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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: 11-19519590-A-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=19519590&ref=A&alt=T&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "NAV2",
"hgnc_id": 15997,
"hgvs_c": "c.75+168563A>T",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "NM_001111018.2",
"verdict": "Benign"
},
{
"benign_score": 12,
"criteria": [
"BP4_Strong",
"BA1"
],
"effects": [
"intron_variant"
],
"gene_symbol": "NAV2-AS4",
"hgnc_id": 40741,
"hgvs_c": "n.338+160T>A",
"hgvs_p": null,
"inheritance_mode": "",
"pathogenic_score": 0,
"score": -12,
"transcript": "NR_033989.1",
"verdict": "Benign"
}
],
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BA1",
"acmg_score": -12,
"allele_count_reference_population": 63280,
"alphamissense_prediction": null,
"alphamissense_score": null,
"alt": "T",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.93,
"chr": "11",
"clinvar_classification": "",
"clinvar_disease": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"computational_prediction_selected": "Benign",
"computational_score_selected": -0.9300000071525574,
"computational_source_selected": "BayesDel_noAF",
"consequences": [
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2365,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10667,
"cdna_start": null,
"cds_end": null,
"cds_length": 7098,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 38,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000360655.8",
"gene_hgnc_id": 15997,
"gene_symbol": "NAV2",
"hgvs_c": "c.75+168563A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000353871.4",
"strand": true,
"transcript": "ENST00000360655.8",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2365,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11097,
"cdna_start": null,
"cds_end": null,
"cds_length": 7098,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 39,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NM_001111018.2",
"gene_hgnc_id": 15997,
"gene_symbol": "NAV2",
"hgvs_c": "c.75+168563A>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_001104488.1",
"strand": true,
"transcript": "NM_001111018.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2424,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11274,
"cdna_start": null,
"cds_end": null,
"cds_length": 7275,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 42,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017018520.3",
"gene_hgnc_id": 15997,
"gene_symbol": "NAV2",
"hgvs_c": "c.75+168563A>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016874009.1",
"strand": true,
"transcript": "XM_017018520.3",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2424,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11663,
"cdna_start": null,
"cds_end": null,
"cds_length": 7275,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 41,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_024448758.2",
"gene_hgnc_id": 15997,
"gene_symbol": "NAV2",
"hgvs_c": "c.75+168563A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_024304526.1",
"strand": true,
"transcript": "XM_024448758.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2401,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11205,
"cdna_start": null,
"cds_end": null,
"cds_length": 7206,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 41,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_017018522.2",
"gene_hgnc_id": 15997,
"gene_symbol": "NAV2",
"hgvs_c": "c.75+168563A>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_016874011.1",
"strand": true,
"transcript": "XM_017018522.2",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2401,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11594,
"cdna_start": null,
"cds_end": null,
"cds_length": 7206,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 40,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047427820.1",
"gene_hgnc_id": 15997,
"gene_symbol": "NAV2",
"hgvs_c": "c.75+168563A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047283776.1",
"strand": true,
"transcript": "XM_047427820.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2388,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11166,
"cdna_start": null,
"cds_end": null,
"cds_length": 7167,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 40,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047427824.1",
"gene_hgnc_id": 15997,
"gene_symbol": "NAV2",
"hgvs_c": "c.75+168563A>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047283780.1",
"strand": true,
"transcript": "XM_047427824.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2361,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11474,
"cdna_start": null,
"cds_end": null,
"cds_length": 7086,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 37,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047427825.1",
"gene_hgnc_id": 15997,
"gene_symbol": "NAV2",
"hgvs_c": "c.75+168563A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047283781.1",
"strand": true,
"transcript": "XM_047427825.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2343,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11031,
"cdna_start": null,
"cds_end": null,
"cds_length": 7032,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 38,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047427828.1",
"gene_hgnc_id": 15997,
"gene_symbol": "NAV2",
"hgvs_c": "c.75+168563A>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047283784.1",
"strand": true,
"transcript": "XM_047427828.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2331,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10995,
"cdna_start": null,
"cds_end": null,
"cds_length": 6996,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 38,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047427830.1",
"gene_hgnc_id": 15997,
"gene_symbol": "NAV2",
"hgvs_c": "c.75+168563A>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047283786.1",
"strand": true,
"transcript": "XM_047427830.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2328,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 10986,
"cdna_start": null,
"cds_end": null,
"cds_length": 6987,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 37,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047427831.1",
"gene_hgnc_id": 15997,
"gene_symbol": "NAV2",
"hgvs_c": "c.75+168563A>T",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047283787.1",
"strand": true,
"transcript": "XM_047427831.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 2328,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11375,
"cdna_start": null,
"cds_end": null,
"cds_length": 6987,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 36,
"exon_rank": null,
"exon_rank_end": null,
"feature": "XM_047427833.1",
"gene_hgnc_id": 15997,
"gene_symbol": "NAV2",
"hgvs_c": "c.75+168563A>T",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "XP_047283789.1",
"strand": true,
"transcript": "XM_047427833.1",
"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": 1181,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000532874.1",
"gene_hgnc_id": 40741,
"gene_symbol": "NAV2-AS4",
"hgvs_c": "n.147+160T>A",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000532874.1",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1379,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000837121.1",
"gene_hgnc_id": 40741,
"gene_symbol": "NAV2-AS4",
"hgvs_c": "n.343+160T>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000837121.1",
"transcript_support_level": null
},
{
"aa_alt": null,
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"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1317,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000837122.1",
"gene_hgnc_id": 40741,
"gene_symbol": "NAV2-AS4",
"hgvs_c": "n.317+160T>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000837122.1",
"transcript_support_level": null
},
{
"aa_alt": null,
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"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1142,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 3,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000837123.1",
"gene_hgnc_id": 40741,
"gene_symbol": "NAV2-AS4",
"hgvs_c": "n.311+160T>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "ENST00000837123.1",
"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": 1369,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 4,
"exon_rank": null,
"exon_rank_end": null,
"feature": "NR_033989.1",
"gene_hgnc_id": 40741,
"gene_symbol": "NAV2-AS4",
"hgvs_c": "n.338+160T>A",
"hgvs_p": null,
"intron_rank": 2,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": false,
"transcript": "NR_033989.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs1487181",
"effect": "intron_variant",
"frequency_reference_population": 0.41630483,
"gene_hgnc_id": 15997,
"gene_symbol": "NAV2",
"gnomad_exomes_ac": null,
"gnomad_exomes_af": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_ac": 63280,
"gnomad_genomes_af": 0.416305,
"gnomad_genomes_homalt": 13620,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 13620,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": null,
"phenotype_combined": null,
"phylop100way_prediction": "Benign",
"phylop100way_score": -0.931,
"pos": 19519590,
"ref": "A",
"revel_prediction": null,
"revel_score": null,
"splice_prediction_selected": null,
"splice_score_selected": null,
"splice_source_selected": null,
"spliceai_max_prediction": null,
"spliceai_max_score": null,
"transcript": "NM_001111018.2"
}
]
}