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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: 8-98193384-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=8&pos=98193384&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "8",
"pos": 98193384,
"ref": "C",
"alt": "T",
"effect": "intron_variant",
"transcript": "ENST00000430223.7",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "NIPAL2",
"gene_hgnc_id": 25854,
"hgvs_c": "c.1040-294G>A",
"hgvs_p": null,
"transcript": "NM_001321635.2",
"protein_id": "NP_001308564.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 383,
"cds_start": -4,
"cds_end": null,
"cds_length": 1152,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4402,
"mane_select": "ENST00000430223.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 10,
"intron_rank_end": null,
"gene_symbol": "NIPAL2",
"gene_hgnc_id": 25854,
"hgvs_c": "c.1040-294G>A",
"hgvs_p": null,
"transcript": "ENST00000430223.7",
"protein_id": "ENSP00000407087.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 383,
"cds_start": -4,
"cds_end": null,
"cds_length": 1152,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4402,
"mane_select": "NM_001321635.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "NIPAL2",
"gene_hgnc_id": 25854,
"hgvs_c": "c.1067+1G>A",
"hgvs_p": null,
"transcript": "NM_024759.3",
"protein_id": "NP_079035.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 368,
"cds_start": -4,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4430,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "NIPAL2",
"gene_hgnc_id": 25854,
"hgvs_c": "c.1067+1G>A",
"hgvs_p": null,
"transcript": "ENST00000341166.3",
"protein_id": "ENSP00000339256.3",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 368,
"cds_start": -4,
"cds_end": null,
"cds_length": 1107,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4581,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "NIPAL2",
"gene_hgnc_id": 25854,
"hgvs_c": "c.945-294G>A",
"hgvs_p": null,
"transcript": "NM_001321636.2",
"protein_id": "NP_001308565.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 327,
"cds_start": -4,
"cds_end": null,
"cds_length": 984,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4307,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 9,
"intron_rank_end": null,
"gene_symbol": "NIPAL2",
"gene_hgnc_id": 25854,
"hgvs_c": "n.1059-294G>A",
"hgvs_p": null,
"transcript": "ENST00000520545.5",
"protein_id": null,
"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": 1391,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "NIPAL2",
"gene_hgnc_id": 25854,
"hgvs_c": "n.1302-294G>A",
"hgvs_p": null,
"transcript": "NR_135745.2",
"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": 4566,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 12,
"intron_rank_end": null,
"gene_symbol": "NIPAL2",
"gene_hgnc_id": 25854,
"hgvs_c": "n.1424-294G>A",
"hgvs_p": null,
"transcript": "NR_135746.2",
"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": 4688,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": 11,
"intron_rank_end": null,
"gene_symbol": "NIPAL2",
"gene_hgnc_id": 25854,
"hgvs_c": "n.1362-294G>A",
"hgvs_p": null,
"transcript": "NR_135747.2",
"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": 4626,
"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": 3,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NIPAL2-AS1",
"gene_hgnc_id": 56271,
"hgvs_c": "n.662+13340C>T",
"hgvs_p": null,
"transcript": "XR_928444.3",
"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": 775,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NIPAL2",
"gene_hgnc_id": 25854,
"dbsnp": "rs3735887",
"frequency_reference_population": 0.52052575,
"hom_count_reference_population": 220036,
"allele_count_reference_population": 839227,
"gnomad_exomes_af": 0.519595,
"gnomad_genomes_af": 0.529465,
"gnomad_exomes_ac": 758742,
"gnomad_genomes_ac": 80485,
"gnomad_exomes_homalt": 198617,
"gnomad_genomes_homalt": 21419,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.7200000286102295,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.7699999809265137,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.72,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.134,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.999074020852647,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -7,
"acmg_classification": "Benign",
"acmg_criteria": "PP3,BA1",
"acmg_by_gene": [
{
"score": -7,
"benign_score": 8,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000430223.7",
"gene_symbol": "NIPAL2",
"hgnc_id": 25854,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1040-294G>A",
"hgvs_p": null
},
{
"score": -7,
"benign_score": 8,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BA1"
],
"verdict": "Benign",
"transcript": "XR_928444.3",
"gene_symbol": "NIPAL2-AS1",
"hgnc_id": 56271,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.662+13340C>T",
"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
}