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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: 2-15468510-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=15468510&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 0,
"criteria": [
"PVS1",
"PM2",
"PP5_Moderate"
],
"effects": [
"stop_gained"
],
"gene_symbol": "NBAS",
"hgnc_id": 15625,
"hgvs_c": "c.1749G>A",
"hgvs_p": "p.Trp583*",
"inheritance_mode": "AR",
"pathogenic_score": 12,
"score": 12,
"transcript": "NM_015909.4",
"verdict": "Pathogenic"
}
],
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Moderate",
"acmg_score": 12,
"allele_count_reference_population": 5,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.66,
"chr": "2",
"clinvar_classification": "Pathogenic",
"clinvar_disease": "Infantile liver failure syndrome 2,NBAS-related disorder,not provided",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "P:1",
"computational_prediction_selected": "Pathogenic",
"computational_score_selected": 0.6600000262260437,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2371,
"aa_ref": "W",
"aa_start": 583,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7278,
"cdna_start": 1779,
"cds_end": null,
"cds_length": 7116,
"cds_start": 1749,
"consequences": [
"stop_gained"
],
"exon_count": 52,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NM_015909.4",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1749G>A",
"hgvs_p": "p.Trp583*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000281513.10",
"protein_coding": true,
"protein_id": "NP_056993.2",
"strand": false,
"transcript": "NM_015909.4",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2371,
"aa_ref": "W",
"aa_start": 583,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 7278,
"cdna_start": 1779,
"cds_end": null,
"cds_length": 7116,
"cds_start": 1749,
"consequences": [
"stop_gained"
],
"exon_count": 52,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000281513.10",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1749G>A",
"hgvs_p": "p.Trp583*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_015909.4",
"protein_coding": true,
"protein_id": "ENSP00000281513.5",
"strand": false,
"transcript": "ENST00000281513.10",
"transcript_support_level": 1
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2326,
"aa_ref": "W",
"aa_start": 583,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7137,
"cdna_start": 1770,
"cds_end": null,
"cds_length": 6981,
"cds_start": 1749,
"consequences": [
"stop_gained"
],
"exon_count": 52,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000914564.1",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1749G>A",
"hgvs_p": "p.Trp583*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000584623.1",
"strand": false,
"transcript": "ENST00000914564.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2265,
"aa_ref": "W",
"aa_start": 477,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6935,
"cdna_start": 1437,
"cds_end": null,
"cds_length": 6798,
"cds_start": 1431,
"consequences": [
"stop_gained"
],
"exon_count": 50,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000914565.1",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1431G>A",
"hgvs_p": "p.Trp477*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000584624.1",
"strand": false,
"transcript": "ENST00000914565.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 796,
"aa_ref": "W",
"aa_start": 422,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 2851,
"cdna_start": 1695,
"cds_end": null,
"cds_length": 2391,
"cds_start": 1266,
"consequences": [
"stop_gained"
],
"exon_count": 22,
"exon_rank": 15,
"exon_rank_end": null,
"feature": "ENST00000700066.1",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1266G>A",
"hgvs_p": "p.Trp422*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000514780.1",
"strand": false,
"transcript": "ENST00000700066.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 628,
"aa_ref": "W",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 1899,
"cdna_start": 1630,
"cds_end": null,
"cds_length": 1889,
"cds_start": 1620,
"consequences": [
"stop_gained"
],
"exon_count": 17,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "ENST00000700069.1",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1620G>A",
"hgvs_p": "p.Trp540*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000514781.1",
"strand": false,
"transcript": "ENST00000700069.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2328,
"aa_ref": "W",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7149,
"cdna_start": 1650,
"cds_end": null,
"cds_length": 6987,
"cds_start": 1620,
"consequences": [
"stop_gained"
],
"exon_count": 51,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_011510357.3",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1620G>A",
"hgvs_p": "p.Trp540*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011508659.1",
"strand": false,
"transcript": "XM_011510357.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2328,
"aa_ref": "W",
"aa_start": 583,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7149,
"cdna_start": 1779,
"cds_end": null,
"cds_length": 6987,
"cds_start": 1749,
"consequences": [
"stop_gained"
],
"exon_count": 51,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_011510358.3",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1749G>A",
"hgvs_p": "p.Trp583*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_011508660.1",
"strand": false,
"transcript": "XM_011510358.3",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2293,
