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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: 3-133755484-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=133755484&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 133755484,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000402696.9",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.624G>A",
"hgvs_p": "p.Ser208Ser",
"transcript": "NM_001063.4",
"protein_id": "NP_001054.2",
"transcript_support_level": null,
"aa_start": 208,
"aa_end": null,
"aa_length": 698,
"cds_start": 624,
"cds_end": null,
"cds_length": 2097,
"cdna_start": 672,
"cdna_end": null,
"cdna_length": 20166,
"mane_select": "ENST00000402696.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.624G>A",
"hgvs_p": "p.Ser208Ser",
"transcript": "ENST00000402696.9",
"protein_id": "ENSP00000385834.3",
"transcript_support_level": 1,
"aa_start": 208,
"aa_end": null,
"aa_length": 698,
"cds_start": 624,
"cds_end": null,
"cds_length": 2097,
"cdna_start": 672,
"cdna_end": null,
"cdna_length": 20166,
"mane_select": "NM_001063.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.492G>A",
"hgvs_p": "p.Ser164Ser",
"transcript": "NM_001354703.2",
"protein_id": "NP_001341632.2",
"transcript_support_level": null,
"aa_start": 164,
"aa_end": null,
"aa_length": 654,
"cds_start": 492,
"cds_end": null,
"cds_length": 1965,
"cdna_start": 1640,
"cdna_end": null,
"cdna_length": 21134,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.243G>A",
"hgvs_p": "p.Ser81Ser",
"transcript": "NM_001354704.2",
"protein_id": "NP_001341633.2",
"transcript_support_level": null,
"aa_start": 81,
"aa_end": null,
"aa_length": 571,
"cds_start": 243,
"cds_end": null,
"cds_length": 1716,
"cdna_start": 499,
"cdna_end": null,
"cdna_length": 19993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "c.243G>A",
"hgvs_p": "p.Ser81Ser",
"transcript": "ENST00000482271.5",
"protein_id": "ENSP00000419338.1",
"transcript_support_level": 4,
"aa_start": 81,
"aa_end": null,
"aa_length": 133,
"cds_start": 243,
"cds_end": null,
"cds_length": 403,
"cdna_start": 499,
"cdna_end": null,
"cdna_length": 659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "n.672G>A",
"hgvs_p": null,
"transcript": "ENST00000493011.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 999,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"hgvs_c": "n.158-1448G>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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 580,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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.*253G>A",
"hgvs_p": null,
"transcript": "ENST00000494430.5",
"protein_id": "ENSP00000418396.1",
"transcript_support_level": 4,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 594,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TF",
"gene_hgnc_id": 11740,
"dbsnp": "rs12769",
"frequency_reference_population": 0.31852436,
"hom_count_reference_population": 85910,
"allele_count_reference_population": 514041,
"gnomad_exomes_af": 0.323495,
"gnomad_genomes_af": 0.270777,
"gnomad_exomes_ac": 472839,
"gnomad_genomes_ac": 41202,
"gnomad_exomes_homalt": 79491,
"gnomad_genomes_homalt": 6419,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.9300000071525574,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.93,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -3.601,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.02,
"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": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000402696.9",
"gene_symbol": "TF",
"hgnc_id": 11740,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.624G>A",
"hgvs_p": "p.Ser208Ser"
}
],
"clinvar_disease": "Atransferrinemia,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:3",
"phenotype_combined": "Atransferrinemia|not specified|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}