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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: 14-74480701-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=14&pos=74480701&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "14",
"pos": 74480701,
"ref": "C",
"alt": "T",
"effect": "splice_donor_variant,intron_variant",
"transcript": "ENST00000555619.6",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.442G>A",
"hgvs_p": "p.Val148Ile",
"transcript": "ENST00000557510.5",
"protein_id": "ENSP00000451206.1",
"transcript_support_level": 1,
"aa_start": 148,
"aa_end": null,
"aa_length": 174,
"cds_start": 442,
"cds_end": null,
"cds_length": 525,
"cdna_start": 515,
"cdna_end": null,
"cdna_length": 1029,
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.441+1G>A",
"hgvs_p": null,
"transcript": "NM_006432.5",
"protein_id": "NP_006423.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 151,
"cds_start": -4,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 821,
"mane_select": "ENST00000555619.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.441+1G>A",
"hgvs_p": null,
"transcript": "ENST00000555619.6",
"protein_id": "ENSP00000451112.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 151,
"cds_start": -4,
"cds_end": null,
"cds_length": 456,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 821,
"mane_select": "NM_006432.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.442G>A",
"hgvs_p": "p.Val148Ile",
"transcript": "ENST00000553490.5",
"protein_id": "ENSP00000451180.1",
"transcript_support_level": 2,
"aa_start": 148,
"aa_end": null,
"aa_length": 220,
"cds_start": 442,
"cds_end": null,
"cds_length": 664,
"cdna_start": 507,
"cdna_end": null,
"cdna_length": 729,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "I",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.442G>A",
"hgvs_p": "p.Val148Ile",
"transcript": "NM_001363688.1",
"protein_id": "NP_001350617.1",
"transcript_support_level": null,
"aa_start": 148,
"aa_end": null,
"aa_length": 174,
"cds_start": 442,
"cds_end": null,
"cds_length": 525,
"cdna_start": 680,
"cdna_end": null,
"cdna_length": 1446,
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.441+1G>A",
"hgvs_p": null,
"transcript": "ENST00000434013.6",
"protein_id": "ENSP00000412103.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 201,
"cds_start": -4,
"cds_end": null,
"cds_length": 606,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 875,
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.504+1G>A",
"hgvs_p": null,
"transcript": "ENST00000556009.5",
"protein_id": "ENSP00000450502.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 172,
"cds_start": -4,
"cds_end": null,
"cds_length": 519,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 699,
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.432+10G>A",
"hgvs_p": null,
"transcript": "ENST00000238633.6",
"protein_id": "ENSP00000238633.2",
"transcript_support_level": 3,
"aa_start": null,
"aa_end": null,
"aa_length": 148,
"cds_start": -4,
"cds_end": null,
"cds_length": 447,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 796,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.364-413G>A",
"hgvs_p": null,
"transcript": "NM_001375440.1",
"protein_id": "NP_001362369.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 125,
"cds_start": -4,
"cds_end": null,
"cds_length": 378,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 743,
"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": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "c.364-413G>A",
"hgvs_p": null,
"transcript": "ENST00000541064.5",
"protein_id": "ENSP00000442488.1",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 125,
"cds_start": -4,
"cds_end": null,
"cds_length": 378,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1436,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"hgvs_c": "n.*74+1G>A",
"hgvs_p": null,
"transcript": "ENST00000554482.1",
"protein_id": "ENSP00000451314.1",
"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": 583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NPC2",
"gene_hgnc_id": 14537,
"dbsnp": "rs140130028",
"frequency_reference_population": 0.006315543,
"hom_count_reference_population": 46,
"allele_count_reference_population": 10185,
"gnomad_exomes_af": 0.00656997,
"gnomad_genomes_af": 0.00387505,
"gnomad_exomes_ac": 9595,
"gnomad_genomes_ac": 590,
"gnomad_exomes_homalt": 43,
"gnomad_genomes_homalt": 3,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2070000022649765,
"computational_prediction_selected": "Benign",
"computational_source_selected": "REVEL",
"splice_score_selected": 0.5540000200271606,
"splice_prediction_selected": "Benign",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.207,
"revel_prediction": "Benign",
"alphamissense_score": 0.1414,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.31,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.037,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.98,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999363729880175,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PVS1_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 9,
"pathogenic_score": 4,
"criteria": [
"PVS1_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000555619.6",
"gene_symbol": "NPC2",
"hgnc_id": 14537,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.441+1G>A",
"hgvs_p": null
}
],
"clinvar_disease": " type C1, type C2,NPC2-related disorder,Niemann-Pick disease,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "P:1 US:10 LB:4 O:1",
"phenotype_combined": "Niemann-Pick disease, type C2|not provided|Niemann-Pick disease, type C1|not specified|NPC2-related disorder",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}