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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: 22-40861499-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=40861499&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 40861499,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_145174.2",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB7",
"gene_hgnc_id": 24986,
"hgvs_c": "c.496G>A",
"hgvs_p": "p.Glu166Lys",
"transcript": "NM_145174.2",
"protein_id": "NP_660157.1",
"transcript_support_level": null,
"aa_start": 166,
"aa_end": null,
"aa_length": 309,
"cds_start": 496,
"cds_end": null,
"cds_length": 930,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000307221.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_145174.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DNAJB7",
"gene_hgnc_id": 24986,
"hgvs_c": "c.496G>A",
"hgvs_p": "p.Glu166Lys",
"transcript": "ENST00000307221.5",
"protein_id": "ENSP00000307197.4",
"transcript_support_level": 6,
"aa_start": 166,
"aa_end": null,
"aa_length": 309,
"cds_start": 496,
"cds_end": null,
"cds_length": 930,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_145174.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000307221.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "XPNPEP3",
"gene_hgnc_id": 28052,
"hgvs_c": "c.64+4254C>T",
"hgvs_p": null,
"transcript": "NM_022098.4",
"protein_id": "NP_071381.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 507,
"cds_start": null,
"cds_end": null,
"cds_length": 1524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000357137.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_022098.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "XPNPEP3",
"gene_hgnc_id": 28052,
"hgvs_c": "c.64+4254C>T",
"hgvs_p": null,
"transcript": "ENST00000357137.9",
"protein_id": "ENSP00000349658.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 507,
"cds_start": null,
"cds_end": null,
"cds_length": 1524,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_022098.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000357137.9"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "XPNPEP3",
"gene_hgnc_id": 28052,
"hgvs_c": "n.266-119C>T",
"hgvs_p": null,
"transcript": "ENST00000482652.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000482652.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "XPNPEP3",
"gene_hgnc_id": 28052,
"hgvs_c": "c.64+4254C>T",
"hgvs_p": null,
"transcript": "ENST00000926395.1",
"protein_id": "ENSP00000596454.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 486,
"cds_start": null,
"cds_end": null,
"cds_length": 1461,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926395.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "XPNPEP3",
"gene_hgnc_id": 28052,
"hgvs_c": "c.64+4254C>T",
"hgvs_p": null,
"transcript": "ENST00000904508.1",
"protein_id": "ENSP00000574567.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 468,
"cds_start": null,
"cds_end": null,
"cds_length": 1407,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904508.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "XPNPEP3",
"gene_hgnc_id": 28052,
"hgvs_c": "c.64+4254C>T",
"hgvs_p": null,
"transcript": "ENST00000904509.1",
"protein_id": "ENSP00000574568.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 448,
"cds_start": null,
"cds_end": null,
"cds_length": 1347,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000904509.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "XPNPEP3",
"gene_hgnc_id": 28052,
"hgvs_c": "c.64+4254C>T",
"hgvs_p": null,
"transcript": "ENST00000950134.1",
"protein_id": "ENSP00000620193.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 371,
"cds_start": null,
"cds_end": null,
"cds_length": 1116,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950134.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "XPNPEP3",
"gene_hgnc_id": 28052,
"hgvs_c": "c.*13-119C>T",
"hgvs_p": null,
"transcript": "NM_001204827.2",
"protein_id": "NP_001191756.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 55,
"cds_start": null,
"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": "NM_001204827.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "XPNPEP3",
"gene_hgnc_id": 28052,
"hgvs_c": "n.169+4254C>T",
"hgvs_p": null,
"transcript": "ENST00000417688.5",
"protein_id": null,
"transcript_support_level": 3,
"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": "retained_intron",
"feature": "ENST00000417688.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "XPNPEP3",
"gene_hgnc_id": 28052,
"hgvs_c": "n.64+4254C>T",
"hgvs_p": null,
"transcript": "ENST00000428799.1",
"protein_id": "ENSP00000394283.1",
"transcript_support_level": 2,
"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": "nonsense_mediated_decay",
"feature": "ENST00000428799.1"
}
],
"gene_symbol": "DNAJB7",
"gene_hgnc_id": 24986,
"dbsnp": "rs138400041",
"frequency_reference_population": 0.000028497478,
"hom_count_reference_population": 0,
"allele_count_reference_population": 46,
"gnomad_exomes_af": 0.0000116292,
"gnomad_genomes_af": 0.000190366,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 29,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.033205002546310425,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.163,
"revel_prediction": "Benign",
"alphamissense_score": 0.0732,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.39,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.406,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -4,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong",
"acmg_by_gene": [
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_145174.2",
"gene_symbol": "DNAJB7",
"hgnc_id": 24986,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.496G>A",
"hgvs_p": "p.Glu166Lys"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_022098.4",
"gene_symbol": "XPNPEP3",
"hgnc_id": 28052,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.64+4254C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}