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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: 6-131851228-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=6&pos=131851228&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "6",
"pos": 131851228,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000647893.1",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENPP1",
"gene_hgnc_id": 3356,
"hgvs_c": "c.517A>C",
"hgvs_p": "p.Lys173Gln",
"transcript": "NM_006208.3",
"protein_id": "NP_006199.2",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 925,
"cds_start": 517,
"cds_end": null,
"cds_length": 2778,
"cdna_start": 533,
"cdna_end": null,
"cdna_length": 7438,
"mane_select": "ENST00000647893.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENPP1",
"gene_hgnc_id": 3356,
"hgvs_c": "c.517A>C",
"hgvs_p": "p.Lys173Gln",
"transcript": "ENST00000647893.1",
"protein_id": "ENSP00000498074.1",
"transcript_support_level": null,
"aa_start": 173,
"aa_end": null,
"aa_length": 925,
"cds_start": 517,
"cds_end": null,
"cds_length": 2778,
"cdna_start": 533,
"cdna_end": null,
"cdna_length": 7438,
"mane_select": "NM_006208.3",
"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": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENPP1",
"gene_hgnc_id": 3356,
"hgvs_c": "n.537A>C",
"hgvs_p": null,
"transcript": "ENST00000486853.1",
"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": 732,
"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": 4,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENPP1",
"gene_hgnc_id": 3356,
"hgvs_c": "n.517A>C",
"hgvs_p": null,
"transcript": "ENST00000513998.5",
"protein_id": "ENSP00000422424.1",
"transcript_support_level": 5,
"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": 3107,
"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": 2,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENPP1",
"gene_hgnc_id": 3356,
"hgvs_c": "n.193A>C",
"hgvs_p": null,
"transcript": "ENST00000650147.1",
"protein_id": "ENSP00000497519.1",
"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": 2146,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "ENPP1",
"gene_hgnc_id": 3356,
"hgvs_c": "n.106+1122A>C",
"hgvs_p": null,
"transcript": "ENST00000650437.1",
"protein_id": "ENSP00000497981.1",
"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": 2090,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ENPP1",
"gene_hgnc_id": 3356,
"dbsnp": "rs1044498",
"frequency_reference_population": 0.17729196,
"hom_count_reference_population": 41008,
"allele_count_reference_population": 286112,
"gnomad_exomes_af": 0.161539,
"gnomad_genomes_af": 0.328638,
"gnomad_exomes_ac": 236113,
"gnomad_genomes_ac": 49999,
"gnomad_exomes_homalt": 26814,
"gnomad_genomes_homalt": 14194,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 9.324463690063567e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.055,
"revel_prediction": "Benign",
"alphamissense_score": 0.0684,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.68,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.445,
"phylop100way_prediction": "Benign",
"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": -11,
"acmg_classification": "Benign",
"acmg_criteria": "PM1,BP4_Strong,BP6,BA1",
"acmg_by_gene": [
{
"score": -11,
"benign_score": 13,
"pathogenic_score": 2,
"criteria": [
"PM1",
"BP4_Strong",
"BP6",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000647893.1",
"gene_symbol": "ENPP1",
"hgnc_id": 3356,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD,AR",
"hgvs_c": "c.517A>C",
"hgvs_p": "p.Lys173Gln"
}
],
"clinvar_disease": " 1, 2, autosomal recessive, generalized, of infancy, susceptibility to,Arterial calcification,Diabetes mellitus type 2,ENPP1-related disorder,Hypophosphatemic rickets,Hypopigmentation-punctate palmoplantar keratoderma syndrome,Inherited obesity,Insulin resistance,Obesity,Type 2 diabetes mellitus,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "LP:1 B:9 O:1",
"phenotype_combined": "Insulin resistance, susceptibility to|Obesity|not specified|Hypophosphatemic rickets, autosomal recessive, 2|Arterial calcification, generalized, of infancy, 1|Hypopigmentation-punctate palmoplantar keratoderma syndrome|Diabetes mellitus type 2, susceptibility to|not provided|Hypophosphatemic rickets|Type 2 diabetes mellitus|ENPP1-related disorder|Hypopigmentation-punctate palmoplantar keratoderma syndrome;Type 2 diabetes mellitus;Arterial calcification, generalized, of infancy, 1;Inherited obesity;Hypophosphatemic rickets, autosomal recessive, 2",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}