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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: 1-231421331-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=231421331&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 231421331,
"ref": "C",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000366641.4",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGLN1",
"gene_hgnc_id": 1232,
"hgvs_c": "c.558G>C",
"hgvs_p": "p.Lys186Asn",
"transcript": "NM_022051.3",
"protein_id": "NP_071334.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 426,
"cds_start": 558,
"cds_end": null,
"cds_length": 1281,
"cdna_start": 957,
"cdna_end": null,
"cdna_length": 4335,
"mane_select": "ENST00000366641.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGLN1",
"gene_hgnc_id": 1232,
"hgvs_c": "c.558G>C",
"hgvs_p": "p.Lys186Asn",
"transcript": "ENST00000366641.4",
"protein_id": "ENSP00000355601.3",
"transcript_support_level": 1,
"aa_start": 186,
"aa_end": null,
"aa_length": 426,
"cds_start": 558,
"cds_end": null,
"cds_length": 1281,
"cdna_start": 957,
"cdna_end": null,
"cdna_length": 4335,
"mane_select": "NM_022051.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ENSG00000287856",
"gene_hgnc_id": null,
"hgvs_c": "c.30+41107G>C",
"hgvs_p": null,
"transcript": "ENST00000662216.1",
"protein_id": "ENSP00000499467.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 139,
"cds_start": -4,
"cds_end": null,
"cds_length": 420,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1361,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGLN1",
"gene_hgnc_id": 1232,
"hgvs_c": "c.558G>C",
"hgvs_p": "p.Lys186Asn",
"transcript": "NM_001377260.1",
"protein_id": "NP_001364189.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 383,
"cds_start": 558,
"cds_end": null,
"cds_length": 1152,
"cdna_start": 957,
"cdna_end": null,
"cdna_length": 4267,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGLN1",
"gene_hgnc_id": 1232,
"hgvs_c": "c.558G>C",
"hgvs_p": "p.Lys186Asn",
"transcript": "NM_001377261.1",
"protein_id": "NP_001364190.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 345,
"cds_start": 558,
"cds_end": null,
"cds_length": 1038,
"cdna_start": 957,
"cdna_end": null,
"cdna_length": 4198,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGLN1",
"gene_hgnc_id": 1232,
"hgvs_c": "c.558G>C",
"hgvs_p": "p.Lys186Asn",
"transcript": "XM_024447734.2",
"protein_id": "XP_024303502.1",
"transcript_support_level": null,
"aa_start": 186,
"aa_end": null,
"aa_length": 345,
"cds_start": 558,
"cds_end": null,
"cds_length": 1038,
"cdna_start": 957,
"cdna_end": null,
"cdna_length": 1480,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "ENSG00000287856",
"gene_hgnc_id": null,
"hgvs_c": "c.30+41107G>C",
"hgvs_p": null,
"transcript": "ENST00000653908.1",
"protein_id": "ENSP00000499669.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 58,
"cds_start": -4,
"cds_end": null,
"cds_length": 177,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3288,
"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": 8,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000287856",
"gene_hgnc_id": null,
"hgvs_c": "n.433+41141G>C",
"hgvs_p": null,
"transcript": "ENST00000653198.1",
"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": 3252,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGLN1",
"gene_hgnc_id": 1232,
"hgvs_c": "c.-70G>C",
"hgvs_p": null,
"transcript": "ENST00000658954.1",
"protein_id": "ENSP00000499299.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 174,
"cds_start": -4,
"cds_end": null,
"cds_length": 525,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1090,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGLN1",
"gene_hgnc_id": 1232,
"hgvs_c": "c.-139G>C",
"hgvs_p": null,
"transcript": "ENST00000667629.1",
"protein_id": "ENSP00000499629.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 113,
"cds_start": -4,
"cds_end": null,
"cds_length": 342,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3108,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGLN1",
"gene_hgnc_id": 1232,
"hgvs_c": "c.-106G>C",
"hgvs_p": null,
"transcript": "ENST00000670301.1",
"protein_id": "ENSP00000499368.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 80,
"cds_start": -4,
"cds_end": null,
"cds_length": 243,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 783,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EGLN1",
"gene_hgnc_id": 1232,
"hgvs_c": "n.-223G>C",
"hgvs_p": null,
"transcript": "ENST00000654803.1",
"protein_id": "ENSP00000499591.1",
"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": 1525,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "EGLN1",
"gene_hgnc_id": 1232,
"dbsnp": "rs201365992",
"frequency_reference_population": 0.00044236478,
"hom_count_reference_population": 0,
"allele_count_reference_population": 713,
"gnomad_exomes_af": 0.000470028,
"gnomad_genomes_af": 0.000177277,
"gnomad_exomes_ac": 686,
"gnomad_genomes_ac": 27,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.07357823848724365,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.04,
"revel_prediction": "Benign",
"alphamissense_score": 0.7145,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": -0.69,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.066,
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Moderate,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 11,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000366641.4",
"gene_symbol": "EGLN1",
"hgnc_id": 1232,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.558G>C",
"hgvs_p": "p.Lys186Asn"
},
{
"score": -3,
"benign_score": 3,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6"
],
"verdict": "Likely_benign",
"transcript": "ENST00000662216.1",
"gene_symbol": "ENSG00000287856",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.30+41107G>C",
"hgvs_p": null
}
],
"clinvar_disease": " 3, familial,Erythrocytosis,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:2 LB:1 B:1",
"phenotype_combined": "Erythrocytosis, familial, 3|not provided|not specified",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}