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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: 21-25639842-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=21&pos=25639842&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "21",
"pos": 25639842,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001270408.2",
"consequences": [
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAM2",
"gene_hgnc_id": 14686,
"hgvs_c": "c.21C>A",
"hgvs_p": "p.His7Gln",
"transcript": "NM_021219.4",
"protein_id": "NP_067042.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 298,
"cds_start": 21,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000480456.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_021219.4"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAM2",
"gene_hgnc_id": 14686,
"hgvs_c": "c.21C>A",
"hgvs_p": "p.His7Gln",
"transcript": "ENST00000480456.6",
"protein_id": "ENSP00000420419.1",
"transcript_support_level": 1,
"aa_start": 7,
"aa_end": null,
"aa_length": 298,
"cds_start": 21,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_021219.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000480456.6"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAM2",
"gene_hgnc_id": 14686,
"hgvs_c": "c.21C>A",
"hgvs_p": "p.His7Gln",
"transcript": "ENST00000400532.5",
"protein_id": "ENSP00000383376.1",
"transcript_support_level": 1,
"aa_start": 7,
"aa_end": null,
"aa_length": 312,
"cds_start": 21,
"cds_end": null,
"cds_length": 939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000400532.5"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAM2",
"gene_hgnc_id": 14686,
"hgvs_c": "c.21C>A",
"hgvs_p": "p.His7Gln",
"transcript": "ENST00000948521.1",
"protein_id": "ENSP00000618580.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 313,
"cds_start": 21,
"cds_end": null,
"cds_length": 942,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000948521.1"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAM2",
"gene_hgnc_id": 14686,
"hgvs_c": "c.21C>A",
"hgvs_p": "p.His7Gln",
"transcript": "NM_001270408.2",
"protein_id": "NP_001257337.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 312,
"cds_start": 21,
"cds_end": null,
"cds_length": 939,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001270408.2"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAM2",
"gene_hgnc_id": 14686,
"hgvs_c": "c.21C>A",
"hgvs_p": "p.His7Gln",
"transcript": "NM_001270407.2",
"protein_id": "NP_001257336.1",
"transcript_support_level": null,
"aa_start": 7,
"aa_end": null,
"aa_length": 262,
"cds_start": 21,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001270407.2"
},
{
"aa_ref": "H",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAM2",
"gene_hgnc_id": 14686,
"hgvs_c": "c.21C>A",
"hgvs_p": "p.His7Gln",
"transcript": "ENST00000312957.9",
"protein_id": "ENSP00000318416.6",
"transcript_support_level": 2,
"aa_start": 7,
"aa_end": null,
"aa_length": 262,
"cds_start": 21,
"cds_end": null,
"cds_length": 789,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000312957.9"
},
{
"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": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "JAM2",
"gene_hgnc_id": 14686,
"hgvs_c": "n.585C>A",
"hgvs_p": null,
"transcript": "NR_072999.2",
"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_072999.2"
}
],
"gene_symbol": "JAM2",
"gene_hgnc_id": 14686,
"dbsnp": "rs8132639",
"frequency_reference_population": 0.0031652732,
"hom_count_reference_population": 125,
"allele_count_reference_population": 5034,
"gnomad_exomes_af": 0.0017054,
"gnomad_genomes_af": 0.0169791,
"gnomad_exomes_ac": 2453,
"gnomad_genomes_ac": 2581,
"gnomad_exomes_homalt": 59,
"gnomad_genomes_homalt": 66,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0020769238471984863,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.035,
"revel_prediction": "Benign",
"alphamissense_score": 0.1543,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.421,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_001270408.2",
"gene_symbol": "JAM2",
"hgnc_id": 14686,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.21C>A",
"hgvs_p": "p.His7Gln"
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}