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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: 17-7218281-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=7218281&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 7218281,
"ref": "T",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000648172.9",
"consequences": [
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG4",
"gene_hgnc_id": 2903,
"hgvs_c": "c.119A>T",
"hgvs_p": "p.Asp40Val",
"transcript": "ENST00000648172.9",
"protein_id": "ENSP00000497806.3",
"transcript_support_level": null,
"aa_start": 40,
"aa_end": null,
"aa_length": 767,
"cds_start": 119,
"cds_end": null,
"cds_length": 2304,
"cdna_start": 1106,
"cdna_end": null,
"cdna_length": 6812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG4",
"gene_hgnc_id": 2903,
"hgvs_c": "c.119A>T",
"hgvs_p": "p.Asp40Val",
"transcript": "ENST00000399510.8",
"protein_id": "ENSP00000382428.3",
"transcript_support_level": 1,
"aa_start": 40,
"aa_end": null,
"aa_length": 764,
"cds_start": 119,
"cds_end": null,
"cds_length": 2295,
"cdna_start": 1106,
"cdna_end": null,
"cdna_length": 4100,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG4",
"gene_hgnc_id": 2903,
"hgvs_c": "n.119A>T",
"hgvs_p": null,
"transcript": "ENST00000491753.2",
"protein_id": "ENSP00000467897.2",
"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": 3505,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG4",
"gene_hgnc_id": 2903,
"hgvs_c": "c.119A>T",
"hgvs_p": "p.Asp40Val",
"transcript": "NM_001365.5",
"protein_id": "NP_001356.1",
"transcript_support_level": null,
"aa_start": 40,
"aa_end": null,
"aa_length": 767,
"cds_start": 119,
"cds_end": null,
"cds_length": 2304,
"cdna_start": 1106,
"cdna_end": null,
"cdna_length": 6812,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "D",
"aa_alt": "V",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG4",
"gene_hgnc_id": 2903,
"hgvs_c": "c.119A>T",
"hgvs_p": "p.Asp40Val",
"transcript": "NM_001321074.1",
"protein_id": "NP_001308003.1",
"transcript_support_level": null,
"aa_start": 40,
"aa_end": null,
"aa_length": 764,
"cds_start": 119,
"cds_end": null,
"cds_length": 2295,
"cdna_start": 1320,
"cdna_end": null,
"cdna_length": 4314,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG4",
"gene_hgnc_id": 2903,
"hgvs_c": "n.25A>T",
"hgvs_p": null,
"transcript": "ENST00000648707.1",
"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": 2357,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DLG4",
"gene_hgnc_id": 2903,
"hgvs_c": "n.1320A>T",
"hgvs_p": null,
"transcript": "NR_135527.1",
"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": 4213,
"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": 21,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ACADVL",
"gene_hgnc_id": 92,
"hgvs_c": "c.131+463T>A",
"hgvs_p": null,
"transcript": "NM_001270447.2",
"protein_id": "NP_001257376.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 678,
"cds_start": -4,
"cds_end": null,
"cds_length": 2037,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2227,
"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": 21,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ACADVL",
"gene_hgnc_id": 92,
"hgvs_c": "c.131+463T>A",
"hgvs_p": null,
"transcript": "ENST00000543245.6",
"protein_id": "ENSP00000438689.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 678,
"cds_start": -4,
"cds_end": null,
"cds_length": 2037,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DLG4",
"gene_hgnc_id": 2903,
"dbsnp": "rs2142949377",
"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": 0.18424773216247559,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.4620000123977661,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.127,
"revel_prediction": "Benign",
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.41,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.493,
"phylop100way_prediction": "Benign",
"spliceai_max_score": null,
"spliceai_max_prediction": null,
"dbscsnv_ada_score": 0.800001763770604,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000648172.9",
"gene_symbol": "DLG4",
"hgnc_id": 2903,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.119A>T",
"hgvs_p": "p.Asp40Val"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_001270447.2",
"gene_symbol": "ACADVL",
"hgnc_id": 92,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.131+463T>A",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}