← Back to variant description
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-100664899-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=100664899&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 100664899,
"ref": "C",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000373004.5",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX2",
"gene_hgnc_id": 30668,
"hgvs_c": "c.481C>A",
"hgvs_p": "p.Arg161Arg",
"transcript": "NM_014467.3",
"protein_id": "NP_055282.1",
"transcript_support_level": null,
"aa_start": 161,
"aa_end": null,
"aa_length": 465,
"cds_start": 481,
"cds_end": null,
"cds_length": 1398,
"cdna_start": 928,
"cdna_end": null,
"cdna_length": 6646,
"mane_select": "ENST00000373004.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX2",
"gene_hgnc_id": 30668,
"hgvs_c": "c.481C>A",
"hgvs_p": "p.Arg161Arg",
"transcript": "ENST00000373004.5",
"protein_id": "ENSP00000362095.3",
"transcript_support_level": 1,
"aa_start": 161,
"aa_end": null,
"aa_length": 465,
"cds_start": 481,
"cds_end": null,
"cds_length": 1398,
"cdna_start": 928,
"cdna_end": null,
"cdna_length": 6646,
"mane_select": "NM_014467.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX2",
"gene_hgnc_id": 30668,
"hgvs_c": "c.505C>A",
"hgvs_p": "p.Arg169Arg",
"transcript": "ENST00000638458.1",
"protein_id": "ENSP00000492168.1",
"transcript_support_level": 5,
"aa_start": 169,
"aa_end": null,
"aa_length": 311,
"cds_start": 505,
"cds_end": null,
"cds_length": 936,
"cdna_start": 505,
"cdna_end": null,
"cdna_length": 936,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "R",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX2",
"gene_hgnc_id": 30668,
"hgvs_c": "c.481C>A",
"hgvs_p": "p.Arg161Arg",
"transcript": "ENST00000640889.1",
"protein_id": "ENSP00000492571.1",
"transcript_support_level": 5,
"aa_start": 161,
"aa_end": null,
"aa_length": 222,
"cds_start": 481,
"cds_end": null,
"cds_length": 671,
"cdna_start": 803,
"cdna_end": null,
"cdna_length": 993,
"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": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX2",
"gene_hgnc_id": 30668,
"hgvs_c": "n.469C>A",
"hgvs_p": null,
"transcript": "ENST00000638319.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 584,
"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": 4,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX2",
"gene_hgnc_id": 30668,
"hgvs_c": "n.484C>A",
"hgvs_p": null,
"transcript": "ENST00000638920.1",
"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": 1493,
"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": 4,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX2",
"gene_hgnc_id": 30668,
"hgvs_c": "n.415C>A",
"hgvs_p": null,
"transcript": "ENST00000677630.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1029,
"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": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SRPX2",
"gene_hgnc_id": 30668,
"hgvs_c": "n.514C>A",
"hgvs_p": null,
"transcript": "ENST00000679590.1",
"protein_id": null,
"transcript_support_level": null,
"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": 1128,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SRPX2",
"gene_hgnc_id": 30668,
"dbsnp": "rs150552508",
"frequency_reference_population": 0.0017363882,
"hom_count_reference_population": 638,
"allele_count_reference_population": 2100,
"gnomad_exomes_af": 0.00181284,
"gnomad_genomes_af": 0.000989014,
"gnomad_exomes_ac": 1989,
"gnomad_genomes_ac": 111,
"gnomad_exomes_homalt": 3,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.1599999964237213,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.029999999329447746,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.16,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.825,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.03,
"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": -14,
"acmg_classification": "Benign",
"acmg_criteria": "BP4,BP6_Very_Strong,BP7,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 14,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6_Very_Strong",
"BP7",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000373004.5",
"gene_symbol": "SRPX2",
"hgnc_id": 30668,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL,AD",
"hgvs_c": "c.481C>A",
"hgvs_p": "p.Arg161Arg"
}
],
"clinvar_disease": " X-linked, and speech dyspraxia, intellectual disability,Rolandic epilepsy,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:4",
"phenotype_combined": "Rolandic epilepsy, intellectual disability, and speech dyspraxia, X-linked|not specified|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}