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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: 3-119503609-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=119503609&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 119503609,
"ref": "G",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000494664.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.438G>T",
"hgvs_p": "p.Val146Val",
"transcript": "NM_016589.4",
"protein_id": "NP_057673.2",
"transcript_support_level": null,
"aa_start": 146,
"aa_end": null,
"aa_length": 285,
"cds_start": 438,
"cds_end": null,
"cds_length": 858,
"cdna_start": 625,
"cdna_end": null,
"cdna_length": 2379,
"mane_select": "ENST00000494664.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.438G>T",
"hgvs_p": "p.Val146Val",
"transcript": "ENST00000494664.6",
"protein_id": "ENSP00000418803.1",
"transcript_support_level": 1,
"aa_start": 146,
"aa_end": null,
"aa_length": 285,
"cds_start": 438,
"cds_end": null,
"cds_length": 858,
"cdna_start": 625,
"cdna_end": null,
"cdna_length": 2379,
"mane_select": "NM_016589.4",
"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": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "n.438G>T",
"hgvs_p": null,
"transcript": "ENST00000264244.7",
"protein_id": "ENSP00000264244.3",
"transcript_support_level": 1,
"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": 1271,
"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": 2,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "n.272G>T",
"hgvs_p": null,
"transcript": "ENST00000492164.5",
"protein_id": "ENSP00000418846.1",
"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": 725,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.194+4682G>T",
"hgvs_p": null,
"transcript": "NM_001438040.1",
"protein_id": "NP_001424969.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 151,
"cds_start": -4,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1168,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.194+4682G>T",
"hgvs_p": null,
"transcript": "ENST00000493694.1",
"protein_id": "ENSP00000419510.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 151,
"cds_start": -4,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 710,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "c.195-345G>T",
"hgvs_p": null,
"transcript": "ENST00000466984.1",
"protein_id": "ENSP00000420122.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 149,
"cds_start": -4,
"cds_end": null,
"cds_length": 452,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 605,
"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": 4,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "n.*177+2749G>T",
"hgvs_p": null,
"transcript": "ENST00000463927.6",
"protein_id": "ENSP00000417205.2",
"transcript_support_level": 5,
"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": 670,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "n.488-345G>T",
"hgvs_p": null,
"transcript": "ENST00000469324.1",
"protein_id": null,
"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": 634,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "n.194+4682G>T",
"hgvs_p": null,
"transcript": "ENST00000486418.5",
"protein_id": "ENSP00000417083.1",
"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": 551,
"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": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"hgvs_c": "n.*2+4676G>T",
"hgvs_p": null,
"transcript": "ENST00000498399.1",
"protein_id": "ENSP00000420812.1",
"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": 684,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TIMMDC1",
"gene_hgnc_id": 1321,
"dbsnp": "rs1131265",
"frequency_reference_population": 6.8683863e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.86839e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.4699999988079071,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.07999999821186066,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.47,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.599,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.08,
"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": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000494664.6",
"gene_symbol": "TIMMDC1",
"hgnc_id": 1321,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.438G>T",
"hgvs_p": "p.Val146Val"
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}