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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: 3-160307663-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=160307663&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 160307663,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "ENST00000326448.12",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1076C>T",
"hgvs_p": "p.Ser359Phe",
"transcript": "NM_020800.3",
"protein_id": "NP_065851.1",
"transcript_support_level": null,
"aa_start": 359,
"aa_end": null,
"aa_length": 777,
"cds_start": 1076,
"cds_end": null,
"cds_length": 2334,
"cdna_start": 1202,
"cdna_end": null,
"cdna_length": 3999,
"mane_select": "ENST00000326448.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.1076C>T",
"hgvs_p": "p.Ser359Phe",
"transcript": "ENST00000326448.12",
"protein_id": "ENSP00000312778.7",
"transcript_support_level": 1,
"aa_start": 359,
"aa_end": null,
"aa_length": 777,
"cds_start": 1076,
"cds_end": null,
"cds_length": 2334,
"cdna_start": 1202,
"cdna_end": null,
"cdna_length": 3999,
"mane_select": "NM_020800.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ser222Phe",
"transcript": "ENST00000483465.5",
"protein_id": "ENSP00000418196.1",
"transcript_support_level": 1,
"aa_start": 222,
"aa_end": null,
"aa_length": 640,
"cds_start": 665,
"cds_end": null,
"cds_length": 1923,
"cdna_start": 1253,
"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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"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.1589C>T",
"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": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ser222Phe",
"transcript": "NM_001190241.2",
"protein_id": "NP_001177170.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 640,
"cds_start": 665,
"cds_end": null,
"cds_length": 1923,
"cdna_start": 1422,
"cdna_end": null,
"cdna_length": 4219,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ser222Phe",
"transcript": "NM_001190242.2",
"protein_id": "NP_001177171.1",
"transcript_support_level": null,
"aa_start": 222,
"aa_end": null,
"aa_length": 640,
"cds_start": 665,
"cds_end": null,
"cds_length": 1923,
"cdna_start": 1363,
"cdna_end": null,
"cdna_length": 4160,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.665C>T",
"hgvs_p": "p.Ser222Phe",
"transcript": "ENST00000496589.5",
"protein_id": "ENSP00000420646.1",
"transcript_support_level": 2,
"aa_start": 222,
"aa_end": null,
"aa_length": 640,
"cds_start": 665,
"cds_end": null,
"cds_length": 1923,
"cdna_start": 1470,
"cdna_end": null,
"cdna_length": 3073,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "c.119C>T",
"hgvs_p": "p.Ser40Phe",
"transcript": "ENST00000483325.1",
"protein_id": "ENSP00000417552.1",
"transcript_support_level": 5,
"aa_start": 40,
"aa_end": null,
"aa_length": 122,
"cds_start": 119,
"cds_end": null,
"cds_length": 369,
"cdna_start": 119,
"cdna_end": null,
"cdna_length": 554,
"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_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "n.507C>T",
"hgvs_p": null,
"transcript": "ENST00000461213.1",
"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": 553,
"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_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "n.*404C>T",
"hgvs_p": null,
"transcript": "ENST00000472555.5",
"protein_id": "ENSP00000420401.1",
"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": 687,
"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_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "n.2295C>T",
"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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"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.1784C>T",
"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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"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.3320C>T",
"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": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"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.3587C>T",
"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
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"hgvs_c": "n.*404C>T",
"hgvs_p": null,
"transcript": "ENST00000472555.5",
"protein_id": "ENSP00000420401.1",
"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": 687,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IFT80",
"gene_hgnc_id": 29262,
"dbsnp": "rs144099135",
"frequency_reference_population": 0.008087984,
"hom_count_reference_population": 99,
"allele_count_reference_population": 11690,
"gnomad_exomes_af": 0.00814088,
"gnomad_genomes_af": 0.00763875,
"gnomad_exomes_ac": 10527,
"gnomad_genomes_ac": 1163,
"gnomad_exomes_homalt": 90,
"gnomad_genomes_homalt": 9,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.008718907833099365,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.75,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.451,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.5263,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.09,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 4.503,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.01,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.992310887004679,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -15,
"acmg_classification": "Benign",
"acmg_criteria": "PP3,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -15,
"benign_score": 16,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000326448.12",
"gene_symbol": "IFT80",
"hgnc_id": 29262,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1076C>T",
"hgvs_p": "p.Ser359Phe"
},
{
"score": -15,
"benign_score": 16,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000483754.1",
"gene_symbol": "TRIM59-IFT80",
"hgnc_id": 56756,
"effects": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.1589C>T",
"hgvs_p": null
}
],
"clinvar_disease": "Asphyxiating thoracic dystrophy 2,Connective tissue disorder,Jeune thoracic dystrophy,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:7",
"phenotype_combined": "not specified|not provided|Jeune thoracic dystrophy|Asphyxiating thoracic dystrophy 2|Connective tissue disorder",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}