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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: 16-58020195-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=16&pos=58020195&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 20,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "USB1",
"hgnc_id": 25792,
"hgvs_c": "c.748C>G",
"hgvs_p": "p.Gln250Glu",
"inheritance_mode": "AR,AD",
"pathogenic_score": 0,
"score": -20,
"transcript": "NM_024598.4",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_score": -20,
"allele_count_reference_population": 121260,
"alphamissense_prediction": null,
"alphamissense_score": 0.0586,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.48,
"chr": "16",
"clinvar_classification": "Benign",
"clinvar_disease": "Poikiloderma with neutropenia,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:5",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.0021330416202545166,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 265,
"aa_ref": "Q",
"aa_start": 250,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2248,
"cdna_start": 825,
"cds_end": null,
"cds_length": 798,
"cds_start": 748,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_024598.4",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "c.748C>G",
"hgvs_p": "p.Gln250Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000219281.8",
"protein_coding": true,
"protein_id": "NP_078874.2",
"strand": true,
"transcript": "NM_024598.4",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 265,
"aa_ref": "Q",
"aa_start": 250,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 2248,
"cdna_start": 825,
"cds_end": null,
"cds_length": 798,
"cds_start": 748,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000219281.8",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "c.748C>G",
"hgvs_p": "p.Gln250Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_024598.4",
"protein_coding": true,
"protein_id": "ENSP00000219281.3",
"strand": true,
"transcript": "ENST00000219281.8",
"transcript_support_level": 1
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 252,
"aa_ref": "Q",
"aa_start": 237,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2227,
"cdna_start": 832,
"cds_end": null,
"cds_length": 759,
"cds_start": 709,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000561568.6",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "c.709C>G",
"hgvs_p": "p.Gln237Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000457322.2",
"strand": true,
"transcript": "ENST00000561568.6",
"transcript_support_level": 4
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 247,
"aa_ref": "Q",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2194,
"cdna_start": 771,
"cds_end": null,
"cds_length": 744,
"cds_start": 694,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "NM_001195302.2",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "c.694C>G",
"hgvs_p": "p.Gln232Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001182231.1",
"strand": true,
"transcript": "NM_001195302.2",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 247,
"aa_ref": "Q",
"aa_start": 232,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1212,
"cdna_start": 773,
"cds_end": null,
"cds_length": 744,
"cds_start": 694,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000539737.6",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "c.694C>G",
"hgvs_p": "p.Gln232Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000446143.2",
"strand": true,
"transcript": "ENST00000539737.6",
"transcript_support_level": 2
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 237,
"aa_ref": "Q",
"aa_start": 222,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1710,
"cdna_start": 749,
"cds_end": null,
"cds_length": 714,
"cds_start": 664,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000896281.1",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "c.664C>G",
"hgvs_p": "p.Gln222Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000566340.1",
"strand": true,
"transcript": "ENST00000896281.1",
"transcript_support_level": null
},
{
"aa_alt": "R",
"aa_end": null,
"aa_length": 228,
"aa_ref": "S",
"aa_start": 214,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2489,
"cdna_start": 1066,
"cds_end": null,
"cds_length": 687,
"cds_start": 642,
"consequences": [
"missense_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000698445.1",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "c.642C>G",
"hgvs_p": "p.Ser214Arg",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000513727.1",
"strand": true,
"transcript": "ENST00000698445.1",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 214,
"aa_ref": "Q",
"aa_start": 199,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2154,
"cdna_start": 731,
"cds_end": null,
"cds_length": 645,
"cds_start": 595,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "NM_001330568.2",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "c.595C>G",
"hgvs_p": "p.Gln199Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001317497.1",
"strand": true,
"transcript": "NM_001330568.2",
"transcript_support_level": null
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 214,
"aa_ref": "Q",
"aa_start": 199,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1135,
"cdna_start": 788,
"cds_end": null,
"cds_length": 645,
"cds_start": 595,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000561743.5",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "c.595C>G",
"hgvs_p": "p.Gln199Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000454928.1",
"strand": true,
"transcript": "ENST00000561743.5",
"transcript_support_level": 3
},
{
"aa_alt": "E",
"aa_end": null,
"aa_length": 214,
"aa_ref": "Q",
"aa_start": 199,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2117,
"cdna_start": 722,
"cds_end": null,
"cds_length": 645,
"cds_start": 595,
"consequences": [
"missense_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000698444.1",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "c.595C>G",
"hgvs_p": "p.Gln199Glu",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000513726.1",
"strand": true,
"transcript": "ENST00000698444.1",
"transcript_support_level": null
},
{
"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": 2168,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000565662.6",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "n.*227C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000513729.1",
"strand": true,
"transcript": "ENST00000565662.6",
"transcript_support_level": 4
},
{
"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": 3888,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 3,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000566082.1",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "n.2466C>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": "ENST00000566082.1",
"transcript_support_level": 2
},
{
"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": 2216,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000698446.1",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "n.*439C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000513728.1",
"strand": true,
"transcript": "ENST00000698446.1",
"transcript_support_level": null
},
{
"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": 2224,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000698447.1",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "n.*405C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000513732.1",
"strand": true,
"transcript": "ENST00000698447.1",
"transcript_support_level": null
},
{
"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": 2168,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000565662.6",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "n.*227C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000513729.1",
"strand": true,
"transcript": "ENST00000565662.6",
"transcript_support_level": 4
},
{
"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": 2216,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 6,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000698446.1",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "n.*439C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000513728.1",
"strand": true,
"transcript": "ENST00000698446.1",
"transcript_support_level": null
},
{
"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": 2224,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"3_prime_UTR_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000698447.1",
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"hgvs_c": "n.*405C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000513732.1",
"strand": true,
"transcript": "ENST00000698447.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs16959641",
"effect": "missense_variant",
"frequency_reference_population": 0.0751262,
"gene_hgnc_id": 25792,
"gene_symbol": "USB1",
"gnomad_exomes_ac": 112366,
"gnomad_exomes_af": 0.076866,
"gnomad_exomes_homalt": 4785,
"gnomad_genomes_ac": 8894,
"gnomad_genomes_af": 0.0584201,
"gnomad_genomes_homalt": 381,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 5166,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign",
"phenotype_combined": "not specified|not provided|Poikiloderma with neutropenia",
"phylop100way_prediction": "Benign",
"phylop100way_score": 3.269,
"pos": 58020195,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.119,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.03999999910593033,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.04,
"transcript": "NM_024598.4"
}
]
}