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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: 4-88697686-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=4&pos=88697686&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "4",
"pos": 88697686,
"ref": "T",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000323061.7",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAP1L5",
"gene_hgnc_id": 19968,
"hgvs_c": "c.69A>T",
"hgvs_p": "p.Ala23Ala",
"transcript": "NM_153757.4",
"protein_id": "NP_715638.1",
"transcript_support_level": null,
"aa_start": 23,
"aa_end": null,
"aa_length": 182,
"cds_start": 69,
"cds_end": null,
"cds_length": 549,
"cdna_start": 144,
"cdna_end": null,
"cdna_length": 1917,
"mane_select": "ENST00000323061.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NAP1L5",
"gene_hgnc_id": 19968,
"hgvs_c": "c.69A>T",
"hgvs_p": "p.Ala23Ala",
"transcript": "ENST00000323061.7",
"protein_id": "ENSP00000320488.5",
"transcript_support_level": 6,
"aa_start": 23,
"aa_end": null,
"aa_length": 182,
"cds_start": 69,
"cds_end": null,
"cds_length": 549,
"cdna_start": 144,
"cdna_end": null,
"cdna_length": 1917,
"mane_select": "NM_153757.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "HERC3",
"gene_hgnc_id": 4876,
"hgvs_c": "c.2658-6412T>A",
"hgvs_p": null,
"transcript": "NM_014606.3",
"protein_id": "NP_055421.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1050,
"cds_start": -4,
"cds_end": null,
"cds_length": 3153,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4914,
"mane_select": "ENST00000402738.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "HERC3",
"gene_hgnc_id": 4876,
"hgvs_c": "c.2658-6412T>A",
"hgvs_p": null,
"transcript": "ENST00000402738.6",
"protein_id": "ENSP00000385684.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 1050,
"cds_start": -4,
"cds_end": null,
"cds_length": 3153,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4914,
"mane_select": "NM_014606.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "HERC3",
"gene_hgnc_id": 4876,
"hgvs_c": "c.2634-6412T>A",
"hgvs_p": null,
"transcript": "ENST00000512194.2",
"protein_id": "ENSP00000421021.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 1042,
"cds_start": -4,
"cds_end": null,
"cds_length": 3129,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4967,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "HERC3",
"gene_hgnc_id": 4876,
"hgvs_c": "c.2655-6412T>A",
"hgvs_p": null,
"transcript": "NM_001375480.1",
"protein_id": "NP_001362409.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1049,
"cds_start": -4,
"cds_end": null,
"cds_length": 3150,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4911,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "HERC3",
"gene_hgnc_id": 4876,
"hgvs_c": "c.2634-6412T>A",
"hgvs_p": null,
"transcript": "NM_001375478.1",
"protein_id": "NP_001362407.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1042,
"cds_start": -4,
"cds_end": null,
"cds_length": 3129,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4890,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "HERC3",
"gene_hgnc_id": 4876,
"hgvs_c": "c.2634-6412T>A",
"hgvs_p": null,
"transcript": "NM_001375479.1",
"protein_id": "NP_001362408.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1042,
"cds_start": -4,
"cds_end": null,
"cds_length": 3129,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5028,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "HERC3",
"gene_hgnc_id": 4876,
"hgvs_c": "c.2634-6412T>A",
"hgvs_p": null,
"transcript": "NM_001375482.1",
"protein_id": "NP_001362411.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1042,
"cds_start": -4,
"cds_end": null,
"cds_length": 3129,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4885,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 26,
"intron_rank": 23,
"intron_rank_end": null,
"gene_symbol": "HERC3",
"gene_hgnc_id": 4876,
"hgvs_c": "c.2634-6412T>A",
"hgvs_p": null,
"transcript": "NM_001375483.1",
"protein_id": "NP_001362412.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1042,
"cds_start": -4,
"cds_end": null,
"cds_length": 3129,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5023,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": 22,
"intron_rank_end": null,
"gene_symbol": "HERC3",
"gene_hgnc_id": 4876,
"hgvs_c": "c.2304-6412T>A",
"hgvs_p": null,
"transcript": "NM_001271602.2",
"protein_id": "NP_001258531.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 932,
"cds_start": -4,
"cds_end": null,
"cds_length": 2799,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4659,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "HERC3",
"gene_hgnc_id": 4876,
"hgvs_c": "c.2280-6412T>A",
"hgvs_p": null,
"transcript": "NM_001375477.1",
"protein_id": "NP_001362406.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 924,
"cds_start": -4,
"cds_end": null,
"cds_length": 2775,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4635,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": 21,
"intron_rank_end": null,
"gene_symbol": "HERC3",
"gene_hgnc_id": 4876,
"hgvs_c": "c.2118-6412T>A",
"hgvs_p": null,
"transcript": "NM_001375481.1",
"protein_id": "NP_001362410.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 870,
"cds_start": -4,
"cds_end": null,
"cds_length": 2613,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4473,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NAP1L5",
"gene_hgnc_id": 19968,
"dbsnp": "rs710834",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": 0,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 0,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7900000214576721,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.79,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.927,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000323061.7",
"gene_symbol": "NAP1L5",
"hgnc_id": 19968,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.69A>T",
"hgvs_p": "p.Ala23Ala"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000402738.6",
"gene_symbol": "HERC3",
"hgnc_id": 4876,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.2658-6412T>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}