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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: 5-129904837-T-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=5&pos=129904837&ref=T&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "5",
"pos": 129904837,
"ref": "T",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_175856.5",
"consequences": [
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHSY3",
"gene_hgnc_id": 24293,
"hgvs_c": "c.8T>G",
"hgvs_p": "p.Val3Gly",
"transcript": "NM_175856.5",
"protein_id": "NP_787052.3",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 882,
"cds_start": 8,
"cds_end": null,
"cds_length": 2649,
"cdna_start": 373,
"cdna_end": null,
"cdna_length": 3857,
"mane_select": "ENST00000305031.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHSY3",
"gene_hgnc_id": 24293,
"hgvs_c": "c.8T>G",
"hgvs_p": "p.Val3Gly",
"transcript": "ENST00000305031.5",
"protein_id": "ENSP00000302629.4",
"transcript_support_level": 1,
"aa_start": 3,
"aa_end": null,
"aa_length": 882,
"cds_start": 8,
"cds_end": null,
"cds_length": 2649,
"cdna_start": 373,
"cdna_end": null,
"cdna_length": 3857,
"mane_select": "NM_175856.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHSY3",
"gene_hgnc_id": 24293,
"hgvs_c": "c.8T>G",
"hgvs_p": "p.Val3Gly",
"transcript": "XM_017009435.3",
"protein_id": "XP_016864924.1",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 449,
"cds_start": 8,
"cds_end": null,
"cds_length": 1350,
"cdna_start": 373,
"cdna_end": null,
"cdna_length": 2192,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHSY3",
"gene_hgnc_id": 24293,
"hgvs_c": "c.8T>G",
"hgvs_p": "p.Val3Gly",
"transcript": "XM_011543365.4",
"protein_id": "XP_011541667.1",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 397,
"cds_start": 8,
"cds_end": null,
"cds_length": 1194,
"cdna_start": 373,
"cdna_end": null,
"cdna_length": 3945,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHSY3",
"gene_hgnc_id": 24293,
"hgvs_c": "c.8T>G",
"hgvs_p": "p.Val3Gly",
"transcript": "XM_005271982.5",
"protein_id": "XP_005272039.1",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 377,
"cds_start": 8,
"cds_end": null,
"cds_length": 1134,
"cdna_start": 373,
"cdna_end": null,
"cdna_length": 2904,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "V",
"aa_alt": "G",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CHSY3",
"gene_hgnc_id": 24293,
"hgvs_c": "c.8T>G",
"hgvs_p": "p.Val3Gly",
"transcript": "XM_005271983.5",
"protein_id": "XP_005272040.1",
"transcript_support_level": null,
"aa_start": 3,
"aa_end": null,
"aa_length": 363,
"cds_start": 8,
"cds_end": null,
"cds_length": 1092,
"cdna_start": 373,
"cdna_end": null,
"cdna_length": 11411,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000251680",
"gene_hgnc_id": 58253,
"hgvs_c": "n.72+1009A>C",
"hgvs_p": null,
"transcript": "ENST00000503616.5",
"protein_id": null,
"transcript_support_level": 3,
"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": 631,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000251680",
"gene_hgnc_id": 58253,
"hgvs_c": "n.82+743A>C",
"hgvs_p": null,
"transcript": "ENST00000515569.1",
"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": 462,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000251680",
"gene_hgnc_id": 58253,
"hgvs_c": "n.149+743A>C",
"hgvs_p": null,
"transcript": "ENST00000653455.2",
"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": 3643,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000251680",
"gene_hgnc_id": 58253,
"hgvs_c": "n.74+1005A>C",
"hgvs_p": null,
"transcript": "ENST00000655036.1",
"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": 3465,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000251680",
"gene_hgnc_id": 58253,
"hgvs_c": "n.33+743A>C",
"hgvs_p": null,
"transcript": "ENST00000661736.1",
"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": 3583,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000251680",
"gene_hgnc_id": 58253,
"hgvs_c": "n.108+743A>C",
"hgvs_p": null,
"transcript": "ENST00000670057.1",
"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": 923,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000251680",
"gene_hgnc_id": 58253,
"hgvs_c": "n.144+743A>C",
"hgvs_p": null,
"transcript": "ENST00000849201.1",
"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": 476,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENSG00000251680",
"gene_hgnc_id": 58253,
"hgvs_c": "n.401+743A>C",
"hgvs_p": null,
"transcript": "ENST00000849202.1",
"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": 836,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CHSY3",
"gene_hgnc_id": 24293,
"hgvs_c": "c.-126+768T>G",
"hgvs_p": null,
"transcript": "XM_011543363.4",
"protein_id": "XP_011541665.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 573,
"cds_start": -4,
"cds_end": null,
"cds_length": 1722,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2781,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "CHSY3-AS1",
"gene_hgnc_id": 58253,
"hgvs_c": "n.86+1005A>C",
"hgvs_p": null,
"transcript": "XR_002956248.2",
"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": 519,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "CHSY3",
"gene_hgnc_id": 24293,
"dbsnp": "rs1760174499",
"frequency_reference_population": 0.000011119466,
"hom_count_reference_population": 0,
"allele_count_reference_population": 16,
"gnomad_exomes_af": 0.0000116572,
"gnomad_genomes_af": 0.00000657186,
"gnomad_exomes_ac": 15,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.11795130372047424,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.025,
"revel_prediction": "Benign",
"alphamissense_score": 0.0988,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.115,
"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": 0,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4_Moderate",
"acmg_by_gene": [
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "NM_175856.5",
"gene_symbol": "CHSY3",
"hgnc_id": 24293,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.8T>G",
"hgvs_p": "p.Val3Gly"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000515569.1",
"gene_symbol": "ENSG00000251680",
"hgnc_id": 58253,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.82+743A>C",
"hgvs_p": null
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "XR_002956248.2",
"gene_symbol": "CHSY3-AS1",
"hgnc_id": 58253,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.86+1005A>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
}