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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-47572946-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=47572946&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 47572946,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006950.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.2036G>A",
"hgvs_p": "p.Arg679Lys",
"transcript": "NM_006950.3",
"protein_id": "NP_008881.2",
"transcript_support_level": null,
"aa_start": 679,
"aa_end": null,
"aa_length": 705,
"cds_start": 2036,
"cds_end": null,
"cds_length": 2118,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000295987.13",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006950.3"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.2036G>A",
"hgvs_p": "p.Arg679Lys",
"transcript": "ENST00000295987.13",
"protein_id": "ENSP00000295987.7",
"transcript_support_level": 2,
"aa_start": 679,
"aa_end": null,
"aa_length": 705,
"cds_start": 2036,
"cds_end": null,
"cds_length": 2118,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_006950.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295987.13"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.1998G>A",
"hgvs_p": "p.Gln666Gln",
"transcript": "ENST00000340666.5",
"protein_id": "ENSP00000343206.4",
"transcript_support_level": 1,
"aa_start": 666,
"aa_end": null,
"aa_length": 669,
"cds_start": 1998,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000340666.5"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.2033G>A",
"hgvs_p": "p.Arg678Lys",
"transcript": "ENST00000950906.1",
"protein_id": "ENSP00000620965.1",
"transcript_support_level": null,
"aa_start": 678,
"aa_end": null,
"aa_length": 704,
"cds_start": 2033,
"cds_end": null,
"cds_length": 2115,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950906.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.1961G>A",
"hgvs_p": "p.Arg654Lys",
"transcript": "ENST00000950907.1",
"protein_id": "ENSP00000620966.1",
"transcript_support_level": null,
"aa_start": 654,
"aa_end": null,
"aa_length": 680,
"cds_start": 1961,
"cds_end": null,
"cds_length": 2043,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950907.1"
},
{
"aa_ref": "R",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.86G>A",
"hgvs_p": "p.Arg29Lys",
"transcript": "ENST00000640721.1",
"protein_id": "ENSP00000492857.1",
"transcript_support_level": 5,
"aa_start": 29,
"aa_end": null,
"aa_length": 55,
"cds_start": 86,
"cds_end": null,
"cds_length": 168,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000640721.1"
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"hgvs_c": "c.1998G>A",
"hgvs_p": "p.Gln666Gln",
"transcript": "NM_133499.2",
"protein_id": "NP_598006.1",
"transcript_support_level": null,
"aa_start": 666,
"aa_end": null,
"aa_length": 669,
"cds_start": 1998,
"cds_end": null,
"cds_length": 2010,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_133499.2"
}
],
"gene_symbol": "SYN1",
"gene_hgnc_id": 11494,
"dbsnp": null,
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2305113971233368,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.05999999865889549,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.048,
"revel_prediction": "Benign",
"alphamissense_score": 0.163,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.54,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.168,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.06,
"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": "PM2,BP4_Moderate,BP6_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_006950.3",
"gene_symbol": "SYN1",
"hgnc_id": 11494,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.2036G>A",
"hgvs_p": "p.Arg679Lys"
}
],
"clinvar_disease": "Inborn genetic diseases",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Inborn genetic diseases",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}