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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: 19-58480356-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=19&pos=58480356&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "19",
"pos": 58480356,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_017908.4",
"consequences": [
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF446",
"gene_hgnc_id": 21036,
"hgvs_c": "c.983C>T",
"hgvs_p": "p.Pro328Leu",
"transcript": "NM_017908.4",
"protein_id": "NP_060378.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 450,
"cds_start": 983,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000594369.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_017908.4"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF446",
"gene_hgnc_id": 21036,
"hgvs_c": "c.983C>T",
"hgvs_p": "p.Pro328Leu",
"transcript": "ENST00000594369.6",
"protein_id": "ENSP00000472802.1",
"transcript_support_level": 1,
"aa_start": 328,
"aa_end": null,
"aa_length": 450,
"cds_start": 983,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_017908.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000594369.6"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF446",
"gene_hgnc_id": 21036,
"hgvs_c": "c.983C>T",
"hgvs_p": "p.Pro328Leu",
"transcript": "ENST00000610298.1",
"protein_id": "ENSP00000478778.1",
"transcript_support_level": 1,
"aa_start": 328,
"aa_end": null,
"aa_length": 422,
"cds_start": 983,
"cds_end": null,
"cds_length": 1269,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000610298.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF446",
"gene_hgnc_id": 21036,
"hgvs_c": "c.983C>T",
"hgvs_p": "p.Pro328Leu",
"transcript": "ENST00000864814.1",
"protein_id": "ENSP00000534873.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 450,
"cds_start": 983,
"cds_end": null,
"cds_length": 1353,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864814.1"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF446",
"gene_hgnc_id": 21036,
"hgvs_c": "c.830C>T",
"hgvs_p": "p.Pro277Leu",
"transcript": "ENST00000596341.5",
"protein_id": "ENSP00000472219.1",
"transcript_support_level": 5,
"aa_start": 277,
"aa_end": null,
"aa_length": 399,
"cds_start": 830,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000596341.5"
},
{
"aa_ref": "P",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF446",
"gene_hgnc_id": 21036,
"hgvs_c": "c.830C>T",
"hgvs_p": "p.Pro277Leu",
"transcript": "ENST00000943129.1",
"protein_id": "ENSP00000613188.1",
"transcript_support_level": null,
"aa_start": 277,
"aa_end": null,
"aa_length": 399,
"cds_start": 830,
"cds_end": null,
"cds_length": 1200,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000943129.1"
},
{
"aa_ref": "P",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF446",
"gene_hgnc_id": 21036,
"hgvs_c": "c.898C>T",
"hgvs_p": "p.Pro300Ser",
"transcript": "ENST00000335841.8",
"protein_id": "ENSP00000336565.4",
"transcript_support_level": 5,
"aa_start": 300,
"aa_end": null,
"aa_length": 336,
"cds_start": 898,
"cds_end": null,
"cds_length": 1011,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000335841.8"
},
{
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ZNF446",
"gene_hgnc_id": 21036,
"hgvs_c": "c.802+337C>T",
"hgvs_p": null,
"transcript": "NM_001304453.1",
"protein_id": "NP_001291382.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 304,
"cds_start": null,
"cds_end": null,
"cds_length": 915,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001304453.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZNF446",
"gene_hgnc_id": 21036,
"hgvs_c": "n.1280C>T",
"hgvs_p": null,
"transcript": "ENST00000391694.4",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000391694.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC27A5",
"gene_hgnc_id": 10999,
"hgvs_c": "n.*710G>A",
"hgvs_p": null,
"transcript": "ENST00000595851.5",
"protein_id": "ENSP00000469512.1",
"transcript_support_level": 2,
"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": "nonsense_mediated_decay",
"feature": "ENST00000595851.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC27A5",
"gene_hgnc_id": 10999,
"hgvs_c": "n.*710G>A",
"hgvs_p": null,
"transcript": "ENST00000595851.5",
"protein_id": "ENSP00000469512.1",
"transcript_support_level": 2,
"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": "nonsense_mediated_decay",
"feature": "ENST00000595851.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SLC27A5",
"gene_hgnc_id": 10999,
"hgvs_c": "c.*471G>A",
"hgvs_p": null,
"transcript": "ENST00000864562.1",
"protein_id": "ENSP00000534621.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 690,
"cds_start": null,
"cds_end": null,
"cds_length": 2073,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000864562.1"
}
],
"gene_symbol": "ZNF446",
"gene_hgnc_id": 21036,
"dbsnp": "rs34732619",
"frequency_reference_population": 0.0077670277,
"hom_count_reference_population": 63,
"allele_count_reference_population": 12453,
"gnomad_exomes_af": 0.00809453,
"gnomad_genomes_af": 0.00464762,
"gnomad_exomes_ac": 11745,
"gnomad_genomes_ac": 708,
"gnomad_exomes_homalt": 59,
"gnomad_genomes_homalt": 4,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.004432052373886108,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.031,
"revel_prediction": "Benign",
"alphamissense_score": 0.1338,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.83,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.465,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -10,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Moderate,BS2",
"acmg_by_gene": [
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_017908.4",
"gene_symbol": "ZNF446",
"hgnc_id": 21036,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.983C>T",
"hgvs_p": "p.Pro328Leu"
},
{
"score": -10,
"benign_score": 10,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Moderate",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000595851.5",
"gene_symbol": "SLC27A5",
"hgnc_id": 10999,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.*710G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}