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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: 17-31259130-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=17&pos=31259130&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "17",
"pos": 31259130,
"ref": "G",
"alt": "A",
"effect": "splice_donor_variant,intron_variant",
"transcript": "NM_001042492.3",
"consequences": [
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "c.4430+1G>A",
"hgvs_p": null,
"transcript": "NM_001042492.3",
"protein_id": "NP_001035957.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2839,
"cds_start": -4,
"cds_end": null,
"cds_length": 8520,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12373,
"mane_select": "ENST00000358273.9",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "c.4430+1G>A",
"hgvs_p": null,
"transcript": "ENST00000358273.9",
"protein_id": "ENSP00000351015.4",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2839,
"cds_start": -4,
"cds_end": null,
"cds_length": 8520,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12373,
"mane_select": "NM_001042492.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": 32,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "c.4367+1G>A",
"hgvs_p": null,
"transcript": "ENST00000356175.7",
"protein_id": "ENSP00000348498.3",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 2818,
"cds_start": -4,
"cds_end": null,
"cds_length": 8457,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12362,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 58,
"intron_rank": 32,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "n.4367+1G>A",
"hgvs_p": null,
"transcript": "ENST00000579081.6",
"protein_id": "ENSP00000462408.2",
"transcript_support_level": 1,
"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": 8788,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "n.403G>A",
"hgvs_p": null,
"transcript": "ENST00000691649.1",
"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": 2459,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": 34,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "c.4460+1G>A",
"hgvs_p": null,
"transcript": "ENST00000691014.1",
"protein_id": "ENSP00000510595.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2849,
"cds_start": -4,
"cds_end": null,
"cds_length": 8550,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12415,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 57,
"intron_rank": 32,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "c.4367+1G>A",
"hgvs_p": null,
"transcript": "NM_000267.4",
"protein_id": "NP_000258.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2818,
"cds_start": -4,
"cds_end": null,
"cds_length": 8457,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12310,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 59,
"intron_rank": 33,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "c.4412+1G>A",
"hgvs_p": null,
"transcript": "ENST00000696138.1",
"protein_id": "ENSP00000512431.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 2807,
"cds_start": -4,
"cds_end": null,
"cds_length": 8424,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12484,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 50,
"intron_rank": 24,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "c.3365+1G>A",
"hgvs_p": null,
"transcript": "ENST00000456735.6",
"protein_id": "ENSP00000389907.2",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 2502,
"cds_start": -4,
"cds_end": null,
"cds_length": 7509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 7787,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "n.*264+1G>A",
"hgvs_p": null,
"transcript": "ENST00000466819.5",
"protein_id": "ENSP00000463819.1",
"transcript_support_level": 5,
"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": 1177,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "n.*264+1G>A",
"hgvs_p": null,
"transcript": "ENST00000479614.1",
"protein_id": "ENSP00000462157.1",
"transcript_support_level": 5,
"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": 1114,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": 15,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "n.2903+1G>A",
"hgvs_p": null,
"transcript": "ENST00000493220.5",
"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": 5691,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "n.218+1G>A",
"hgvs_p": null,
"transcript": "ENST00000581113.7",
"protein_id": "ENSP00000492721.2",
"transcript_support_level": 5,
"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": 2335,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 27,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "n.1075+1G>A",
"hgvs_p": null,
"transcript": "ENST00000687863.1",
"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": 5018,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "n.536+1G>A",
"hgvs_p": null,
"transcript": "ENST00000696140.1",
"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": 1318,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_donor_variant",
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"hgvs_c": "n.*323+1G>A",
"hgvs_p": null,
"transcript": "ENST00000696141.1",
"protein_id": "ENSP00000512433.1",
"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": 827,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NF1",
"gene_hgnc_id": 7765,
"dbsnp": "rs773151680",
"frequency_reference_population": 6.943104e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.9431e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3499999940395355,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.9259999990463257,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.35,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.303,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 1,
"spliceai_max_prediction": "Pathogenic",
"dbscsnv_ada_score": 0.999989072007339,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "NM_001042492.3",
"gene_symbol": "NF1",
"hgnc_id": 7765,
"effects": [
"splice_donor_variant",
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.4430+1G>A",
"hgvs_p": null
}
],
"clinvar_disease": " type 1,Neoplasm,Neurofibromatosis,not provided",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:5 US:1",
"phenotype_combined": "Neurofibromatosis, type 1|not provided|Neoplasm",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}