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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: 21-40013093-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=40013093&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 40013093,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_001389.5",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DSCAM",
"gene_hgnc_id": 3039,
"hgvs_c": "c.5980G>A",
"hgvs_p": "p.Asp1994Asn",
"transcript": "NM_001389.5",
"protein_id": "NP_001380.2",
"transcript_support_level": null,
"aa_start": 1994,
"aa_end": null,
"aa_length": 2012,
"cds_start": 5980,
"cds_end": null,
"cds_length": 6039,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000400454.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001389.5"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DSCAM",
"gene_hgnc_id": 3039,
"hgvs_c": "c.5980G>A",
"hgvs_p": "p.Asp1994Asn",
"transcript": "ENST00000400454.6",
"protein_id": "ENSP00000383303.1",
"transcript_support_level": 1,
"aa_start": 1994,
"aa_end": null,
"aa_length": 2012,
"cds_start": 5980,
"cds_end": null,
"cds_length": 6039,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001389.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000400454.6"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 29,
"exon_rank_end": null,
"exon_count": 29,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DSCAM",
"gene_hgnc_id": 3039,
"hgvs_c": "c.5182G>A",
"hgvs_p": "p.Asp1728Asn",
"transcript": "ENST00000404019.2",
"protein_id": "ENSP00000385342.2",
"transcript_support_level": 1,
"aa_start": 1728,
"aa_end": null,
"aa_length": 1746,
"cds_start": 5182,
"cds_end": null,
"cds_length": 5241,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000404019.2"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DSCAM",
"gene_hgnc_id": 3039,
"hgvs_c": "c.5926G>A",
"hgvs_p": "p.Asp1976Asn",
"transcript": "NM_001271534.3",
"protein_id": "NP_001258463.1",
"transcript_support_level": null,
"aa_start": 1976,
"aa_end": null,
"aa_length": 1994,
"cds_start": 5926,
"cds_end": null,
"cds_length": 5985,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001271534.3"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DSCAM",
"gene_hgnc_id": 3039,
"hgvs_c": "c.5485G>A",
"hgvs_p": "p.Asp1829Asn",
"transcript": "ENST00000617870.4",
"protein_id": "ENSP00000478698.1",
"transcript_support_level": 5,
"aa_start": 1829,
"aa_end": null,
"aa_length": 1847,
"cds_start": 5485,
"cds_end": null,
"cds_length": 5544,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000617870.4"
},
{
"aa_ref": "D",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 30,
"exon_rank_end": null,
"exon_count": 30,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DSCAM",
"gene_hgnc_id": 3039,
"hgvs_c": "c.5272G>A",
"hgvs_p": "p.Asp1758Asn",
"transcript": "XM_017028281.2",
"protein_id": "XP_016883770.1",
"transcript_support_level": null,
"aa_start": 1758,
"aa_end": null,
"aa_length": 1776,
"cds_start": 5272,
"cds_end": null,
"cds_length": 5331,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_017028281.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 33,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DSCAM",
"gene_hgnc_id": 3039,
"hgvs_c": "n.6286G>A",
"hgvs_p": null,
"transcript": "NR_073202.3",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_073202.3"
}
],
"gene_symbol": "DSCAM",
"gene_hgnc_id": 3039,
"dbsnp": "rs370041442",
"frequency_reference_population": 0.000025138925,
"hom_count_reference_population": 0,
"allele_count_reference_population": 40,
"gnomad_exomes_af": 0.0000271007,
"gnomad_genomes_af": 0.0000065754,
"gnomad_exomes_ac": 39,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3651028275489807,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.28,
"revel_prediction": "Benign",
"alphamissense_score": 0.1568,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.42,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 7.344,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_001389.5",
"gene_symbol": "DSCAM",
"hgnc_id": 3039,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.5980G>A",
"hgvs_p": "p.Asp1994Asn"
}
],
"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
}