"aa_ref": "W",
"aa_start": 583,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7118,
"cdna_start": 1779,
"cds_end": null,
"cds_length": 6882,
"cds_start": 1749,
"consequences": [
"stop_gained"
],
"exon_count": 53,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_017004317.2",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1749G>A",
"hgvs_p": "p.Trp583*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016859806.1",
"strand": false,
"transcript": "XM_017004317.2",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2293,
"aa_ref": "W",
"aa_start": 583,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7367,
"cdna_start": 1779,
"cds_end": null,
"cds_length": 6882,
"cds_start": 1749,
"consequences": [
"stop_gained"
],
"exon_count": 53,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XM_047444733.1",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1749G>A",
"hgvs_p": "p.Trp583*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047300689.1",
"strand": false,
"transcript": "XM_047444733.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2285,
"aa_ref": "W",
"aa_start": 540,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 7020,
"cdna_start": 1650,
"cds_end": null,
"cds_length": 6858,
"cds_start": 1620,
"consequences": [
"stop_gained"
],
"exon_count": 50,
"exon_rank": 16,
"exon_rank_end": null,
"feature": "XM_047444734.1",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1620G>A",
"hgvs_p": "p.Trp540*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047300690.1",
"strand": false,
"transcript": "XM_047444734.1",
"transcript_support_level": null
},
{
"aa_alt": "*",
"aa_end": null,
"aa_length": 2158,
"aa_ref": "W",
"aa_start": 370,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 6693,
"cdna_start": 1194,
"cds_end": null,
"cds_length": 6477,
"cds_start": 1110,
"consequences": [
"stop_gained"
],
"exon_count": 46,
"exon_rank": 11,
"exon_rank_end": null,
"feature": "XM_047444735.1",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1110G>A",
"hgvs_p": "p.Trp370*",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047300691.1",
"strand": false,
"transcript": "XM_047444735.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1753,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 5399,
"cdna_start": null,
"cds_end": null,
"cds_length": 5262,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 39,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000957312.1",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1083+20384G>A",
"hgvs_p": null,
"intron_rank": 12,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000627371.1",
"strand": false,
"transcript": "ENST00000957312.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 1339,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 4177,
"cdna_start": null,
"cds_end": null,
"cds_length": 4020,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 29,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000901626.1",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "c.1083+20384G>A",
"hgvs_p": null,
"intron_rank": 12,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000571685.1",
"strand": false,
"transcript": "ENST00000901626.1",
"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": 9548,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 41,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000700065.1",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "n.1762G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000700065.1",
"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": 2784,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 22,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000700067.1",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "n.1764G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000700067.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3977,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 21,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "ENST00000700068.1",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "n.1764G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000700068.1",
"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": 7082,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 51,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "NR_052013.3",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "n.1779G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_052013.3",
"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": 7254,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 54,
"exon_rank": 17,
"exon_rank_end": null,
"feature": "XR_007076390.1",
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"hgvs_c": "n.1779G>A",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "XR_007076390.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs770446752",
"effect": "stop_gained",
"frequency_reference_population": 0.0000034205764,
"gene_hgnc_id": 15625,
"gene_symbol": "NBAS",
"gnomad_exomes_ac": 5,
"gnomad_exomes_af": 0.00000342058,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_ac": null,
"gnomad_genomes_af": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 0,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Pathogenic",
"phenotype_combined": "Infantile liver failure syndrome 2|not provided|NBAS-related disorder",
"phylop100way_prediction": "Pathogenic",
"phylop100way_score": 7.905,
"pos": 15468510,
"ref": "C",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0,
"transcript": "NM_015909.4"
}
]
}