← Back to variant description
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: 3-160279351-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=160279351&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 160279351,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000326448.12",
"consequences": [
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1678A>G",
"hgvs_p": "p.Asn560Asp",
"transcript": "NM_020800.3",
"protein_id": "NP_065851.1",
"transcript_support_level": null,
"aa_start": 560,
"aa_end": null,
"aa_length": 777,
"cds_start": 1678,
"cds_end": null,
"cds_length": 2334,
"cdna_start": 1804,
"cdna_end": null,
"cdna_length": 3999,
"mane_select": "ENST00000326448.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1678A>G",
"hgvs_p": "p.Asn560Asp",
"transcript": "ENST00000326448.12",
"protein_id": "ENSP00000312778.7",
"transcript_support_level": 1,
"aa_start": 560,
"aa_end": null,
"aa_length": 777,
"cds_start": 1678,
"cds_end": null,
"cds_length": 2334,
"cdna_start": 1804,
"cdna_end": null,
"cdna_length": 3999,
"mane_select": "NM_020800.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1267A>G",
"hgvs_p": "p.Asn423Asp",
"transcript": "ENST00000483465.5",
"protein_id": "ENSP00000418196.1",
"transcript_support_level": 1,
"aa_start": 423,
"aa_end": null,
"aa_length": 640,
"cds_start": 1267,
"cds_end": null,
"cds_length": 1923,
"cdna_start": 1855,
"cdna_end": null,
"cdna_length": 4044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM59-IFT80",
"gene_hgnc_id": 56756,
"hgvs_c": "n.2191A>G",
"hgvs_p": null,
"transcript": "ENST00000483754.1",
"protein_id": "ENSP00000456272.1",
"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": 3360,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1267A>G",
"hgvs_p": "p.Asn423Asp",
"transcript": "NM_001190241.2",
"protein_id": "NP_001177170.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 640,
"cds_start": 1267,
"cds_end": null,
"cds_length": 1923,
"cdna_start": 2024,
"cdna_end": null,
"cdna_length": 4219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1267A>G",
"hgvs_p": "p.Asn423Asp",
"transcript": "NM_001190242.2",
"protein_id": "NP_001177171.1",
"transcript_support_level": null,
"aa_start": 423,
"aa_end": null,
"aa_length": 640,
"cds_start": 1267,
"cds_end": null,
"cds_length": 1923,
"cdna_start": 1965,
"cdna_end": null,
"cdna_length": 4160,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "N",
"aa_alt": "D",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1267A>G",
"hgvs_p": "p.Asn423Asp",
"transcript": "ENST00000496589.5",
"protein_id": "ENSP00000420646.1",
"transcript_support_level": 2,
"aa_start": 423,
"aa_end": null,
"aa_length": 640,
"cds_start": 1267,
"cds_end": null,
"cds_length": 1923,
"cdna_start": 2072,
"cdna_end": null,
"cdna_length": 3073,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "n.2897A>G",
"hgvs_p": null,
"transcript": "ENST00000487943.5",
"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": 3893,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 14,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM59-IFT80",
"gene_hgnc_id": 56756,
"hgvs_c": "n.2386A>G",
"hgvs_p": null,
"transcript": "NR_148401.1",
"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": 3369,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM59-IFT80",
"gene_hgnc_id": 56756,
"hgvs_c": "n.3922A>G",
"hgvs_p": null,
"transcript": "NR_148402.1",
"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": 6117,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM59-IFT80",
"gene_hgnc_id": 56756,
"hgvs_c": "n.4189A>G",
"hgvs_p": null,
"transcript": "NR_148403.1",
"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": 6384,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"dbsnp": "rs202145480",
"frequency_reference_population": 0.00008059117,
"hom_count_reference_population": 0,
"allele_count_reference_population": 130,
"gnomad_exomes_af": 0.000077346,
"gnomad_genomes_af": 0.00011176,
"gnomad_exomes_ac": 113,
"gnomad_genomes_ac": 17,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.02032238245010376,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.195,
"revel_prediction": "Benign",
"alphamissense_score": 0.1791,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.33,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.386,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Strong,BP6",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000326448.12",
"gene_symbol": "IFT80",
"hgnc_id": 29262,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1678A>G",
"hgvs_p": "p.Asn560Asp"
},
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000483754.1",
"gene_symbol": "TRIM59-IFT80",
"hgnc_id": 56756,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.2191A>G",
"hgvs_p": null
}
],
"clinvar_disease": "Asphyxiating thoracic dystrophy 2,Inborn genetic diseases,Jeune thoracic dystrophy",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:3 LB:1",
"phenotype_combined": "Jeune thoracic dystrophy|Asphyxiating thoracic dystrophy 2|Inborn genetic diseases",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}