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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: 1-77942797-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=77942797&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 77942797,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000334785.12",
"consequences": [
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEXN",
"gene_hgnc_id": 29557,
"hgvs_c": "c.1996A>G",
"hgvs_p": "p.Thr666Ala",
"transcript": "NM_144573.4",
"protein_id": "NP_653174.3",
"transcript_support_level": null,
"aa_start": 666,
"aa_end": null,
"aa_length": 675,
"cds_start": 1996,
"cds_end": null,
"cds_length": 2028,
"cdna_start": 2184,
"cdna_end": null,
"cdna_length": 3282,
"mane_select": "ENST00000334785.12",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEXN",
"gene_hgnc_id": 29557,
"hgvs_c": "c.1996A>G",
"hgvs_p": "p.Thr666Ala",
"transcript": "ENST00000334785.12",
"protein_id": "ENSP00000333938.7",
"transcript_support_level": 1,
"aa_start": 666,
"aa_end": null,
"aa_length": 675,
"cds_start": 1996,
"cds_end": null,
"cds_length": 2028,
"cdna_start": 2184,
"cdna_end": null,
"cdna_length": 3282,
"mane_select": "NM_144573.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEXN",
"gene_hgnc_id": 29557,
"hgvs_c": "c.1693A>G",
"hgvs_p": "p.Thr565Ala",
"transcript": "ENST00000342754.5",
"protein_id": "ENSP00000343928.5",
"transcript_support_level": 1,
"aa_start": 565,
"aa_end": null,
"aa_length": 575,
"cds_start": 1693,
"cds_end": null,
"cds_length": 1728,
"cdna_start": 1695,
"cdna_end": null,
"cdna_length": 2712,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEXN",
"gene_hgnc_id": 29557,
"hgvs_c": "c.1804A>G",
"hgvs_p": "p.Thr602Ala",
"transcript": "NM_001172309.2",
"protein_id": "NP_001165780.1",
"transcript_support_level": null,
"aa_start": 602,
"aa_end": null,
"aa_length": 611,
"cds_start": 1804,
"cds_end": null,
"cds_length": 1836,
"cdna_start": 1992,
"cdna_end": null,
"cdna_length": 3090,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEXN",
"gene_hgnc_id": 29557,
"hgvs_c": "c.1804A>G",
"hgvs_p": "p.Thr602Ala",
"transcript": "ENST00000330010.12",
"protein_id": "ENSP00000327363.8",
"transcript_support_level": 2,
"aa_start": 602,
"aa_end": null,
"aa_length": 611,
"cds_start": 1804,
"cds_end": null,
"cds_length": 1836,
"cdna_start": 2101,
"cdna_end": null,
"cdna_length": 3195,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEXN",
"gene_hgnc_id": 29557,
"hgvs_c": "c.1996A>G",
"hgvs_p": "p.Thr666Ala",
"transcript": "XM_005271322.5",
"protein_id": "XP_005271379.1",
"transcript_support_level": null,
"aa_start": 666,
"aa_end": null,
"aa_length": 676,
"cds_start": 1996,
"cds_end": null,
"cds_length": 2031,
"cdna_start": 2184,
"cdna_end": null,
"cdna_length": 3201,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEXN",
"gene_hgnc_id": 29557,
"hgvs_c": "c.1954A>G",
"hgvs_p": "p.Thr652Ala",
"transcript": "XM_005271323.5",
"protein_id": "XP_005271380.1",
"transcript_support_level": null,
"aa_start": 652,
"aa_end": null,
"aa_length": 662,
"cds_start": 1954,
"cds_end": null,
"cds_length": 1989,
"cdna_start": 2142,
"cdna_end": null,
"cdna_length": 3159,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEXN",
"gene_hgnc_id": 29557,
"hgvs_c": "c.1804A>G",
"hgvs_p": "p.Thr602Ala",
"transcript": "XM_005271324.6",
"protein_id": "XP_005271381.1",
"transcript_support_level": null,
"aa_start": 602,
"aa_end": null,
"aa_length": 612,
"cds_start": 1804,
"cds_end": null,
"cds_length": 1839,
"cdna_start": 1992,
"cdna_end": null,
"cdna_length": 3009,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEXN",
"gene_hgnc_id": 29557,
"hgvs_c": "c.1774A>G",
"hgvs_p": "p.Thr592Ala",
"transcript": "XM_005271325.5",
"protein_id": "XP_005271382.1",
"transcript_support_level": null,
"aa_start": 592,
"aa_end": null,
"aa_length": 602,
"cds_start": 1774,
"cds_end": null,
"cds_length": 1809,
"cdna_start": 1962,
"cdna_end": null,
"cdna_length": 2979,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "T",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEXN",
"gene_hgnc_id": 29557,
"hgvs_c": "c.1579A>G",
"hgvs_p": "p.Thr527Ala",
"transcript": "XM_005271327.5",
"protein_id": "XP_005271384.1",
"transcript_support_level": null,
"aa_start": 527,
"aa_end": null,
"aa_length": 537,
"cds_start": 1579,
"cds_end": null,
"cds_length": 1614,
"cdna_start": 1767,
"cdna_end": null,
"cdna_length": 2784,
"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": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEXN",
"gene_hgnc_id": 29557,
"hgvs_c": "n.1570A>G",
"hgvs_p": null,
"transcript": "ENST00000480732.2",
"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": 1972,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NEXN",
"gene_hgnc_id": 29557,
"hgvs_c": "n.*44A>G",
"hgvs_p": null,
"transcript": "ENST00000470735.1",
"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": 791,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "NEXN",
"gene_hgnc_id": 29557,
"dbsnp": "rs374000722",
"frequency_reference_population": 0.00006891799,
"hom_count_reference_population": 0,
"allele_count_reference_population": 111,
"gnomad_exomes_af": 0.0000685625,
"gnomad_genomes_af": 0.0000723275,
"gnomad_exomes_ac": 100,
"gnomad_genomes_ac": 11,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.4270494282245636,
"computational_prediction_selected": "Uncertain_significance",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.253,
"revel_prediction": "Benign",
"alphamissense_score": 0.2567,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.2,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.325,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.02,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BS1_Supporting,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BS1_Supporting",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "ENST00000334785.12",
"gene_symbol": "NEXN",
"hgnc_id": 29557,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.1996A>G",
"hgvs_p": "p.Thr666Ala"
}
],
"clinvar_disease": "Cardiomyopathy,Cardiovascular phenotype,Dilated cardiomyopathy 1CC,Hypertrophic cardiomyopathy 20,NEXN-related disorder,Primary familial hypertrophic cardiomyopathy,not provided,not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:6",
"phenotype_combined": "not specified|Primary familial hypertrophic cardiomyopathy|Cardiomyopathy|not provided|Dilated cardiomyopathy 1CC;Hypertrophic cardiomyopathy 20|NEXN-related disorder|Cardiovascular phenotype",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}