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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: 19-57399238-C-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=57399238&ref=C&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 57399238,
"ref": "C",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001172773.2",
"consequences": [
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF548",
"gene_hgnc_id": 26561,
"hgvs_c": "c.987C>A",
"hgvs_p": "p.Phe329Leu",
"transcript": "NM_001172773.2",
"protein_id": "NP_001166244.1",
"transcript_support_level": null,
"aa_start": 329,
"aa_end": null,
"aa_length": 545,
"cds_start": 987,
"cds_end": null,
"cds_length": 1638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000336128.12",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001172773.2"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF548",
"gene_hgnc_id": 26561,
"hgvs_c": "c.987C>A",
"hgvs_p": "p.Phe329Leu",
"transcript": "ENST00000336128.12",
"protein_id": "ENSP00000337555.6",
"transcript_support_level": 2,
"aa_start": 329,
"aa_end": null,
"aa_length": 545,
"cds_start": 987,
"cds_end": null,
"cds_length": 1638,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001172773.2",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000336128.12"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF548",
"gene_hgnc_id": 26561,
"hgvs_c": "c.951C>A",
"hgvs_p": "p.Phe317Leu",
"transcript": "ENST00000366197.10",
"protein_id": "ENSP00000379482.3",
"transcript_support_level": 1,
"aa_start": 317,
"aa_end": null,
"aa_length": 533,
"cds_start": 951,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000366197.10"
},
{
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000269533",
"gene_hgnc_id": null,
"hgvs_c": "c.51+5015C>A",
"hgvs_p": null,
"transcript": "ENST00000596400.1",
"protein_id": "ENSP00000472277.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 178,
"cds_start": null,
"cds_end": null,
"cds_length": 538,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000596400.1"
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000268533",
"gene_hgnc_id": null,
"hgvs_c": "c.39+5015C>A",
"hgvs_p": null,
"transcript": "ENST00000597410.1",
"protein_id": "ENSP00000472152.1",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 71,
"cds_start": null,
"cds_end": null,
"cds_length": 216,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000597410.1"
},
{
"aa_ref": "F",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF548",
"gene_hgnc_id": 26561,
"hgvs_c": "c.951C>A",
"hgvs_p": "p.Phe317Leu",
"transcript": "NM_152909.4",
"protein_id": "NP_690873.2",
"transcript_support_level": null,
"aa_start": 317,
"aa_end": null,
"aa_length": 533,
"cds_start": 951,
"cds_end": null,
"cds_length": 1602,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152909.4"
},
{
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000269533",
"gene_hgnc_id": null,
"hgvs_c": "c.178+2064C>A",
"hgvs_p": null,
"transcript": "ENST00000596617.5",
"protein_id": "ENSP00000471870.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": 105,
"cds_start": null,
"cds_end": null,
"cds_length": 320,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000596617.5"
},
{
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000269533",
"gene_hgnc_id": null,
"hgvs_c": "n.291+2064C>A",
"hgvs_p": null,
"transcript": "ENST00000600421.1",
"protein_id": null,
"transcript_support_level": 4,
"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": "ENST00000600421.1"
}
],
"gene_symbol": "ZNF548",
"gene_hgnc_id": 26561,
"dbsnp": "rs779076002",
"frequency_reference_population": 0.000059492235,
"hom_count_reference_population": 0,
"allele_count_reference_population": 96,
"gnomad_exomes_af": 0.0000622484,
"gnomad_genomes_af": 0.0000329442,
"gnomad_exomes_ac": 91,
"gnomad_genomes_ac": 5,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.02593371272087097,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.061,
"revel_prediction": "Benign",
"alphamissense_score": 0.8454,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.67,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.619,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_001172773.2",
"gene_symbol": "ZNF548",
"hgnc_id": 26561,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.987C>A",
"hgvs_p": "p.Phe329Leu"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000597410.1",
"gene_symbol": "ENSG00000268533",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.39+5015C>A",
"hgvs_p": null
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000596400.1",
"gene_symbol": "ENSG00000269533",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.51+5015C>A",
"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
}