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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: 11-66423839-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=66423839&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NPAS4",
"hgnc_id": 18983,
"hgvs_c": "c.949A>G",
"hgvs_p": "p.Met317Val",
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_178864.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 2,
"alphamissense_prediction": "Benign",
"alphamissense_score": 0.0712,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.67,
"chr": "11",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "not specified",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.055741071701049805,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 802,
"aa_ref": "M",
"aa_start": 317,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3272,
"cdna_start": 1094,
"cds_end": null,
"cds_length": 2409,
"cds_start": 949,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_178864.4",
"gene_hgnc_id": 18983,
"gene_symbol": "NPAS4",
"hgvs_c": "c.949A>G",
"hgvs_p": "p.Met317Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000311034.7",
"protein_coding": true,
"protein_id": "NP_849195.2",
"strand": true,
"transcript": "NM_178864.4",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 802,
"aa_ref": "M",
"aa_start": 317,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 3272,
"cdna_start": 1094,
"cds_end": null,
"cds_length": 2409,
"cds_start": 949,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000311034.7",
"gene_hgnc_id": 18983,
"gene_symbol": "NPAS4",
"hgvs_c": "c.949A>G",
"hgvs_p": "p.Met317Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_178864.4",
"protein_coding": true,
"protein_id": "ENSP00000311196.2",
"strand": true,
"transcript": "ENST00000311034.7",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2454,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000525148.1",
"gene_hgnc_id": 18983,
"gene_symbol": "NPAS4",
"hgvs_c": "n.*134A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000433135.1",
"strand": true,
"transcript": "ENST00000525148.1",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2454,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000525148.1",
"gene_hgnc_id": 18983,
"gene_symbol": "NPAS4",
"hgvs_c": "n.*134A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000433135.1",
"strand": true,
"transcript": "ENST00000525148.1",
"transcript_support_level": 1
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 592,
"aa_ref": "M",
"aa_start": 107,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3192,
"cdna_start": 1015,
"cds_end": null,
"cds_length": 1779,
"cds_start": 319,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001318804.1",
"gene_hgnc_id": 18983,
"gene_symbol": "NPAS4",
"hgvs_c": "c.319A>G",
"hgvs_p": "p.Met107Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001305733.1",
"strand": true,
"transcript": "NM_001318804.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 879,
"aa_ref": "M",
"aa_start": 394,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4620,
"cdna_start": 2442,
"cds_end": null,
"cds_length": 2640,
"cds_start": 1180,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047426764.1",
"gene_hgnc_id": 18983,
"gene_symbol": "NPAS4",
"hgvs_c": "c.1180A>G",
"hgvs_p": "p.Met394Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047282720.1",
"strand": true,
"transcript": "XM_047426764.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 879,
"aa_ref": "M",
"aa_start": 394,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3944,
"cdna_start": 1766,
"cds_end": null,
"cds_length": 2640,
"cds_start": 1180,
"consequences": [
"missense_variant"
],
"exon_count": 11,
"exon_rank": 10,
"exon_rank_end": null,
"feature": "XM_047426765.1",
"gene_hgnc_id": 18983,
"gene_symbol": "NPAS4",
"hgvs_c": "c.1180A>G",
"hgvs_p": "p.Met394Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047282721.1",
"strand": true,
"transcript": "XM_047426765.1",
"transcript_support_level": null
},
{
"aa_alt": "V",
"aa_end": null,
"aa_length": 523,
"aa_ref": "M",
"aa_start": 38,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2455,
"cdna_start": 277,
"cds_end": null,
"cds_length": 1572,
"cds_start": 112,
"consequences": [
"missense_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_017017538.2",
"gene_hgnc_id": 18983,
"gene_symbol": "NPAS4",
"hgvs_c": "c.112A>G",
"hgvs_p": "p.Met38Val",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016873027.1",
"strand": true,
"transcript": "XM_017017538.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 234,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1221,
"cdna_start": null,
"cds_end": null,
"cds_length": 705,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_017017539.1",
"gene_hgnc_id": 18983,
"gene_symbol": "NPAS4",
"hgvs_c": "c.*255A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016873028.1",
"strand": true,
"transcript": "XM_017017539.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 326,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 2,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000524617.1",
"gene_hgnc_id": 18983,
"gene_symbol": "NPAS4",
"hgvs_c": "n.320A>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000524617.1",
"transcript_support_level": 3
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs76159120",
"effect": "missense_variant",
"frequency_reference_population": 0.0000013739434,
"gene_hgnc_id": 18983,
"gene_symbol": "NPAS4",
"gnomad_exomes_ac": 2,
"gnomad_exomes_af": 0.00000137394,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.169,
"pos": 66423839,
"ref": "A",
"revel_prediction": "Benign",
"revel_score": 0.046,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_178864.4"
}
]
}