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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: 2-112238467-T-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=112238467&ref=T&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 112238467,
"ref": "T",
"alt": "C",
"effect": "missense_variant",
"transcript": "NM_032494.3",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZC3H8",
"gene_hgnc_id": 30941,
"hgvs_c": "c.218A>G",
"hgvs_p": "p.Tyr73Cys",
"transcript": "NM_032494.3",
"protein_id": "NP_115883.2",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 291,
"cds_start": 218,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000409573.7",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_032494.3"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZC3H8",
"gene_hgnc_id": 30941,
"hgvs_c": "c.218A>G",
"hgvs_p": "p.Tyr73Cys",
"transcript": "ENST00000409573.7",
"protein_id": "ENSP00000386488.1",
"transcript_support_level": 5,
"aa_start": 73,
"aa_end": null,
"aa_length": 291,
"cds_start": 218,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_032494.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000409573.7"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZC3H8",
"gene_hgnc_id": 30941,
"hgvs_c": "c.218A>G",
"hgvs_p": "p.Tyr73Cys",
"transcript": "ENST00000866700.1",
"protein_id": "ENSP00000536759.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 291,
"cds_start": 218,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866700.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZC3H8",
"gene_hgnc_id": 30941,
"hgvs_c": "c.218A>G",
"hgvs_p": "p.Tyr73Cys",
"transcript": "ENST00000866701.1",
"protein_id": "ENSP00000536760.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 291,
"cds_start": 218,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866701.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZC3H8",
"gene_hgnc_id": 30941,
"hgvs_c": "c.218A>G",
"hgvs_p": "p.Tyr73Cys",
"transcript": "ENST00000924270.1",
"protein_id": "ENSP00000594329.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 291,
"cds_start": 218,
"cds_end": null,
"cds_length": 876,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000924270.1"
},
{
"aa_ref": "Y",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZC3H8",
"gene_hgnc_id": 30941,
"hgvs_c": "c.218A>G",
"hgvs_p": "p.Tyr73Cys",
"transcript": "ENST00000866699.1",
"protein_id": "ENSP00000536758.1",
"transcript_support_level": null,
"aa_start": 73,
"aa_end": null,
"aa_length": 252,
"cds_start": 218,
"cds_end": null,
"cds_length": 759,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000866699.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ZC3H8",
"gene_hgnc_id": 30941,
"hgvs_c": "c.157-5096A>G",
"hgvs_p": null,
"transcript": "ENST00000957654.1",
"protein_id": "ENSP00000627713.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 136,
"cds_start": null,
"cds_end": null,
"cds_length": 411,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000957654.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZC3H8",
"gene_hgnc_id": 30941,
"hgvs_c": "n.292A>G",
"hgvs_p": null,
"transcript": "ENST00000464305.1",
"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": "ENST00000464305.1"
},
{
"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": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZC3H8",
"gene_hgnc_id": 30941,
"hgvs_c": "n.125A>G",
"hgvs_p": null,
"transcript": "ENST00000466259.1",
"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": "ENST00000466259.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZC3H8",
"gene_hgnc_id": 30941,
"hgvs_c": "n.398A>G",
"hgvs_p": null,
"transcript": "ENST00000474234.5",
"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": "ENST00000474234.5"
},
{
"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": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ZC3H8",
"gene_hgnc_id": 30941,
"hgvs_c": "n.279A>G",
"hgvs_p": null,
"transcript": "XR_001738994.2",
"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": "XR_001738994.2"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "FBLN7",
"gene_hgnc_id": 26740,
"hgvs_c": "n.10509-654T>C",
"hgvs_p": null,
"transcript": "XR_007069507.1",
"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": "XR_007069507.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": 8,
"intron_rank_end": null,
"gene_symbol": "FBLN7",
"gene_hgnc_id": 26740,
"hgvs_c": "n.10509-4482T>C",
"hgvs_p": null,
"transcript": "XR_007069508.1",
"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": "XR_007069508.1"
}
],
"gene_symbol": "ZC3H8",
"gene_hgnc_id": 30941,
"dbsnp": "rs61762973",
"frequency_reference_population": 0.00018722807,
"hom_count_reference_population": 2,
"allele_count_reference_population": 302,
"gnomad_exomes_af": 0.000191678,
"gnomad_genomes_af": 0.000144526,
"gnomad_exomes_ac": 280,
"gnomad_genomes_ac": 22,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.3159356415271759,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.328,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.154,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.06,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.088,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -1,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4",
"acmg_by_gene": [
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "NM_032494.3",
"gene_symbol": "ZC3H8",
"hgnc_id": 30941,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.218A>G",
"hgvs_p": "p.Tyr73Cys"
},
{
"score": -1,
"benign_score": 1,
"pathogenic_score": 0,
"criteria": [
"BP4"
],
"verdict": "Likely_benign",
"transcript": "XR_007069507.1",
"gene_symbol": "FBLN7",
"hgnc_id": 26740,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "n.10509-654T>C",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}