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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: 2-232879665-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=232879665&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 232879665,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_019850.3",
"consequences": [
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.1957G>A",
"hgvs_p": "p.Glu653Lys",
"transcript": "NM_019850.3",
"protein_id": "NP_062824.2",
"transcript_support_level": null,
"aa_start": 653,
"aa_end": null,
"aa_length": 710,
"cds_start": 1957,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000264051.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_019850.3"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.1957G>A",
"hgvs_p": "p.Glu653Lys",
"transcript": "ENST00000264051.8",
"protein_id": "ENSP00000264051.3",
"transcript_support_level": 1,
"aa_start": 653,
"aa_end": null,
"aa_length": 710,
"cds_start": 1957,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_019850.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000264051.8"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.2056G>A",
"hgvs_p": "p.Glu686Lys",
"transcript": "ENST00000905022.1",
"protein_id": "ENSP00000575081.1",
"transcript_support_level": null,
"aa_start": 686,
"aa_end": null,
"aa_length": 743,
"cds_start": 2056,
"cds_end": null,
"cds_length": 2232,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905022.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.2056G>A",
"hgvs_p": "p.Glu686Lys",
"transcript": "ENST00000965357.1",
"protein_id": "ENSP00000635416.1",
"transcript_support_level": null,
"aa_start": 686,
"aa_end": null,
"aa_length": 743,
"cds_start": 2056,
"cds_end": null,
"cds_length": 2232,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965357.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.1957G>A",
"hgvs_p": "p.Glu653Lys",
"transcript": "ENST00000905023.1",
"protein_id": "ENSP00000575082.1",
"transcript_support_level": null,
"aa_start": 653,
"aa_end": null,
"aa_length": 710,
"cds_start": 1957,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905023.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 16,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.1957G>A",
"hgvs_p": "p.Glu653Lys",
"transcript": "ENST00000965358.1",
"protein_id": "ENSP00000635417.1",
"transcript_support_level": null,
"aa_start": 653,
"aa_end": null,
"aa_length": 710,
"cds_start": 1957,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000965358.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.1915G>A",
"hgvs_p": "p.Glu639Lys",
"transcript": "ENST00000905024.1",
"protein_id": "ENSP00000575083.1",
"transcript_support_level": null,
"aa_start": 639,
"aa_end": null,
"aa_length": 696,
"cds_start": 1915,
"cds_end": null,
"cds_length": 2091,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000905024.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.1681G>A",
"hgvs_p": "p.Glu561Lys",
"transcript": "NM_001114090.2",
"protein_id": "NP_001107562.1",
"transcript_support_level": null,
"aa_start": 561,
"aa_end": null,
"aa_length": 618,
"cds_start": 1681,
"cds_end": null,
"cds_length": 1857,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001114090.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.1681G>A",
"hgvs_p": "p.Glu561Lys",
"transcript": "ENST00000373552.8",
"protein_id": "ENSP00000362653.4",
"transcript_support_level": 2,
"aa_start": 561,
"aa_end": null,
"aa_length": 618,
"cds_start": 1681,
"cds_end": null,
"cds_length": 1857,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000373552.8"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 15,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.1957G>A",
"hgvs_p": "p.Glu653Lys",
"transcript": "XM_011510923.4",
"protein_id": "XP_011509225.1",
"transcript_support_level": null,
"aa_start": 653,
"aa_end": null,
"aa_length": 710,
"cds_start": 1957,
"cds_end": null,
"cds_length": 2133,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510923.4"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.1483G>A",
"hgvs_p": "p.Glu495Lys",
"transcript": "XM_047443880.1",
"protein_id": "XP_047299836.1",
"transcript_support_level": null,
"aa_start": 495,
"aa_end": null,
"aa_length": 552,
"cds_start": 1483,
"cds_end": null,
"cds_length": 1659,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_047443880.1"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.1126G>A",
"hgvs_p": "p.Glu376Lys",
"transcript": "XM_011510924.2",
"protein_id": "XP_011509226.1",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 433,
"cds_start": 1126,
"cds_end": null,
"cds_length": 1302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510924.2"
},
{
"aa_ref": "E",
"aa_alt": "K",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"hgvs_c": "c.1126G>A",
"hgvs_p": "p.Glu376Lys",
"transcript": "XM_011510925.2",
"protein_id": "XP_011509227.1",
"transcript_support_level": null,
"aa_start": 376,
"aa_end": null,
"aa_length": 433,
"cds_start": 1126,
"cds_end": null,
"cds_length": 1302,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "XM_011510925.2"
}
],
"gene_symbol": "NGEF",
"gene_hgnc_id": 7807,
"dbsnp": "rs544040415",
"frequency_reference_population": 0.000015503703,
"hom_count_reference_population": 0,
"allele_count_reference_population": 25,
"gnomad_exomes_af": 0.000014382,
"gnomad_genomes_af": 0.0000262543,
"gnomad_exomes_ac": 21,
"gnomad_genomes_ac": 4,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.5952172875404358,
"computational_prediction_selected": "Uncertain_significance",
"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": 0.9442,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.09,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.69,
"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": 2,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2",
"acmg_by_gene": [
{
"score": 2,
"benign_score": 0,
"pathogenic_score": 2,
"criteria": [
"PM2"
],
"verdict": "Uncertain_significance",
"transcript": "NM_019850.3",
"gene_symbol": "NGEF",
"hgnc_id": 7807,
"effects": [
"missense_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.1957G>A",
"hgvs_p": "p.Glu653Lys"
}
],
"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
}