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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: 3-133777188-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=133777188&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 133777188,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001063.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.2012G>A",
"hgvs_p": "p.Gly671Glu",
"transcript": "NM_001063.4",
"protein_id": "NP_001054.2",
"transcript_support_level": null,
"aa_start": 671,
"aa_end": null,
"aa_length": 698,
"cds_start": 2012,
"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": "G",
"aa_alt": "E",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.2012G>A",
"hgvs_p": "p.Gly671Glu",
"transcript": "ENST00000402696.9",
"protein_id": "ENSP00000385834.3",
"transcript_support_level": 1,
"aa_start": 671,
"aa_end": null,
"aa_length": 698,
"cds_start": 2012,
"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": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "n.3006G>A",
"hgvs_p": null,
"transcript": "ENST00000467842.1",
"protein_id": null,
"transcript_support_level": 1,
"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": "ENST00000467842.1"
},
{
"aa_ref": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.1880G>A",
"hgvs_p": "p.Gly627Glu",
"transcript": "NM_001354703.2",
"protein_id": "NP_001341632.2",
"transcript_support_level": null,
"aa_start": 627,
"aa_end": null,
"aa_length": 654,
"cds_start": 1880,
"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": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.1631G>A",
"hgvs_p": "p.Gly544Glu",
"transcript": "NM_001354704.2",
"protein_id": "NP_001341633.2",
"transcript_support_level": null,
"aa_start": 544,
"aa_end": null,
"aa_length": 571,
"cds_start": 1631,
"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": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.1364G>A",
"hgvs_p": "p.Gly455Glu",
"transcript": "ENST00000877249.1",
"protein_id": "ENSP00000547308.1",
"transcript_support_level": null,
"aa_start": 455,
"aa_end": null,
"aa_length": 482,
"cds_start": 1364,
"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": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.1025G>A",
"hgvs_p": "p.Gly342Glu",
"transcript": "ENST00000877246.1",
"protein_id": "ENSP00000547305.1",
"transcript_support_level": null,
"aa_start": 342,
"aa_end": null,
"aa_length": 369,
"cds_start": 1025,
"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": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.1007G>A",
"hgvs_p": "p.Gly336Glu",
"transcript": "ENST00000877245.1",
"protein_id": "ENSP00000547304.1",
"transcript_support_level": null,
"aa_start": 336,
"aa_end": null,
"aa_length": 363,
"cds_start": 1007,
"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": "G",
"aa_alt": "E",
"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": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.758G>A",
"hgvs_p": "p.Gly253Glu",
"transcript": "ENST00000877248.1",
"protein_id": "ENSP00000547307.1",
"transcript_support_level": null,
"aa_start": 253,
"aa_end": null,
"aa_length": 280,
"cds_start": 758,
"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": "G",
"aa_alt": "E",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.368G>A",
"hgvs_p": "p.Gly123Glu",
"transcript": "ENST00000877247.1",
"protein_id": "ENSP00000547306.1",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 150,
"cds_start": 368,
"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": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "n.*312G>A",
"hgvs_p": null,
"transcript": "ENST00000461695.1",
"protein_id": "ENSP00000419714.1",
"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": "ENST00000461695.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "n.*312G>A",
"hgvs_p": null,
"transcript": "ENST00000461695.1",
"protein_id": "ENSP00000419714.1",
"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": "ENST00000461695.1"
}
],
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"dbsnp": "rs121918677",
"frequency_reference_population": 0.0038537555,
"hom_count_reference_population": 17,
"allele_count_reference_population": 6220,
"gnomad_exomes_af": 0.00394875,
"gnomad_genomes_af": 0.00294191,
"gnomad_exomes_ac": 5772,
"gnomad_genomes_ac": 448,
"gnomad_exomes_homalt": 14,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.019947469234466553,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.386,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.7741,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 5.209,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_001063.4",
"gene_symbol": "TF",
"hgnc_id": 11740,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2012G>A",
"hgvs_p": "p.Gly671Glu"
}
],
"clinvar_disease": "Atransferrinemia,TF-related disorder,Transferrin variant B2,not provided,not specified",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LB:5",
"phenotype_combined": "Transferrin variant B2|Atransferrinemia|not provided|not specified|TF-related disorder",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}