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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: 2-1648888-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=1648888&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 1648888,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000252804.9",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.2892C>T",
"hgvs_p": "p.Asn964Asn",
"transcript": "NM_012293.3",
"protein_id": "NP_036425.1",
"transcript_support_level": null,
"aa_start": 964,
"aa_end": null,
"aa_length": 1479,
"cds_start": 2892,
"cds_end": null,
"cds_length": 4440,
"cdna_start": 2952,
"cdna_end": null,
"cdna_length": 6817,
"mane_select": "ENST00000252804.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.2892C>T",
"hgvs_p": "p.Asn964Asn",
"transcript": "ENST00000252804.9",
"protein_id": "ENSP00000252804.4",
"transcript_support_level": 1,
"aa_start": 964,
"aa_end": null,
"aa_length": 1479,
"cds_start": 2892,
"cds_end": null,
"cds_length": 4440,
"cdna_start": 2952,
"cdna_end": null,
"cdna_length": 6817,
"mane_select": "NM_012293.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.2820C>T",
"hgvs_p": "p.Asn940Asn",
"transcript": "XM_005264707.4",
"protein_id": "XP_005264764.1",
"transcript_support_level": null,
"aa_start": 940,
"aa_end": null,
"aa_length": 1455,
"cds_start": 2820,
"cds_end": null,
"cds_length": 4368,
"cdna_start": 2880,
"cdna_end": null,
"cdna_length": 6745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.2343C>T",
"hgvs_p": "p.Asn781Asn",
"transcript": "XM_011510396.2",
"protein_id": "XP_011508698.1",
"transcript_support_level": null,
"aa_start": 781,
"aa_end": null,
"aa_length": 1296,
"cds_start": 2343,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 2790,
"cdna_end": null,
"cdna_length": 6655,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.2343C>T",
"hgvs_p": "p.Asn781Asn",
"transcript": "XM_047445788.1",
"protein_id": "XP_047301744.1",
"transcript_support_level": null,
"aa_start": 781,
"aa_end": null,
"aa_length": 1296,
"cds_start": 2343,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 2750,
"cdna_end": null,
"cdna_length": 6615,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "c.2343C>T",
"hgvs_p": "p.Asn781Asn",
"transcript": "XM_047445789.1",
"protein_id": "XP_047301745.1",
"transcript_support_level": null,
"aa_start": 781,
"aa_end": null,
"aa_length": 1296,
"cds_start": 2343,
"cds_end": null,
"cds_length": 3891,
"cdna_start": 2714,
"cdna_end": null,
"cdna_length": 6579,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"hgvs_c": "n.2697-4136C>T",
"hgvs_p": null,
"transcript": "ENST00000478155.5",
"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": 3840,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "PXDN",
"gene_hgnc_id": 14966,
"dbsnp": "rs3811613",
"frequency_reference_population": 0.2871886,
"hom_count_reference_population": 67217,
"allele_count_reference_population": 459917,
"gnomad_exomes_af": 0.291527,
"gnomad_genomes_af": 0.245786,
"gnomad_exomes_ac": 422585,
"gnomad_genomes_ac": 37332,
"gnomad_exomes_homalt": 62270,
"gnomad_genomes_homalt": 4947,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.5,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.5,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.045,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000252804.9",
"gene_symbol": "PXDN",
"hgnc_id": 14966,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2892C>T",
"hgvs_p": "p.Asn964Asn"
}
],
"clinvar_disease": "Anterior segment dysgenesis 7,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"phenotype_combined": "not specified|not provided|Anterior segment dysgenesis 7",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}