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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-47605326-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=47605326&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 47605326,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000295987.13",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.581G>T",
"hgvs_p": "p.Arg194Leu",
"transcript": "NM_006950.3",
"protein_id": "NP_008881.2",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 705,
"cds_start": 581,
"cds_end": null,
"cds_length": 2118,
"cdna_start": 710,
"cdna_end": null,
"cdna_length": 3210,
"mane_select": "ENST00000295987.13",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.581G>T",
"hgvs_p": "p.Arg194Leu",
"transcript": "ENST00000295987.13",
"protein_id": "ENSP00000295987.7",
"transcript_support_level": 2,
"aa_start": 194,
"aa_end": null,
"aa_length": 705,
"cds_start": 581,
"cds_end": null,
"cds_length": 2118,
"cdna_start": 710,
"cdna_end": null,
"cdna_length": 3210,
"mane_select": "NM_006950.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.581G>T",
"hgvs_p": "p.Arg194Leu",
"transcript": "ENST00000340666.5",
"protein_id": "ENSP00000343206.4",
"transcript_support_level": 1,
"aa_start": 194,
"aa_end": null,
"aa_length": 669,
"cds_start": 581,
"cds_end": null,
"cds_length": 2010,
"cdna_start": 710,
"cdna_end": null,
"cdna_length": 3172,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.581G>T",
"hgvs_p": "p.Arg194Leu",
"transcript": "NM_133499.2",
"protein_id": "NP_598006.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 669,
"cds_start": 581,
"cds_end": null,
"cds_length": 2010,
"cdna_start": 710,
"cdna_end": null,
"cdna_length": 3172,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.239G>T",
"hgvs_p": "p.Arg80Leu",
"transcript": "ENST00000639776.1",
"protein_id": "ENSP00000492521.1",
"transcript_support_level": 3,
"aa_start": 80,
"aa_end": null,
"aa_length": 147,
"cds_start": 239,
"cds_end": null,
"cds_length": 444,
"cdna_start": 240,
"cdna_end": null,
"cdna_length": 688,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "n.124G>T",
"hgvs_p": null,
"transcript": "ENST00000638337.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 585,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000283743",
"gene_hgnc_id": null,
"hgvs_c": "n.3037G>T",
"hgvs_p": null,
"transcript": "ENST00000638776.2",
"protein_id": null,
"transcript_support_level": 5,
"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": 3761,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"dbsnp": "rs373152478",
"frequency_reference_population": 0.0000089221185,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": null,
"gnomad_genomes_af": 0.00000892212,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.15506437420845032,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.142,
"revel_prediction": "Benign",
"alphamissense_score": 0.2744,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.57,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.842,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000295987.13",
"gene_symbol": "SYN1",
"hgnc_id": 11494,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.581G>T",
"hgvs_p": "p.Arg194Leu"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000638776.2",
"gene_symbol": "ENSG00000283743",
"hgnc_id": null,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.3037G>T",
"hgvs_p": null
}
],
"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
}