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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: 9-99828473-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=99828473&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 99828473,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_006981.4",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR4A3",
"gene_hgnc_id": 7982,
"hgvs_c": "c.431C>G",
"hgvs_p": "p.Thr144Ser",
"transcript": "NM_006981.4",
"protein_id": "NP_008912.2",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 626,
"cds_start": 431,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 1130,
"cdna_end": null,
"cdna_length": 5604,
"mane_select": "ENST00000395097.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR4A3",
"gene_hgnc_id": 7982,
"hgvs_c": "c.431C>G",
"hgvs_p": "p.Thr144Ser",
"transcript": "ENST00000395097.7",
"protein_id": "ENSP00000378531.2",
"transcript_support_level": 1,
"aa_start": 144,
"aa_end": null,
"aa_length": 626,
"cds_start": 431,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 1130,
"cdna_end": null,
"cdna_length": 5604,
"mane_select": "NM_006981.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR4A3",
"gene_hgnc_id": 7982,
"hgvs_c": "c.431C>G",
"hgvs_p": "p.Thr144Ser",
"transcript": "ENST00000338488.8",
"protein_id": "ENSP00000340301.4",
"transcript_support_level": 1,
"aa_start": 144,
"aa_end": null,
"aa_length": 443,
"cds_start": 431,
"cds_end": null,
"cds_length": 1332,
"cdna_start": 1160,
"cdna_end": null,
"cdna_length": 2588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR4A3",
"gene_hgnc_id": 7982,
"hgvs_c": "c.464C>G",
"hgvs_p": "p.Thr155Ser",
"transcript": "NM_173200.3",
"protein_id": "NP_775292.1",
"transcript_support_level": null,
"aa_start": 155,
"aa_end": null,
"aa_length": 637,
"cds_start": 464,
"cds_end": null,
"cds_length": 1914,
"cdna_start": 1202,
"cdna_end": null,
"cdna_length": 5676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR4A3",
"gene_hgnc_id": 7982,
"hgvs_c": "c.464C>G",
"hgvs_p": "p.Thr155Ser",
"transcript": "ENST00000330847.1",
"protein_id": "ENSP00000333122.1",
"transcript_support_level": 5,
"aa_start": 155,
"aa_end": null,
"aa_length": 637,
"cds_start": 464,
"cds_end": null,
"cds_length": 1914,
"cdna_start": 508,
"cdna_end": null,
"cdna_length": 4982,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR4A3",
"gene_hgnc_id": 7982,
"hgvs_c": "c.464C>G",
"hgvs_p": "p.Thr155Ser",
"transcript": "ENST00000618101.4",
"protein_id": "ENSP00000482027.1",
"transcript_support_level": 5,
"aa_start": 155,
"aa_end": null,
"aa_length": 637,
"cds_start": 464,
"cds_end": null,
"cds_length": 1914,
"cdna_start": 1232,
"cdna_end": null,
"cdna_length": 5706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR4A3",
"gene_hgnc_id": 7982,
"hgvs_c": "c.431C>G",
"hgvs_p": "p.Thr144Ser",
"transcript": "NM_173199.4",
"protein_id": "NP_775291.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 443,
"cds_start": 431,
"cds_end": null,
"cds_length": 1332,
"cdna_start": 1130,
"cdna_end": null,
"cdna_length": 2800,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NR4A3",
"gene_hgnc_id": 7982,
"hgvs_c": "c.431C>G",
"hgvs_p": "p.Thr144Ser",
"transcript": "XM_017015162.2",
"protein_id": "XP_016870651.1",
"transcript_support_level": null,
"aa_start": 144,
"aa_end": null,
"aa_length": 626,
"cds_start": 431,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 718,
"cdna_end": null,
"cdna_length": 5192,
"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": 6,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "NAMA",
"gene_hgnc_id": 42408,
"hgvs_c": "n.268+10513G>C",
"hgvs_p": null,
"transcript": "ENST00000655615.1",
"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": 2308,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "NAMA",
"gene_hgnc_id": 42408,
"hgvs_c": "n.126+10513G>C",
"hgvs_p": null,
"transcript": "ENST00000715777.1",
"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": 1919,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "NAMA",
"gene_hgnc_id": 42408,
"hgvs_c": "n.266+10513G>C",
"hgvs_p": null,
"transcript": "ENST00000725618.1",
"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": 666,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "NAMA",
"gene_hgnc_id": 42408,
"hgvs_c": "n.235+10513G>C",
"hgvs_p": null,
"transcript": "ENST00000725628.1",
"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": 1825,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "NAMA",
"gene_hgnc_id": 42408,
"hgvs_c": "n.280+10513G>C",
"hgvs_p": null,
"transcript": "ENST00000725629.1",
"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": 1450,
"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": 4,
"intron_rank_end": null,
"gene_symbol": "NAMA",
"gene_hgnc_id": 42408,
"hgvs_c": "n.394+10513G>C",
"hgvs_p": null,
"transcript": "ENST00000725630.1",
"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": 1394,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "NAMA",
"gene_hgnc_id": 42408,
"hgvs_c": "n.278+10513G>C",
"hgvs_p": null,
"transcript": "ENST00000725631.1",
"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": 1143,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "NAMA",
"gene_hgnc_id": 42408,
"hgvs_c": "n.256+10513G>C",
"hgvs_p": null,
"transcript": "ENST00000725639.1",
"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": 508,
"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": 3,
"intron_rank_end": null,
"gene_symbol": "NAMA",
"gene_hgnc_id": 42408,
"hgvs_c": "n.262+10513G>C",
"hgvs_p": null,
"transcript": "ENST00000725641.1",
"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": 811,
"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": 2,
"intron_rank_end": null,
"gene_symbol": "NAMA",
"gene_hgnc_id": 42408,
"hgvs_c": "n.217-8080G>C",
"hgvs_p": null,
"transcript": "ENST00000725643.1",
"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": 531,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NR4A3",
"gene_hgnc_id": 7982,
"dbsnp": "rs372573982",
"frequency_reference_population": null,
"hom_count_reference_population": 0,
"allele_count_reference_population": 0,
"gnomad_exomes_af": null,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": null,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": null,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07438924908638,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.206,
"revel_prediction": "Benign",
"alphamissense_score": 0.1003,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.32,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.606,
"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_006981.4",
"gene_symbol": "NR4A3",
"hgnc_id": 7982,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.431C>G",
"hgvs_p": "p.Thr144Ser"
},
{
"score": 0,
"benign_score": 2,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000655615.1",
"gene_symbol": "NAMA",
"hgnc_id": 42408,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.268+10513G>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
}