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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: 9-72700517-GAGA-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=72700517&ref=GAGA&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 16,
"criteria": [
"PM4_Supporting",
"PP3_Moderate",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"effects": [
"conservative_inframe_deletion"
],
"gene_symbol": "TMC1",
"hgnc_id": 16513,
"hgvs_c": "c.247_249delGAA",
"hgvs_p": "p.Glu83del",
"inheritance_mode": "Unknown,AR,AD,SD",
"pathogenic_score": 3,
"score": -13,
"transcript": "NM_138691.3",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "PM4_Supporting,PP3_Moderate,BP6_Very_Strong,BS1,BS2",
"acmg_score": -13,
"allele_count_reference_population": 18914,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": null,
"bayesdelnoaf_score": null,
"chr": "9",
"clinvar_classification": "Benign/Likely benign",
"clinvar_disease": " Dominant, autosomal recessive,Hearing loss,Nonsyndromic Hearing Loss,not provided,not specified",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:2 B:8",
"computational_prediction_selected": null,
"computational_score_selected": null,
"computational_source_selected": null,
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 760,
"aa_ref": "E",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5340,
"cdna_start": 980,
"cds_end": null,
"cds_length": 2283,
"cds_start": 247,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 24,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "NM_138691.3",
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"hgvs_c": "c.247_249delGAA",
"hgvs_p": "p.Glu83del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000297784.10",
"protein_coding": true,
"protein_id": "NP_619636.2",
"strand": true,
"transcript": "NM_138691.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 760,
"aa_ref": "E",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5340,
"cdna_start": 980,
"cds_end": null,
"cds_length": 2283,
"cds_start": 247,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 24,
"exon_rank": 8,
"exon_rank_end": null,
"feature": "ENST00000297784.10",
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"hgvs_c": "c.247_249delGAA",
"hgvs_p": "p.Glu83del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_138691.3",
"protein_coding": true,
"protein_id": "ENSP00000297784.6",
"strand": true,
"transcript": "ENST00000297784.10",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 760,
"aa_ref": "E",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 3068,
"cdna_start": 654,
"cds_end": null,
"cds_length": 2283,
"cds_start": 247,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 22,
"exon_rank": 6,
"exon_rank_end": null,
"feature": "ENST00000340019.4",
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"hgvs_c": "c.247_249delGAA",
"hgvs_p": "p.Glu83del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000341433.3",
"strand": true,
"transcript": "ENST00000340019.4",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 760,
"aa_ref": "E",
"aa_start": 83,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5142,
"cdna_start": 788,
"cds_end": null,
"cds_length": 2283,
"cds_start": 247,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 23,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000645208.2",
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"hgvs_c": "c.247_249delGAA",
"hgvs_p": "p.Glu83del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000494684.1",
"strand": true,
"transcript": "ENST00000645208.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 761,
"aa_ref": "E",
"aa_start": 84,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4870,
"cdna_start": 510,
"cds_end": null,
"cds_length": 2286,
"cds_start": 250,
"consequences": [
"conservative_inframe_deletion"
],
"exon_count": 21,
"exon_rank": 5,
"exon_rank_end": null,
"feature": "XM_017014256.2",
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"hgvs_c": "c.250_252delGAA",
"hgvs_p": "p.Glu84del",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016869745.1",
"strand": true,
"transcript": "XM_017014256.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 687,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2454,
"cdna_start": null,
"cds_end": null,
"cds_length": 2064,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 20,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000645773.1",
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"hgvs_c": "c.236+5814_236+5816delGAA",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493698.1",
"strand": true,
"transcript": "ENST00000645773.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 636,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4707,
"cdna_start": null,
"cds_end": null,
"cds_length": 1911,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 20,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000651183.1",
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"hgvs_c": "c.-77+5814_-77+5816delGAA",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000498723.1",
"strand": true,
"transcript": "ENST00000651183.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 626,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2221,
"cdna_start": null,
"cds_end": null,
"cds_length": 1881,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 18,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000646619.1",
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"hgvs_c": "c.-77+5814_-77+5816delGAA",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000493726.1",
"strand": true,
"transcript": "ENST00000646619.1",
"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": 2514,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 20,
"exon_rank": 4,
"exon_rank_end": null,
"feature": "ENST00000645787.1",
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"hgvs_c": "n.287_289delGAA",
"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": "ENST00000645787.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 905,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 7,
"exon_rank": 7,
"exon_rank_end": null,
"feature": "ENST00000646244.1",
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"hgvs_c": "n.697_699delGAA",
"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": "ENST00000646244.1",
"transcript_support_level": null
},
{
"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": 2477,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 20,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000644967.1",
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"hgvs_c": "n.-77+5814_-77+5816delGAA",
"hgvs_p": null,
"intron_rank": 3,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000496159.1",
"strand": true,
"transcript": "ENST00000644967.1",
"transcript_support_level": null
},
{
"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": 4445,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 19,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000645053.1",
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"hgvs_c": "n.-77+5814_-77+5816delGAA",
"hgvs_p": null,
"intron_rank": 5,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000493838.1",
"strand": true,
"transcript": "ENST00000645053.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 2122,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 15,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000650689.1",
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"hgvs_c": "n.660+5814_660+5816delGAA",
"hgvs_p": null,
"intron_rank": 6,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000650689.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs376040866",
"effect": "conservative_inframe_deletion",
"frequency_reference_population": 0.011908419,
"gene_hgnc_id": 16513,
"gene_symbol": "TMC1",
"gnomad_exomes_ac": 17463,
"gnomad_exomes_af": 0.0121542,
"gnomad_exomes_homalt": 141,
"gnomad_genomes_ac": 1451,
"gnomad_genomes_af": 0.0095773,
"gnomad_genomes_homalt": 16,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 157,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Benign/Likely benign",
"phenotype_combined": "not specified|Nonsyndromic Hearing Loss, Dominant|not provided|Hearing loss, autosomal recessive",
"phylop100way_prediction": "Uncertain_significance",
"phylop100way_score": 5.687,
"pos": 72700517,
"ref": "GAGA",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Pathogenic",
"splice_score_selected": 0.9599999785423279,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Pathogenic",
"spliceai_max_score": 0.96,
"transcript": "NM_138691.3"
}
]
}