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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: 9-72789207-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=72789207&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 72789207,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "ENST00000297784.10",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMC1",
"gene_hgnc_id": 16513,
"hgvs_c": "c.1114G>A",
"hgvs_p": "p.Val372Met",
"transcript": "NM_138691.3",
"protein_id": "NP_619636.2",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 760,
"cds_start": 1114,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 1847,
"cdna_end": null,
"cdna_length": 5340,
"mane_select": "ENST00000297784.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMC1",
"gene_hgnc_id": 16513,
"hgvs_c": "c.1114G>A",
"hgvs_p": "p.Val372Met",
"transcript": "ENST00000297784.10",
"protein_id": "ENSP00000297784.6",
"transcript_support_level": 1,
"aa_start": 372,
"aa_end": null,
"aa_length": 760,
"cds_start": 1114,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 1847,
"cdna_end": null,
"cdna_length": 5340,
"mane_select": "NM_138691.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMC1",
"gene_hgnc_id": 16513,
"hgvs_c": "c.1114G>A",
"hgvs_p": "p.Val372Met",
"transcript": "ENST00000340019.4",
"protein_id": "ENSP00000341433.3",
"transcript_support_level": 5,
"aa_start": 372,
"aa_end": null,
"aa_length": 760,
"cds_start": 1114,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 1521,
"cdna_end": null,
"cdna_length": 3068,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMC1",
"gene_hgnc_id": 16513,
"hgvs_c": "c.1114G>A",
"hgvs_p": "p.Val372Met",
"transcript": "ENST00000645208.2",
"protein_id": "ENSP00000494684.1",
"transcript_support_level": null,
"aa_start": 372,
"aa_end": null,
"aa_length": 760,
"cds_start": 1114,
"cds_end": null,
"cds_length": 2283,
"cdna_start": 1655,
"cdna_end": null,
"cdna_length": 5142,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMC1",
"gene_hgnc_id": 16513,
"hgvs_c": "c.988G>A",
"hgvs_p": "p.Val330Met",
"transcript": "ENST00000645773.1",
"protein_id": "ENSP00000493698.1",
"transcript_support_level": null,
"aa_start": 330,
"aa_end": null,
"aa_length": 687,
"cds_start": 988,
"cds_end": null,
"cds_length": 2064,
"cdna_start": 1378,
"cdna_end": null,
"cdna_length": 2454,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMC1",
"gene_hgnc_id": 16513,
"hgvs_c": "c.676G>A",
"hgvs_p": "p.Val226Met",
"transcript": "ENST00000651183.1",
"protein_id": "ENSP00000498723.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 636,
"cds_start": 676,
"cds_end": null,
"cds_length": 1911,
"cdna_start": 1291,
"cdna_end": null,
"cdna_length": 4707,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMC1",
"gene_hgnc_id": 16513,
"hgvs_c": "c.676G>A",
"hgvs_p": "p.Val226Met",
"transcript": "ENST00000646619.1",
"protein_id": "ENSP00000493726.1",
"transcript_support_level": null,
"aa_start": 226,
"aa_end": null,
"aa_length": 626,
"cds_start": 676,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 1016,
"cdna_end": null,
"cdna_length": 2221,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMC1",
"gene_hgnc_id": 16513,
"hgvs_c": "c.1117G>A",
"hgvs_p": "p.Val373Met",
"transcript": "XM_017014256.2",
"protein_id": "XP_016869745.1",
"transcript_support_level": null,
"aa_start": 373,
"aa_end": null,
"aa_length": 761,
"cds_start": 1117,
"cds_end": null,
"cds_length": 2286,
"cdna_start": 1377,
"cdna_end": null,
"cdna_length": 4870,
"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": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMC1",
"gene_hgnc_id": 16513,
"hgvs_c": "n.676G>A",
"hgvs_p": null,
"transcript": "ENST00000644967.1",
"protein_id": "ENSP00000496159.1",
"transcript_support_level": null,
"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": 2477,
"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": 12,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMC1",
"gene_hgnc_id": 16513,
"hgvs_c": "n.676G>A",
"hgvs_p": null,
"transcript": "ENST00000645053.1",
"protein_id": "ENSP00000493838.1",
"transcript_support_level": null,
"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": 4445,
"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": 11,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMC1",
"gene_hgnc_id": 16513,
"hgvs_c": "n.1154G>A",
"hgvs_p": null,
"transcript": "ENST00000645787.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2514,
"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": 13,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TMC1",
"gene_hgnc_id": 16513,
"hgvs_c": "n.1412G>A",
"hgvs_p": null,
"transcript": "ENST00000650689.1",
"protein_id": null,
"transcript_support_level": null,
"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": 2122,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "TMC1",
"gene_hgnc_id": 16513,
"dbsnp": "rs367924428",
"frequency_reference_population": 0.00007002133,
"hom_count_reference_population": 0,
"allele_count_reference_population": 113,
"gnomad_exomes_af": 0.0000718356,
"gnomad_genomes_af": 0.0000525887,
"gnomad_exomes_ac": 105,
"gnomad_genomes_ac": 8,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.6846906542778015,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.09000000357627869,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.699,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8548,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.17,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 2.892,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.09,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PP2,PP5",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PP2",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000297784.10",
"gene_symbol": "TMC1",
"hgnc_id": 16513,
"effects": [
"missense_variant"
],
"inheritance_mode": "SD,AR,AD",
"hgvs_c": "c.1114G>A",
"hgvs_p": "p.Val372Met"
}
],
"clinvar_disease": " autosomal recessive,Autosomal dominant nonsyndromic hearing loss 36,Autosomal recessive nonsyndromic hearing loss 7,Hearing loss,Nonsyndromic genetic hearing loss,not provided",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 LP:3 US:1",
"phenotype_combined": "not provided|Nonsyndromic genetic hearing loss|Autosomal recessive nonsyndromic hearing loss 7;Autosomal dominant nonsyndromic hearing loss 36|Hearing loss, autosomal recessive",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}