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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: 7-107694694-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=107694694&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"effects": [
"stop_gained"
],
"gene_symbol": "SLC26A4",
"hgnc_id": 8818,
"hgvs_c": "c.1415G>A",
"hgvs_p": "p.Trp472*",
"inheritance_mode": "AR,AD",
"pathogenic_score": 18,
"score": 18,
"transcript": "NM_000441.2",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_score": 18,
"allele_count_reference_population": 0,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "A",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.66,
"chr": "7",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_disease": "Autosomal recessive nonsyndromic hearing loss 4,Pendred syndrome,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:2",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.6600000262260437,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 780,
"aa_ref": "W",
"aa_start": 472,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4737,
"cdna_start": 1446,
"cds_end": null,
"cds_length": 2343,
"cds_start": 1415,
"consequences": [
"stop_gained"
],
"exon_count": 21,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "NM_000441.2",
"gene_hgnc_id": 8818,
"gene_symbol": "SLC26A4",
"hgvs_c": "c.1415G>A",
"hgvs_p": "p.Trp472*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000644269.2",
"protein_coding": true,
"protein_id": "NP_000432.1",
"strand": true,
"transcript": "NM_000441.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 780,
"aa_ref": "W",
"aa_start": 472,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 4737,
"cdna_start": 1446,
"cds_end": null,
"cds_length": 2343,
"cds_start": 1415,
"consequences": [
"stop_gained"
],
"exon_count": 21,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000644269.2",
"gene_hgnc_id": 8818,
"gene_symbol": "SLC26A4",
"hgvs_c": "c.1415G>A",
"hgvs_p": "p.Trp472*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_000441.2",
"protein_coding": true,
"protein_id": "ENSP00000494017.1",
"strand": true,
"transcript": "ENST00000644269.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 780,
"aa_ref": "W",
"aa_start": 472,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4373,
"cdna_start": 2463,
"cds_end": null,
"cds_length": 2343,
"cds_start": 1415,
"consequences": [
"stop_gained"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000888701.1",
"gene_hgnc_id": 8818,
"gene_symbol": "SLC26A4",
"hgvs_c": "c.1415G>A",
"hgvs_p": "p.Trp472*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000558760.1",
"strand": true,
"transcript": "ENST00000888701.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 754,
"aa_ref": "W",
"aa_start": 446,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4066,
"cdna_start": 1372,
"cds_end": null,
"cds_length": 2265,
"cds_start": 1337,
"consequences": [
"stop_gained"
],
"exon_count": 20,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "ENST00000888700.1",
"gene_hgnc_id": 8818,
"gene_symbol": "SLC26A4",
"hgvs_c": "c.1337G>A",
"hgvs_p": "p.Trp446*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000558759.1",
"strand": true,
"transcript": "ENST00000888700.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 750,
"aa_ref": "W",
"aa_start": 442,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4054,
"cdna_start": 1360,
"cds_end": null,
"cds_length": 2253,
"cds_start": 1325,
"consequences": [
"stop_gained"
],
"exon_count": 21,
"exon_rank": 12,
"exon_rank_end": null,
"feature": "ENST00000888699.1",
"gene_hgnc_id": 8818,
"gene_symbol": "SLC26A4",
"hgvs_c": "c.1325G>A",
"hgvs_p": "p.Trp442*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000558758.1",
"strand": true,
"transcript": "ENST00000888699.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 572,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 4,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000460748.1",
"gene_hgnc_id": 8818,
"gene_symbol": "SLC26A4",
"hgvs_c": "n.518G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000460748.1",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 554,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000477350.5",
"gene_hgnc_id": 8818,
"gene_symbol": "SLC26A4",
"hgvs_c": "n.262G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000477350.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 710,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 3,
"exon_rank_end": null,
"feature": "ENST00000480841.5",
"gene_hgnc_id": 8818,
"gene_symbol": "SLC26A4",
"hgvs_c": "n.264G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000480841.5",
"transcript_support_level": 3
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 559,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000497446.5",
"gene_hgnc_id": 8818,
"gene_symbol": "SLC26A4",
"hgvs_c": "n.430G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000497446.5",
"transcript_support_level": 4
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "nonsense_mediated_decay",
"canonical": false,
"cdna_end": null,
"cdna_length": 2905,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 10,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000644846.1",
"gene_hgnc_id": 8818,
"gene_symbol": "SLC26A4",
"hgvs_c": "n.125G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000494344.1",
"strand": true,
"transcript": "ENST00000644846.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1554359693",
"effect": "stop_gained",
"frequency_reference_population": null,
"gene_hgnc_id": 8818,
"gene_symbol": "SLC26A4",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"phenotype_combined": "Pendred syndrome|not provided|Autosomal recessive nonsyndromic hearing loss 4",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 8.844,
"pos": 107694694,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.03999999910593033,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.04,
"transcript": "NM_000441.2"
}
]
}