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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: 9-99828487-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=99828487&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 99828487,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_006981.4",
"consequences": [
{
"aa_ref": "P",
"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.445C>T",
"hgvs_p": "p.Pro149Ser",
"transcript": "NM_006981.4",
"protein_id": "NP_008912.2",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 626,
"cds_start": 445,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 1144,
"cdna_end": null,
"cdna_length": 5604,
"mane_select": "ENST00000395097.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"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.445C>T",
"hgvs_p": "p.Pro149Ser",
"transcript": "ENST00000395097.7",
"protein_id": "ENSP00000378531.2",
"transcript_support_level": 1,
"aa_start": 149,
"aa_end": null,
"aa_length": 626,
"cds_start": 445,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 1144,
"cdna_end": null,
"cdna_length": 5604,
"mane_select": "NM_006981.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"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.445C>T",
"hgvs_p": "p.Pro149Ser",
"transcript": "ENST00000338488.8",
"protein_id": "ENSP00000340301.4",
"transcript_support_level": 1,
"aa_start": 149,
"aa_end": null,
"aa_length": 443,
"cds_start": 445,
"cds_end": null,
"cds_length": 1332,
"cdna_start": 1174,
"cdna_end": null,
"cdna_length": 2588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"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.478C>T",
"hgvs_p": "p.Pro160Ser",
"transcript": "NM_173200.3",
"protein_id": "NP_775292.1",
"transcript_support_level": null,
"aa_start": 160,
"aa_end": null,
"aa_length": 637,
"cds_start": 478,
"cds_end": null,
"cds_length": 1914,
"cdna_start": 1216,
"cdna_end": null,
"cdna_length": 5676,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"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.478C>T",
"hgvs_p": "p.Pro160Ser",
"transcript": "ENST00000330847.1",
"protein_id": "ENSP00000333122.1",
"transcript_support_level": 5,
"aa_start": 160,
"aa_end": null,
"aa_length": 637,
"cds_start": 478,
"cds_end": null,
"cds_length": 1914,
"cdna_start": 522,
"cdna_end": null,
"cdna_length": 4982,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"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.478C>T",
"hgvs_p": "p.Pro160Ser",
"transcript": "ENST00000618101.4",
"protein_id": "ENSP00000482027.1",
"transcript_support_level": 5,
"aa_start": 160,
"aa_end": null,
"aa_length": 637,
"cds_start": 478,
"cds_end": null,
"cds_length": 1914,
"cdna_start": 1246,
"cdna_end": null,
"cdna_length": 5706,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"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.445C>T",
"hgvs_p": "p.Pro149Ser",
"transcript": "NM_173199.4",
"protein_id": "NP_775291.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 443,
"cds_start": 445,
"cds_end": null,
"cds_length": 1332,
"cdna_start": 1144,
"cdna_end": null,
"cdna_length": 2800,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "P",
"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.445C>T",
"hgvs_p": "p.Pro149Ser",
"transcript": "XM_017015162.2",
"protein_id": "XP_016870651.1",
"transcript_support_level": null,
"aa_start": 149,
"aa_end": null,
"aa_length": 626,
"cds_start": 445,
"cds_end": null,
"cds_length": 1881,
"cdna_start": 732,
"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+10499G>A",
"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+10499G>A",
"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+10499G>A",
"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+10499G>A",
"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+10499G>A",
"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+10499G>A",
"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+10499G>A",
"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+10499G>A",
"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+10499G>A",
"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.217-8094G>A",
"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": "rs1827361012",
"frequency_reference_population": 0.0000018997827,
"hom_count_reference_population": 0,
"allele_count_reference_population": 3,
"gnomad_exomes_af": 0.00000140136,
"gnomad_genomes_af": 0.00000658146,
"gnomad_exomes_ac": 2,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.2703063189983368,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.59,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.0709,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.04,
"bayesdelnoaf_prediction": "Uncertain_significance",
"phylop100way_score": 3.891,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_006981.4",
"gene_symbol": "NR4A3",
"hgnc_id": 7982,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.445C>T",
"hgvs_p": "p.Pro149Ser"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000655615.1",
"gene_symbol": "NAMA",
"hgnc_id": 42408,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.268+10499G>A",
"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
}