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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: 3-133759306-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=133759306&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 133759306,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001063.4",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.1180G>A",
"hgvs_p": "p.Glu394Lys",
"transcript": "NM_001063.4",
"protein_id": "NP_001054.2",
"transcript_support_level": null,
"aa_start": 394,
"aa_end": null,
"aa_length": 698,
"cds_start": 1180,
"cds_end": null,
"cds_length": 2097,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000402696.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001063.4"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.1180G>A",
"hgvs_p": "p.Glu394Lys",
"transcript": "ENST00000402696.9",
"protein_id": "ENSP00000385834.3",
"transcript_support_level": 1,
"aa_start": 394,
"aa_end": null,
"aa_length": 698,
"cds_start": 1180,
"cds_end": null,
"cds_length": 2097,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001063.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000402696.9"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.1048G>A",
"hgvs_p": "p.Glu350Lys",
"transcript": "NM_001354703.2",
"protein_id": "NP_001341632.2",
"transcript_support_level": null,
"aa_start": 350,
"aa_end": null,
"aa_length": 654,
"cds_start": 1048,
"cds_end": null,
"cds_length": 1965,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001354703.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.799G>A",
"hgvs_p": "p.Glu267Lys",
"transcript": "NM_001354704.2",
"protein_id": "NP_001341633.2",
"transcript_support_level": null,
"aa_start": 267,
"aa_end": null,
"aa_length": 571,
"cds_start": 799,
"cds_end": null,
"cds_length": 1716,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001354704.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.532G>A",
"hgvs_p": "p.Glu178Lys",
"transcript": "ENST00000877249.1",
"protein_id": "ENSP00000547308.1",
"transcript_support_level": null,
"aa_start": 178,
"aa_end": null,
"aa_length": 482,
"cds_start": 532,
"cds_end": null,
"cds_length": 1449,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877249.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.175G>A",
"hgvs_p": "p.Glu59Lys",
"transcript": "ENST00000877245.1",
"protein_id": "ENSP00000547304.1",
"transcript_support_level": null,
"aa_start": 59,
"aa_end": null,
"aa_length": 363,
"cds_start": 175,
"cds_end": null,
"cds_length": 1092,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877245.1"
},
{
"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": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.217-4876G>A",
"hgvs_p": null,
"transcript": "ENST00000877246.1",
"protein_id": "ENSP00000547305.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 369,
"cds_start": null,
"cds_end": null,
"cds_length": 1110,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877246.1"
},
{
"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": 8,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.44-5569G>A",
"hgvs_p": null,
"transcript": "ENST00000877248.1",
"protein_id": "ENSP00000547307.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 280,
"cds_start": null,
"cds_end": null,
"cds_length": 843,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877248.1"
},
{
"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": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.43+12823G>A",
"hgvs_p": null,
"transcript": "ENST00000877247.1",
"protein_id": "ENSP00000547306.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 150,
"cds_start": null,
"cds_end": null,
"cds_length": 453,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000877247.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "n.*236G>A",
"hgvs_p": null,
"transcript": "ENST00000485977.1",
"protein_id": "ENSP00000418716.1",
"transcript_support_level": 3,
"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": "ENST00000485977.1"
}
],
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"dbsnp": "rs121918680",
"frequency_reference_population": 0.0000024792332,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000205266,
"gnomad_genomes_af": 0.00000658397,
"gnomad_exomes_ac": 3,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8221797943115234,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.316,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.303,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.752,
"phylop100way_prediction": "Uncertain_significance",
"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": 3,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,PP3",
"acmg_by_gene": [
{
"score": 3,
"benign_score": 0,
"pathogenic_score": 3,
"criteria": [
"PM2",
"PP3"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001063.4",
"gene_symbol": "TF",
"hgnc_id": 11740,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1180G>A",
"hgvs_p": "p.Glu394Lys"
}
],
"clinvar_disease": "Atransferrinemia,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "Atransferrinemia|not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}