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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: 15-34348299-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=34348299&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 2,
"criteria": [
"BP4_Moderate"
],
"effects": [
"missense_variant"
],
"gene_symbol": "NUTM1",
"hgnc_id": 29919,
"hgvs_c": "c.431C>T",
"hgvs_p": "p.Ser144Leu",
"inheritance_mode": "AR",
"pathogenic_score": 0,
"score": -2,
"transcript": "NM_001284292.2",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_score": -2,
"allele_count_reference_population": 121,
"alphamissense_prediction": null,
"alphamissense_score": 0.0865,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.54,
"chr": "15",
"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": 0.0834081768989563,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1160,
"aa_ref": "S",
"aa_start": 144,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4109,
"cdna_start": 813,
"cds_end": null,
"cds_length": 3483,
"cds_start": 431,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_001284292.2",
"gene_hgnc_id": 29919,
"gene_symbol": "NUTM1",
"hgvs_c": "c.431C>T",
"hgvs_p": "p.Ser144Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000537011.6",
"protein_coding": true,
"protein_id": "NP_001271221.2",
"strand": true,
"transcript": "NM_001284292.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1160,
"aa_ref": "S",
"aa_start": 144,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4109,
"cdna_start": 813,
"cds_end": null,
"cds_length": 3483,
"cds_start": 431,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000537011.6",
"gene_hgnc_id": 29919,
"gene_symbol": "NUTM1",
"hgvs_c": "c.431C>T",
"hgvs_p": "p.Ser144Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001284292.2",
"protein_coding": true,
"protein_id": "ENSP00000444896.1",
"strand": true,
"transcript": "ENST00000537011.6",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1132,
"aa_ref": "S",
"aa_start": 116,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4196,
"cdna_start": 898,
"cds_end": null,
"cds_length": 3399,
"cds_start": 347,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000333756.5",
"gene_hgnc_id": 29919,
"gene_symbol": "NUTM1",
"hgvs_c": "c.347C>T",
"hgvs_p": "p.Ser116Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000329448.4",
"strand": true,
"transcript": "ENST00000333756.5",
"transcript_support_level": 1
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1150,
"aa_ref": "S",
"aa_start": 134,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4015,
"cdna_start": 719,
"cds_end": null,
"cds_length": 3453,
"cds_start": 401,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001284293.2",
"gene_hgnc_id": 29919,
"gene_symbol": "NUTM1",
"hgvs_c": "c.401C>T",
"hgvs_p": "p.Ser134Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001271222.2",
"strand": true,
"transcript": "NM_001284293.2",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1150,
"aa_ref": "S",
"aa_start": 134,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3922,
"cdna_start": 624,
"cds_end": null,
"cds_length": 3453,
"cds_start": 401,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000438749.7",
"gene_hgnc_id": 29919,
"gene_symbol": "NUTM1",
"hgvs_c": "c.401C>T",
"hgvs_p": "p.Ser134Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000407031.3",
"strand": true,
"transcript": "ENST00000438749.7",
"transcript_support_level": 2
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1132,
"aa_ref": "S",
"aa_start": 116,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4194,
"cdna_start": 898,
"cds_end": null,
"cds_length": 3399,
"cds_start": 347,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "NM_175741.3",
"gene_hgnc_id": 29919,
"gene_symbol": "NUTM1",
"hgvs_c": "c.347C>T",
"hgvs_p": "p.Ser116Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_786883.2",
"strand": true,
"transcript": "NM_175741.3",
"transcript_support_level": null
},
{
"aa_alt": "L",
"aa_end": null,
"aa_length": 1132,
"aa_ref": "S",
"aa_start": 116,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4197,
"cdna_start": 901,
"cds_end": null,
"cds_length": 3399,
"cds_start": 347,
"consequences": [
"missense_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "XM_047432341.1",
"gene_hgnc_id": 29919,
"gene_symbol": "NUTM1",
"hgvs_c": "c.347C>T",
"hgvs_p": "p.Ser116Leu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047288297.1",
"strand": true,
"transcript": "XM_047432341.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs199644358",
"effect": "missense_variant",
"frequency_reference_population": 0.000074964,
"gene_hgnc_id": 29919,
"gene_symbol": "NUTM1",
"gnomad_exomes_ac": 112,
"gnomad_exomes_af": 0.0000766139,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 9,
"gnomad_genomes_af": 0.0000591203,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "not specified",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.361,
"pos": 34348299,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.045,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_001284292.2"
}
]
}