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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: 3-160268487-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=160268487&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 160268487,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_020800.3",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.2149G>A",
"hgvs_p": "p.Ala717Thr",
"transcript": "NM_020800.3",
"protein_id": "NP_065851.1",
"transcript_support_level": null,
"aa_start": 717,
"aa_end": null,
"aa_length": 777,
"cds_start": 2149,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000326448.12",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_020800.3"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.2149G>A",
"hgvs_p": "p.Ala717Thr",
"transcript": "ENST00000326448.12",
"protein_id": "ENSP00000312778.7",
"transcript_support_level": 1,
"aa_start": 717,
"aa_end": null,
"aa_length": 777,
"cds_start": 2149,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_020800.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000326448.12"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1738G>A",
"hgvs_p": "p.Ala580Thr",
"transcript": "ENST00000483465.5",
"protein_id": "ENSP00000418196.1",
"transcript_support_level": 1,
"aa_start": 580,
"aa_end": null,
"aa_length": 640,
"cds_start": 1738,
"cds_end": null,
"cds_length": 1923,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000483465.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 17,
"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.2662G>A",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000483754.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.2149G>A",
"hgvs_p": "p.Ala717Thr",
"transcript": "ENST00000915648.1",
"protein_id": "ENSP00000585707.1",
"transcript_support_level": null,
"aa_start": 717,
"aa_end": null,
"aa_length": 777,
"cds_start": 2149,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000915648.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.2149G>A",
"hgvs_p": "p.Ala717Thr",
"transcript": "ENST00000967444.1",
"protein_id": "ENSP00000637503.1",
"transcript_support_level": null,
"aa_start": 717,
"aa_end": null,
"aa_length": 777,
"cds_start": 2149,
"cds_end": null,
"cds_length": 2334,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000967444.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.2059G>A",
"hgvs_p": "p.Ala687Thr",
"transcript": "ENST00000866738.1",
"protein_id": "ENSP00000536797.1",
"transcript_support_level": null,
"aa_start": 687,
"aa_end": null,
"aa_length": 747,
"cds_start": 2059,
"cds_end": null,
"cds_length": 2244,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866738.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1969G>A",
"hgvs_p": "p.Ala657Thr",
"transcript": "ENST00000866737.1",
"protein_id": "ENSP00000536796.1",
"transcript_support_level": null,
"aa_start": 657,
"aa_end": null,
"aa_length": 717,
"cds_start": 1969,
"cds_end": null,
"cds_length": 2154,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866737.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 17,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1948G>A",
"hgvs_p": "p.Ala650Thr",
"transcript": "ENST00000866736.1",
"protein_id": "ENSP00000536795.1",
"transcript_support_level": null,
"aa_start": 650,
"aa_end": null,
"aa_length": 710,
"cds_start": 1948,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866736.1"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1738G>A",
"hgvs_p": "p.Ala580Thr",
"transcript": "NM_001190241.2",
"protein_id": "NP_001177170.1",
"transcript_support_level": null,
"aa_start": 580,
"aa_end": null,
"aa_length": 640,
"cds_start": 1738,
"cds_end": null,
"cds_length": 1923,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001190241.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1738G>A",
"hgvs_p": "p.Ala580Thr",
"transcript": "NM_001190242.2",
"protein_id": "NP_001177171.1",
"transcript_support_level": null,
"aa_start": 580,
"aa_end": null,
"aa_length": 640,
"cds_start": 1738,
"cds_end": null,
"cds_length": 1923,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001190242.2"
},
{
"aa_ref": "A",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1738G>A",
"hgvs_p": "p.Ala580Thr",
"transcript": "ENST00000496589.5",
"protein_id": "ENSP00000420646.1",
"transcript_support_level": 2,
"aa_start": 580,
"aa_end": null,
"aa_length": 640,
"cds_start": 1738,
"cds_end": null,
"cds_length": 1923,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000496589.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "n.297G>A",
"hgvs_p": null,
"transcript": "ENST00000463240.1",
"protein_id": null,
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "ENST00000463240.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "n.275G>A",
"hgvs_p": null,
"transcript": "ENST00000478278.1",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000478278.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 19,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "n.3368G>A",
"hgvs_p": null,
"transcript": "ENST00000487943.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "retained_intron",
"feature": "ENST00000487943.5"
},
{
"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": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "TRIM59-IFT80",
"gene_hgnc_id": 56756,
"hgvs_c": "n.2857G>A",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_148401.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"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.4393G>A",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_148402.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 20,
"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.4660G>A",
"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": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "pseudogene",
"feature": "NR_148403.1"
}
],
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"dbsnp": "rs370294182",
"frequency_reference_population": 0.000016738124,
"hom_count_reference_population": 0,
"allele_count_reference_population": 27,
"gnomad_exomes_af": 0.0000177962,
"gnomad_genomes_af": 0.00000657471,
"gnomad_exomes_ac": 26,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.44667714834213257,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.433,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5267,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.03,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 7.253,
"phylop100way_prediction": "Uncertain_significance",
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_020800.3",
"gene_symbol": "IFT80",
"hgnc_id": 29262,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2149G>A",
"hgvs_p": "p.Ala717Thr"
},
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000483754.1",
"gene_symbol": "TRIM59-IFT80",
"hgnc_id": 56756,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.2662G>A",
"hgvs_p": null
}
],
"clinvar_disease": "Inborn genetic diseases,Jeune thoracic dystrophy,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:3",
"phenotype_combined": "Jeune thoracic dystrophy|not provided|Inborn genetic diseases",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}