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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-136648280-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=136648280&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 136648280,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_000074.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD40LG",
"gene_hgnc_id": 11935,
"hgvs_c": "c.32G>A",
"hgvs_p": "p.Arg11Gln",
"transcript": "NM_000074.3",
"protein_id": "NP_000065.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 261,
"cds_start": 32,
"cds_end": null,
"cds_length": 786,
"cdna_start": 123,
"cdna_end": null,
"cdna_length": 1852,
"mane_select": "ENST00000370629.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD40LG",
"gene_hgnc_id": 11935,
"hgvs_c": "c.32G>A",
"hgvs_p": "p.Arg11Gln",
"transcript": "ENST00000370629.7",
"protein_id": "ENSP00000359663.2",
"transcript_support_level": 1,
"aa_start": 11,
"aa_end": null,
"aa_length": 261,
"cds_start": 32,
"cds_end": null,
"cds_length": 786,
"cdna_start": 123,
"cdna_end": null,
"cdna_length": 1852,
"mane_select": "NM_000074.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD40LG",
"gene_hgnc_id": 11935,
"hgvs_c": "c.32G>A",
"hgvs_p": "p.Arg11Gln",
"transcript": "ENST00000370628.2",
"protein_id": "ENSP00000359662.2",
"transcript_support_level": 1,
"aa_start": 11,
"aa_end": null,
"aa_length": 240,
"cds_start": 32,
"cds_end": null,
"cds_length": 723,
"cdna_start": 54,
"cdna_end": null,
"cdna_length": 1720,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD40LG",
"gene_hgnc_id": 11935,
"hgvs_c": "c.32G>A",
"hgvs_p": "p.Arg11Gln",
"transcript": "ENST00000695724.1",
"protein_id": "ENSP00000512122.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 107,
"cds_start": 32,
"cds_end": null,
"cds_length": 324,
"cdna_start": 117,
"cdna_end": null,
"cdna_length": 1786,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD40LG",
"gene_hgnc_id": 11935,
"hgvs_c": "c.32G>A",
"hgvs_p": "p.Arg11Gln",
"transcript": "ENST00000695725.1",
"protein_id": "ENSP00000512123.1",
"transcript_support_level": null,
"aa_start": 11,
"aa_end": null,
"aa_length": 63,
"cds_start": 32,
"cds_end": null,
"cds_length": 192,
"cdna_start": 104,
"cdna_end": null,
"cdna_length": 1472,
"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": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD40LG",
"gene_hgnc_id": 11935,
"hgvs_c": "n.75G>A",
"hgvs_p": null,
"transcript": "ENST00000695726.1",
"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": 3622,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD40LG",
"gene_hgnc_id": 11935,
"hgvs_c": "n.19G>A",
"hgvs_p": null,
"transcript": "ENST00000695727.1",
"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": 448,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CD40LG",
"gene_hgnc_id": 11935,
"hgvs_c": "n.19G>A",
"hgvs_p": null,
"transcript": "ENST00000695728.1",
"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": 2219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CD40LG",
"gene_hgnc_id": 11935,
"dbsnp": "rs145115086",
"frequency_reference_population": 0.0002654661,
"hom_count_reference_population": 109,
"allele_count_reference_population": 319,
"gnomad_exomes_af": 0.000268655,
"gnomad_genomes_af": 0.00023415,
"gnomad_exomes_ac": 293,
"gnomad_genomes_ac": 26,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.356791615486145,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.297,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.1314,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 4.201,
"phylop100way_prediction": "Uncertain_significance",
"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": -17,
"acmg_classification": "Benign",
"acmg_criteria": "BP4,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -17,
"benign_score": 17,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_000074.3",
"gene_symbol": "CD40LG",
"hgnc_id": 11935,
"effects": [
"missense_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.32G>A",
"hgvs_p": "p.Arg11Gln"
}
],
"clinvar_disease": "Hyper-IgM syndrome type 1,not provided",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:1",
"phenotype_combined": "Hyper-IgM syndrome type 1|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}