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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: 20-63895150-G-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=63895150&ref=G&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"5_prime_UTR_variant"
],
"gene_symbol": "DNAJC5",
"hgnc_id": 16235,
"hgvs_c": "c.-185G>T",
"hgvs_p": null,
"inheritance_mode": "AD",
"pathogenic_score": 2,
"score": -2,
"transcript": "NM_025219.3",
"verdict": "Likely_benign"
},
{
"benign_score": 4,
"criteria": [
"PM2",
"BP4_Strong"
],
"effects": [
"intron_variant"
],
"gene_symbol": "ENSG00000290226",
"hgnc_id": null,
"hgvs_c": "n.453+12330G>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 2,
"score": -2,
"transcript": "ENST00000703636.1",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_score": -2,
"allele_count_reference_population": 1,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.73,
"chr": "20",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": " 4 (Kufs type), Recessive, neuronal,Ceroid lipofuscinosis,Neuronal Ceroid-Lipofuscinosis",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.7300000190734863,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 198,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5249,
"cdna_start": null,
"cds_end": null,
"cds_length": 597,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "NM_025219.3",
"gene_hgnc_id": 16235,
"gene_symbol": "DNAJC5",
"hgvs_c": "c.-185G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000360864.9",
"protein_coding": true,
"protein_id": "NP_079495.1",
"strand": true,
"transcript": "NM_025219.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 198,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 5249,
"cdna_start": null,
"cds_end": null,
"cds_length": 597,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000360864.9",
"gene_hgnc_id": 16235,
"gene_symbol": "DNAJC5",
"hgvs_c": "c.-185G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_025219.3",
"protein_coding": true,
"protein_id": "ENSP00000354111.4",
"strand": true,
"transcript": "ENST00000360864.9",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 198,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5266,
"cdna_start": null,
"cds_end": null,
"cds_length": 597,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000898575.1",
"gene_hgnc_id": 16235,
"gene_symbol": "DNAJC5",
"hgvs_c": "c.-180G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000568634.1",
"strand": true,
"transcript": "ENST00000898575.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 198,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5247,
"cdna_start": null,
"cds_end": null,
"cds_length": 597,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "ENST00000921989.1",
"gene_hgnc_id": 16235,
"gene_symbol": "DNAJC5",
"hgvs_c": "c.-97G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592048.1",
"strand": true,
"transcript": "ENST00000921989.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 198,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6934,
"cdna_start": null,
"cds_end": null,
"cds_length": 597,
"cds_start": null,
"consequences": [
"5_prime_UTR_variant"
],
"exon_count": 5,
"exon_rank": 1,
"exon_rank_end": null,
"feature": "XM_047440509.1",
"gene_hgnc_id": 16235,
"gene_symbol": "DNAJC5",
"hgvs_c": "c.-1870G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047296465.1",
"strand": true,
"transcript": "XM_047440509.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 198,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4481,
"cdna_start": null,
"cds_end": null,
"cds_length": 597,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000921990.1",
"gene_hgnc_id": 16235,
"gene_symbol": "DNAJC5",
"hgvs_c": "c.-12+27G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000592049.1",
"strand": true,
"transcript": "ENST00000921990.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 198,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5080,
"cdna_start": null,
"cds_end": null,
"cds_length": 597,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000961697.1",
"gene_hgnc_id": 16235,
"gene_symbol": "DNAJC5",
"hgvs_c": "c.-12+470G>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000631756.1",
"strand": true,
"transcript": "ENST00000961697.1",
"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": 571,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 5,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000703636.1",
"gene_hgnc_id": null,
"gene_symbol": "ENSG00000290226",
"hgvs_c": "n.453+12330G>T",
"hgvs_p": null,
"intron_rank": 4,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000703636.1",
"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": 5287,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"upstream_gene_variant"
],
"exon_count": 6,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000470551.1",
"gene_hgnc_id": 16235,
"gene_symbol": "DNAJC5",
"hgvs_c": "n.-185G>T",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": "ENSP00000434744.1",
"strand": true,
"transcript": "ENST00000470551.1",
"transcript_support_level": 2
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs886056928",
"effect": "5_prime_UTR_variant",
"frequency_reference_population": 0.0000066472567,
"gene_hgnc_id": 16235,
"gene_symbol": "DNAJC5",
"gnomad_exomes_ac": 0,
"gnomad_exomes_af": 0,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": 1,
"gnomad_genomes_af": 0.00000664726,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Neuronal Ceroid-Lipofuscinosis, Recessive|Ceroid lipofuscinosis, neuronal, 4 (Kufs type)",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.63,
"pos": 63895150,
"ref": "G",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_025219.3"
}
]
}