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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: 1-153816507-TCC-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=153816507&ref=TCC&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 153816507,
"ref": "TCC",
"alt": "T",
"effect": "frameshift_variant",
"transcript": "NM_020699.4",
"consequences": [
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.980_981delGG",
"hgvs_p": "p.Gly327fs",
"transcript": "NM_020699.4",
"protein_id": "NP_065750.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 593,
"cds_start": 980,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000368655.5",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020699.4"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.980_981delGG",
"hgvs_p": "p.Gly327fs",
"transcript": "ENST00000368655.5",
"protein_id": "ENSP00000357644.4",
"transcript_support_level": 1,
"aa_start": 327,
"aa_end": null,
"aa_length": 593,
"cds_start": 980,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020699.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000368655.5"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.980_981delGG",
"hgvs_p": "p.Gly327fs",
"transcript": "ENST00000634544.1",
"protein_id": "ENSP00000489184.1",
"transcript_support_level": 5,
"aa_start": 327,
"aa_end": null,
"aa_length": 593,
"cds_start": 980,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000634544.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.980_981delGG",
"hgvs_p": "p.Gly327fs",
"transcript": "ENST00000867096.1",
"protein_id": "ENSP00000537155.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 593,
"cds_start": 980,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000867096.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.980_981delGG",
"hgvs_p": "p.Gly327fs",
"transcript": "ENST00000867097.1",
"protein_id": "ENSP00000537156.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 593,
"cds_start": 980,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000867097.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.980_981delGG",
"hgvs_p": "p.Gly327fs",
"transcript": "ENST00000867098.1",
"protein_id": "ENSP00000537157.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 593,
"cds_start": 980,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000867098.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.932_933delGG",
"hgvs_p": "p.Gly311fs",
"transcript": "ENST00000634408.1",
"protein_id": "ENSP00000489595.1",
"transcript_support_level": 5,
"aa_start": 311,
"aa_end": null,
"aa_length": 577,
"cds_start": 932,
"cds_end": null,
"cds_length": 1734,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000634408.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.557_558delGG",
"hgvs_p": "p.Gly186fs",
"transcript": "ENST00000703630.1",
"protein_id": "ENSP00000515408.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 263,
"cds_start": 557,
"cds_end": null,
"cds_length": 793,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000703630.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.233_234delGG",
"hgvs_p": "p.Gly78fs",
"transcript": "ENST00000634564.1",
"protein_id": "ENSP00000489309.1",
"transcript_support_level": 5,
"aa_start": 78,
"aa_end": null,
"aa_length": 261,
"cds_start": 233,
"cds_end": null,
"cds_length": 787,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000634564.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.983_984delGG",
"hgvs_p": "p.Gly328fs",
"transcript": "XM_047426115.1",
"protein_id": "XP_047282071.1",
"transcript_support_level": null,
"aa_start": 328,
"aa_end": null,
"aa_length": 594,
"cds_start": 983,
"cds_end": null,
"cds_length": 1785,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426115.1"
},
{
"aa_ref": "G",
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"frameshift_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"hgvs_c": "c.980_981delGG",
"hgvs_p": "p.Gly327fs",
"transcript": "XM_047426117.1",
"protein_id": "XP_047282073.1",
"transcript_support_level": null,
"aa_start": 327,
"aa_end": null,
"aa_length": 593,
"cds_start": 980,
"cds_end": null,
"cds_length": 1782,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047426117.1"
},
{
"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": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000291199",
"gene_hgnc_id": null,
"hgvs_c": "n.297-11456_297-11455delCC",
"hgvs_p": null,
"transcript": "ENST00000820544.1",
"protein_id": null,
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000820544.1"
}
],
"gene_symbol": "GATAD2B",
"gene_hgnc_id": 30778,
"dbsnp": "rs797045594",
"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": 0.1899999976158142,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": null,
"bayesdelnoaf_prediction": null,
"phylop100way_score": 3.019,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.19,
"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": 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": "NM_020699.4",
"gene_symbol": "GATAD2B",
"hgnc_id": 30778,
"effects": [
"frameshift_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.980_981delGG",
"hgvs_p": "p.Gly327fs"
},
{
"score": 4,
"benign_score": 0,
"pathogenic_score": 4,
"criteria": [
"PM2",
"PP5_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000820544.1",
"gene_symbol": "ENSG00000291199",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.297-11456_297-11455delCC",
"hgvs_p": null
}
],
"clinvar_disease": "Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome",
"clinvar_classification": "Likely pathogenic",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LP:1",
"phenotype_combined": "Severe intellectual disability-poor language-strabismus-grimacing face-long fingers syndrome",
"pathogenicity_classification_combined": "Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}