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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: 1-40835019-T-TACGAC (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=40835019&ref=T&alt=TACGAC&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 40835019,
"ref": "T",
"alt": "TACGAC",
"effect": "frameshift_variant",
"transcript": "ENST00000347132.10",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "TT?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ4",
"gene_hgnc_id": 6298,
"hgvs_c": "c.1667_1671dupACGAC",
"hgvs_p": "p.Val558fs",
"transcript": "NM_004700.4",
"protein_id": "NP_004691.2",
"transcript_support_level": null,
"aa_start": 558,
"aa_end": null,
"aa_length": 695,
"cds_start": 1672,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 1979,
"cdna_end": null,
"cdna_length": 4324,
"mane_select": "ENST00000347132.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "TT?",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ4",
"gene_hgnc_id": 6298,
"hgvs_c": "c.1667_1671dupACGAC",
"hgvs_p": "p.Val558fs",
"transcript": "ENST00000347132.10",
"protein_id": "ENSP00000262916.6",
"transcript_support_level": 1,
"aa_start": 558,
"aa_end": null,
"aa_length": 695,
"cds_start": 1672,
"cds_end": null,
"cds_length": 2088,
"cdna_start": 1979,
"cdna_end": null,
"cdna_length": 4324,
"mane_select": "NM_004700.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "TT?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ4",
"gene_hgnc_id": 6298,
"hgvs_c": "c.1505_1509dupACGAC",
"hgvs_p": "p.Val504fs",
"transcript": "NM_172163.3",
"protein_id": "NP_751895.1",
"transcript_support_level": null,
"aa_start": 504,
"aa_end": null,
"aa_length": 641,
"cds_start": 1510,
"cds_end": null,
"cds_length": 1926,
"cdna_start": 1817,
"cdna_end": null,
"cdna_length": 4162,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "TT?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ4",
"gene_hgnc_id": 6298,
"hgvs_c": "c.1505_1509dupACGAC",
"hgvs_p": "p.Val504fs",
"transcript": "ENST00000509682.6",
"protein_id": "ENSP00000423756.2",
"transcript_support_level": 5,
"aa_start": 504,
"aa_end": null,
"aa_length": 641,
"cds_start": 1510,
"cds_end": null,
"cds_length": 1926,
"cdna_start": 1510,
"cdna_end": null,
"cdna_length": 1926,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "TT?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ4",
"gene_hgnc_id": 6298,
"hgvs_c": "c.1247_1251dupACGAC",
"hgvs_p": "p.Val418fs",
"transcript": "ENST00000443478.3",
"protein_id": "ENSP00000406735.3",
"transcript_support_level": 5,
"aa_start": 418,
"aa_end": null,
"aa_length": 555,
"cds_start": 1252,
"cds_end": null,
"cds_length": 1668,
"cdna_start": 1253,
"cdna_end": null,
"cdna_length": 2435,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "TT?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ4",
"gene_hgnc_id": 6298,
"hgvs_c": "c.1667_1671dupACGAC",
"hgvs_p": "p.Val558fs",
"transcript": "XM_047434057.1",
"protein_id": "XP_047290013.1",
"transcript_support_level": null,
"aa_start": 558,
"aa_end": null,
"aa_length": 687,
"cds_start": 1672,
"cds_end": null,
"cds_length": 2064,
"cdna_start": 1979,
"cdna_end": null,
"cdna_length": 2400,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "TT?",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"frameshift_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ4",
"gene_hgnc_id": 6298,
"hgvs_c": "c.650_654dupACGAC",
"hgvs_p": "p.Val219fs",
"transcript": "XM_017002792.2",
"protein_id": "XP_016858281.1",
"transcript_support_level": null,
"aa_start": 219,
"aa_end": null,
"aa_length": 356,
"cds_start": 655,
"cds_end": null,
"cds_length": 1071,
"cdna_start": 995,
"cdna_end": null,
"cdna_length": 3340,
"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": 9,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ4",
"gene_hgnc_id": 6298,
"hgvs_c": "n.986_990dupACGAC",
"hgvs_p": null,
"transcript": "ENST00000506017.1",
"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": 3335,
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ4",
"gene_hgnc_id": 6298,
"hgvs_c": "n.1443_1447dupACGAC",
"hgvs_p": null,
"transcript": "XR_007064876.1",
"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": 1609,
"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": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "KCNQ4",
"gene_hgnc_id": 6298,
"hgvs_c": "n.1443_1447dupACGAC",
"hgvs_p": null,
"transcript": "XR_007064877.1",
"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": 1608,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "KCNQ4",
"gene_hgnc_id": 6298,
"dbsnp": "rs1553168601",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": null,
"computational_prediction_selected": null,
"computational_source_selected": null,
"splice_score_selected": null,
"splice_prediction_selected": null,
"splice_source_selected": null,
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 9.317,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 12,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"verdict": "Pathogenic",
"transcript": "ENST00000347132.10",
"gene_symbol": "KCNQ4",
"hgnc_id": 6298,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.1667_1671dupACGAC",
"hgvs_p": "p.Val558fs"
}
],
"clinvar_disease": "Rare genetic deafness",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Rare genetic deafness",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}