"protein_id": "ENSP00000359386.1",
"transcript_support_level": 5,
"aa_start": 110,
"aa_end": null,
"aa_length": 156,
"cds_start": 330,
"cds_end": null,
"cds_length": 471,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000370361.5"
},
{
"aa_ref": "G",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_region_variant",
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VMA21",
"gene_hgnc_id": 22082,
"hgvs_c": "c.156C>T",
"hgvs_p": "p.Gly52Gly",
"transcript": "ENST00000932111.1",
"protein_id": "ENSP00000602170.1",
"transcript_support_level": null,
"aa_start": 52,
"aa_end": null,
"aa_length": 98,
"cds_start": 156,
"cds_end": null,
"cds_length": 297,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000932111.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "VMA21",
"gene_hgnc_id": 22082,
"hgvs_c": "n.245C>T",
"hgvs_p": null,
"transcript": "ENST00000477649.1",
"protein_id": null,
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000477649.1"
}
],
"gene_symbol": "VMA21",
"gene_hgnc_id": 22082,
"dbsnp": "rs146017753",
"frequency_reference_population": 0.0017765487,
"hom_count_reference_population": 704,
"allele_count_reference_population": 2138,
"gnomad_exomes_af": 0.00185778,
"gnomad_genomes_af": 0.000948617,
"gnomad_exomes_ac": 2036,
"gnomad_genomes_ac": 102,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.41999998688697815,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.00800000037997961,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.002,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000431336363966869,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -9,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Moderate,BP7,BS2",
"acmg_by_gene": [
{
"score": -9,
"benign_score": 9,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001363810.1",
"gene_symbol": "VMA21",
"hgnc_id": 22082,
"effects": [
"splice_region_variant",
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.330C>T",
"hgvs_p": "p.Gly110Gly"
}
],
"clinvar_disease": "X-linked myopathy with excessive autophagy",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "B:1",
"phenotype_combined": "X-linked myopathy with excessive autophagy",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}