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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: X-108736282-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=X&pos=108736282&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "X",
"pos": 108736282,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000372129.4",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRS4",
"gene_hgnc_id": 6128,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Ala21Ala",
"transcript": "NM_001379150.1",
"protein_id": "NP_001366079.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 1256,
"cds_start": 63,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 282,
"cdna_end": null,
"cdna_length": 6563,
"mane_select": "ENST00000372129.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRS4",
"gene_hgnc_id": 6128,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Ala21Ala",
"transcript": "ENST00000372129.4",
"protein_id": "ENSP00000361202.3",
"transcript_support_level": 6,
"aa_start": 21,
"aa_end": null,
"aa_length": 1256,
"cds_start": 63,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 282,
"cdna_end": null,
"cdna_length": 6563,
"mane_select": "NM_001379150.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRS4",
"gene_hgnc_id": 6128,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Ala21Ala",
"transcript": "NM_001440817.1",
"protein_id": "NP_001427746.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 1300,
"cds_start": 63,
"cds_end": null,
"cds_length": 3903,
"cdna_start": 282,
"cdna_end": null,
"cdna_length": 6589,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRS4",
"gene_hgnc_id": 6128,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Ala21Ala",
"transcript": "NM_003604.2",
"protein_id": "NP_003595.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 1257,
"cds_start": 63,
"cds_end": null,
"cds_length": 3774,
"cdna_start": 96,
"cdna_end": null,
"cdna_length": 3881,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRS4",
"gene_hgnc_id": 6128,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Ala21Ala",
"transcript": "ENST00000564206.2",
"protein_id": "ENSP00000505547.1",
"transcript_support_level": 6,
"aa_start": 21,
"aa_end": null,
"aa_length": 1257,
"cds_start": 63,
"cds_end": null,
"cds_length": 3774,
"cdna_start": 128,
"cdna_end": null,
"cdna_length": 16461,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRS4",
"gene_hgnc_id": 6128,
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Ala21Ala",
"transcript": "XM_006724713.4",
"protein_id": "XP_006724776.1",
"transcript_support_level": null,
"aa_start": 21,
"aa_end": null,
"aa_length": 1256,
"cds_start": 63,
"cds_end": null,
"cds_length": 3771,
"cdna_start": 282,
"cdna_end": null,
"cdna_length": 15937,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRS4-AS1",
"gene_hgnc_id": 55650,
"hgvs_c": "n.272C>T",
"hgvs_p": null,
"transcript": "ENST00000608811.1",
"protein_id": null,
"transcript_support_level": 4,
"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": 551,
"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": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRS4-AS1",
"gene_hgnc_id": 55650,
"hgvs_c": "n.274C>T",
"hgvs_p": null,
"transcript": "ENST00000668534.2",
"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": 1690,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRS4-AS1",
"gene_hgnc_id": 55650,
"hgvs_c": "n.-231C>T",
"hgvs_p": null,
"transcript": "ENST00000436013.2",
"protein_id": null,
"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": 1489,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRS4-AS1",
"gene_hgnc_id": 55650,
"hgvs_c": "n.-199C>T",
"hgvs_p": null,
"transcript": "ENST00000656850.2",
"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": 1533,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRS4-AS1",
"gene_hgnc_id": 55650,
"hgvs_c": "n.-203C>T",
"hgvs_p": null,
"transcript": "ENST00000664433.1",
"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": 1561,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRS4-AS1",
"gene_hgnc_id": 55650,
"hgvs_c": "n.-245C>T",
"hgvs_p": null,
"transcript": "ENST00000746040.1",
"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": 934,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "IRS4-AS1",
"gene_hgnc_id": 55650,
"hgvs_c": "n.-198C>T",
"hgvs_p": null,
"transcript": "ENST00000746041.1",
"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": 297,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "IRS4",
"gene_hgnc_id": 6128,
"dbsnp": "rs2073114",
"frequency_reference_population": 0.2693589,
"hom_count_reference_population": 141783,
"allele_count_reference_population": 323851,
"gnomad_exomes_af": 0.258477,
"gnomad_genomes_af": 0.377494,
"gnomad_exomes_ac": 282352,
"gnomad_genomes_ac": 41499,
"gnomad_exomes_homalt": 31968,
"gnomad_genomes_homalt": 7404,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.46000000834465027,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.671,
"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": -19,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -19,
"benign_score": 19,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000372129.4",
"gene_symbol": "IRS4",
"hgnc_id": 6128,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "XL",
"hgvs_c": "c.63G>A",
"hgvs_p": "p.Ala21Ala"
},
{
"score": -18,
"benign_score": 18,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000608811.1",
"gene_symbol": "IRS4-AS1",
"hgnc_id": 55650,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.272C>T",
"hgvs_p": null
}
],
"clinvar_disease": " 9, congenital, nongoitrous,Hypothyroidism,not provided",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:2",
"phenotype_combined": "Hypothyroidism, congenital, nongoitrous, 9|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}