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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: 20-63930841-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=63930841&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 63930841,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000360864.9",
"consequences": [
{
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "DNAJC5",
"gene_hgnc_id": 16235,
"hgvs_c": "c.322-10C>T",
"hgvs_p": null,
"transcript": "NM_025219.3",
"protein_id": "NP_079495.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": -4,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5249,
"mane_select": "ENST00000360864.9",
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "DNAJC5",
"gene_hgnc_id": 16235,
"hgvs_c": "c.322-10C>T",
"hgvs_p": null,
"transcript": "ENST00000360864.9",
"protein_id": "ENSP00000354111.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": -4,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5249,
"mane_select": "NM_025219.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "DNAJC5",
"gene_hgnc_id": 16235,
"hgvs_c": "n.322-10C>T",
"hgvs_p": null,
"transcript": "ENST00000470551.1",
"protein_id": "ENSP00000434744.1",
"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": 5287,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"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": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "DNAJC5",
"gene_hgnc_id": 16235,
"hgvs_c": "n.322-10C>T",
"hgvs_p": null,
"transcript": "ENST00000703637.1",
"protein_id": "ENSP00000515413.1",
"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": 4037,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "DNAJC5",
"gene_hgnc_id": 16235,
"hgvs_c": "c.322-10C>T",
"hgvs_p": null,
"transcript": "XM_011529048.3",
"protein_id": "XP_011527350.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": -4,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5684,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "DNAJC5",
"gene_hgnc_id": 16235,
"hgvs_c": "c.322-10C>T",
"hgvs_p": null,
"transcript": "XM_047440508.1",
"protein_id": "XP_047296464.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": -4,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5867,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "DNAJC5",
"gene_hgnc_id": 16235,
"hgvs_c": "c.322-10C>T",
"hgvs_p": null,
"transcript": "XM_047440509.1",
"protein_id": "XP_047296465.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": -4,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 6934,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "DNAJC5",
"gene_hgnc_id": 16235,
"hgvs_c": "c.322-10C>T",
"hgvs_p": null,
"transcript": "XM_047440510.1",
"protein_id": "XP_047296466.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": -4,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5793,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "DNAJC5",
"gene_hgnc_id": 16235,
"hgvs_c": "c.322-10C>T",
"hgvs_p": null,
"transcript": "XM_047440511.1",
"protein_id": "XP_047296467.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": -4,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5196,
"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": 5,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "DNAJC5",
"gene_hgnc_id": 16235,
"hgvs_c": "c.322-10C>T",
"hgvs_p": null,
"transcript": "XM_047440512.1",
"protein_id": "XP_047296468.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 198,
"cds_start": -4,
"cds_end": null,
"cds_length": 597,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5072,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DNAJC5",
"gene_hgnc_id": 16235,
"dbsnp": "rs78457562",
"frequency_reference_population": 0.07248074,
"hom_count_reference_population": 4963,
"allele_count_reference_population": 116842,
"gnomad_exomes_af": 0.0722726,
"gnomad_genomes_af": 0.0744758,
"gnomad_exomes_ac": 105498,
"gnomad_genomes_ac": 11344,
"gnomad_exomes_homalt": 4431,
"gnomad_genomes_homalt": 532,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.8199999928474426,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.82,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.529,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.0000135031423102131,
"dbscsnv_ada_prediction": "Benign",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000360864.9",
"gene_symbol": "DNAJC5",
"hgnc_id": 16235,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.322-10C>T",
"hgvs_p": null
}
],
"clinvar_disease": " 4 (Kufs type), Recessive, neuronal,Ceroid lipofuscinosis,Neuronal Ceroid-Lipofuscinosis,Neuronal ceroid lipofuscinosis,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|Neuronal Ceroid-Lipofuscinosis, Recessive|not provided|Ceroid lipofuscinosis, neuronal, 4 (Kufs type)|Neuronal ceroid lipofuscinosis",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}