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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: 1-155139987-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=155139987&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 155139987,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "ENST00000368400.5",
"consequences": [
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM3",
"gene_hgnc_id": 3007,
"hgvs_c": "c.254T>C",
"hgvs_p": "p.Leu85Ser",
"transcript": "NM_153741.2",
"protein_id": "NP_714963.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 92,
"cds_start": 254,
"cds_end": null,
"cds_length": 279,
"cdna_start": 300,
"cdna_end": null,
"cdna_length": 396,
"mane_select": "ENST00000368400.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM3",
"gene_hgnc_id": 3007,
"hgvs_c": "c.254T>C",
"hgvs_p": "p.Leu85Ser",
"transcript": "ENST00000368400.5",
"protein_id": "ENSP00000357385.5",
"transcript_support_level": 1,
"aa_start": 85,
"aa_end": null,
"aa_length": 92,
"cds_start": 254,
"cds_end": null,
"cds_length": 279,
"cdna_start": 300,
"cdna_end": null,
"cdna_length": 396,
"mane_select": "NM_153741.2",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM3",
"gene_hgnc_id": 3007,
"hgvs_c": "c.344T>C",
"hgvs_p": "p.Leu115Ser",
"transcript": "NM_018973.4",
"protein_id": "NP_061846.2",
"transcript_support_level": null,
"aa_start": 115,
"aa_end": null,
"aa_length": 122,
"cds_start": 344,
"cds_end": null,
"cds_length": 369,
"cdna_start": 421,
"cdna_end": null,
"cdna_length": 517,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 1,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM3",
"gene_hgnc_id": 3007,
"hgvs_c": "c.344T>C",
"hgvs_p": "p.Leu115Ser",
"transcript": "ENST00000368399.1",
"protein_id": "ENSP00000357384.1",
"transcript_support_level": 6,
"aa_start": 115,
"aa_end": null,
"aa_length": 122,
"cds_start": 344,
"cds_end": null,
"cds_length": 369,
"cdna_start": 421,
"cdna_end": null,
"cdna_length": 517,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM3",
"gene_hgnc_id": 3007,
"hgvs_c": "c.254T>C",
"hgvs_p": "p.Leu85Ser",
"transcript": "ENST00000341298.3",
"protein_id": "ENSP00000344338.3",
"transcript_support_level": 2,
"aa_start": 85,
"aa_end": null,
"aa_length": 92,
"cds_start": 254,
"cds_end": null,
"cds_length": 279,
"cdna_start": 390,
"cdna_end": null,
"cdna_length": 486,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "L",
"aa_alt": "S",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DPM3",
"gene_hgnc_id": 3007,
"hgvs_c": "c.254T>C",
"hgvs_p": "p.Leu85Ser",
"transcript": "XM_017001498.2",
"protein_id": "XP_016856987.1",
"transcript_support_level": null,
"aa_start": 85,
"aa_end": null,
"aa_length": 92,
"cds_start": 254,
"cds_end": null,
"cds_length": 279,
"cdna_start": 326,
"cdna_end": null,
"cdna_length": 422,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "DPM3",
"gene_hgnc_id": 3007,
"dbsnp": "rs121908155",
"frequency_reference_population": 6.8461827e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.84618e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9865809679031372,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.869,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.9224,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.4,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 8.133,
"phylop100way_prediction": "Pathogenic",
"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": 10,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PM1,PM2,PP2,PP3_Strong,PP5",
"acmg_by_gene": [
{
"score": 10,
"benign_score": 0,
"pathogenic_score": 10,
"criteria": [
"PM1",
"PM2",
"PP2",
"PP3_Strong",
"PP5"
],
"verdict": "Pathogenic",
"transcript": "ENST00000368400.5",
"gene_symbol": "DPM3",
"hgnc_id": 3007,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.254T>C",
"hgvs_p": "p.Leu85Ser"
}
],
"clinvar_disease": "DPM3-congenital disorder of glycosylation",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "O:1",
"phenotype_combined": "DPM3-congenital disorder of glycosylation",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}