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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: 15-52153947-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=15&pos=52153947&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "15",
"pos": 52153947,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_016194.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB5",
"gene_hgnc_id": 4401,
"hgvs_c": "c.368C>T",
"hgvs_p": "p.Ser123Leu",
"transcript": "NM_016194.4",
"protein_id": "NP_057278.2",
"transcript_support_level": null,
"aa_start": 123,
"aa_end": null,
"aa_length": 395,
"cds_start": 368,
"cds_end": null,
"cds_length": 1188,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000261837.12",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016194.4"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB5",
"gene_hgnc_id": 4401,
"hgvs_c": "c.368C>T",
"hgvs_p": "p.Ser123Leu",
"transcript": "ENST00000261837.12",
"protein_id": "ENSP00000261837.7",
"transcript_support_level": 5,
"aa_start": 123,
"aa_end": null,
"aa_length": 395,
"cds_start": 368,
"cds_end": null,
"cds_length": 1188,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016194.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000261837.12"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB5",
"gene_hgnc_id": 4401,
"hgvs_c": "c.242C>T",
"hgvs_p": "p.Ser81Leu",
"transcript": "ENST00000358784.11",
"protein_id": "ENSP00000351635.7",
"transcript_support_level": 1,
"aa_start": 81,
"aa_end": null,
"aa_length": 353,
"cds_start": 242,
"cds_end": null,
"cds_length": 1062,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000358784.11"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB5",
"gene_hgnc_id": 4401,
"hgvs_c": "c.242C>T",
"hgvs_p": "p.Ser81Leu",
"transcript": "ENST00000396335.8",
"protein_id": "ENSP00000379626.4",
"transcript_support_level": 1,
"aa_start": 81,
"aa_end": null,
"aa_length": 283,
"cds_start": 242,
"cds_end": null,
"cds_length": 852,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000396335.8"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB5",
"gene_hgnc_id": 4401,
"hgvs_c": "c.242C>T",
"hgvs_p": "p.Ser81Leu",
"transcript": "ENST00000560116.1",
"protein_id": "ENSP00000453176.1",
"transcript_support_level": 1,
"aa_start": 81,
"aa_end": null,
"aa_length": 126,
"cds_start": 242,
"cds_end": null,
"cds_length": 381,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000560116.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB5",
"gene_hgnc_id": 4401,
"hgvs_c": "c.242C>T",
"hgvs_p": "p.Ser81Leu",
"transcript": "NM_006578.4",
"protein_id": "NP_006569.1",
"transcript_support_level": null,
"aa_start": 81,
"aa_end": null,
"aa_length": 353,
"cds_start": 242,
"cds_end": null,
"cds_length": 1062,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_006578.4"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB5",
"gene_hgnc_id": 4401,
"hgvs_c": "c.86C>T",
"hgvs_p": "p.Ser29Leu",
"transcript": "NM_001379343.1",
"protein_id": "NP_001366272.1",
"transcript_support_level": null,
"aa_start": 29,
"aa_end": null,
"aa_length": 301,
"cds_start": 86,
"cds_end": null,
"cds_length": 906,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001379343.1"
},
{
"aa_ref": "S",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB5",
"gene_hgnc_id": 4401,
"hgvs_c": "c.242C>T",
"hgvs_p": "p.Ser81Leu",
"transcript": "XM_011521162.4",
"protein_id": "XP_011519464.1",
"transcript_support_level": null,
"aa_start": 81,
"aa_end": null,
"aa_length": 353,
"cds_start": 242,
"cds_end": null,
"cds_length": 1062,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011521162.4"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB5",
"gene_hgnc_id": 4401,
"hgvs_c": "n.399C>T",
"hgvs_p": null,
"transcript": "ENST00000560075.1",
"protein_id": null,
"transcript_support_level": 5,
"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": "retained_intron",
"feature": "ENST00000560075.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "GNB5",
"gene_hgnc_id": 4401,
"hgvs_c": "n.242C>T",
"hgvs_p": null,
"transcript": "ENST00000561313.5",
"protein_id": "ENSP00000454185.1",
"transcript_support_level": 4,
"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": "nonsense_mediated_decay",
"feature": "ENST00000561313.5"
}
],
"gene_symbol": "GNB5",
"gene_hgnc_id": 4401,
"dbsnp": "rs761399728",
"frequency_reference_population": 0.000019239458,
"hom_count_reference_population": 0,
"allele_count_reference_population": 31,
"gnomad_exomes_af": 0.0000205609,
"gnomad_genomes_af": 0.00000657073,
"gnomad_exomes_ac": 30,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.8653452396392822,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.64,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.9915,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.23,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.825,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0,
"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": "PM5,PP3_Moderate,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 12,
"benign_score": 0,
"pathogenic_score": 12,
"criteria": [
"PM5",
"PP3_Moderate",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_016194.4",
"gene_symbol": "GNB5",
"hgnc_id": 4401,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,Unknown",
"hgvs_c": "c.368C>T",
"hgvs_p": "p.Ser123Leu"
}
],
"clinvar_disease": "Attention deficit hyperactivity disorder,Delayed speech and language development,Global developmental delay,Gnb5-related intellectual disability-cardiac arrhythmia syndrome,Inborn genetic diseases,Language delay and attention deficit-hyperactivity disorder/cognitive impairment with or without cardiac arrhythmia,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:4 O:2",
"phenotype_combined": "Global developmental delay;Attention deficit hyperactivity disorder;Delayed speech and language development|not provided|Language delay and attention deficit-hyperactivity disorder/cognitive impairment with or without cardiac arrhythmia|Inborn genetic diseases|Gnb5-related intellectual disability-cardiac arrhythmia syndrome;Language delay and attention deficit-hyperactivity disorder/cognitive impairment with or without cardiac arrhythmia|Gnb5-related intellectual disability-cardiac arrhythmia syndrome",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}