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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: 20-10413396-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=20&pos=10413396&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "20",
"pos": 10413396,
"ref": "G",
"alt": "C",
"effect": "stop_gained",
"transcript": "ENST00000347364.7",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKKS",
"gene_hgnc_id": 7108,
"hgvs_c": "c.119C>G",
"hgvs_p": "p.Ser40*",
"transcript": "NM_170784.3",
"protein_id": "NP_740754.1",
"transcript_support_level": null,
"aa_start": 40,
"aa_end": null,
"aa_length": 570,
"cds_start": 119,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 6714,
"mane_select": "ENST00000347364.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKKS",
"gene_hgnc_id": 7108,
"hgvs_c": "c.119C>G",
"hgvs_p": "p.Ser40*",
"transcript": "ENST00000347364.7",
"protein_id": "ENSP00000246062.4",
"transcript_support_level": 1,
"aa_start": 40,
"aa_end": null,
"aa_length": 570,
"cds_start": 119,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 882,
"cdna_end": null,
"cdna_length": 6714,
"mane_select": "NM_170784.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKKS",
"gene_hgnc_id": 7108,
"hgvs_c": "c.119C>G",
"hgvs_p": "p.Ser40*",
"transcript": "ENST00000399054.6",
"protein_id": "ENSP00000382008.2",
"transcript_support_level": 1,
"aa_start": 40,
"aa_end": null,
"aa_length": 570,
"cds_start": 119,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 1006,
"cdna_end": null,
"cdna_length": 2663,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKKS",
"gene_hgnc_id": 7108,
"hgvs_c": "c.119C>G",
"hgvs_p": "p.Ser40*",
"transcript": "NM_018848.3",
"protein_id": "NP_061336.1",
"transcript_support_level": null,
"aa_start": 40,
"aa_end": null,
"aa_length": 570,
"cds_start": 119,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 1009,
"cdna_end": null,
"cdna_length": 3070,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "S",
"aa_alt": "*",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"stop_gained"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MKKS",
"gene_hgnc_id": 7108,
"hgvs_c": "c.119C>G",
"hgvs_p": "p.Ser40*",
"transcript": "ENST00000651692.1",
"protein_id": "ENSP00000498849.1",
"transcript_support_level": null,
"aa_start": 40,
"aa_end": null,
"aa_length": 570,
"cds_start": 119,
"cds_end": null,
"cds_length": 1713,
"cdna_start": 961,
"cdna_end": null,
"cdna_length": 6181,
"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": 7,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "MKKS",
"gene_hgnc_id": 7108,
"hgvs_c": "n.458+400C>G",
"hgvs_p": null,
"transcript": "ENST00000652676.1",
"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": 1669,
"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": 5,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "MKKS",
"gene_hgnc_id": 7108,
"hgvs_c": "n.347-4593C>G",
"hgvs_p": null,
"transcript": "NR_072977.2",
"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": 5312,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"downstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000285508",
"gene_hgnc_id": null,
"hgvs_c": "c.*339C>G",
"hgvs_p": null,
"transcript": "ENST00000609375.1",
"protein_id": "ENSP00000477297.2",
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": 50,
"cds_start": -4,
"cds_end": null,
"cds_length": 153,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 882,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "MKKS",
"gene_hgnc_id": 7108,
"dbsnp": "rs753338844",
"frequency_reference_population": 0.0000034229836,
"hom_count_reference_population": 0,
"allele_count_reference_population": 5,
"gnomad_exomes_af": 0.00000342298,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 5,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.28999999165534973,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": 0.29,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 1.381,
"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": 18,
"acmg_classification": "Pathogenic",
"acmg_criteria": "PVS1,PM2,PP5_Very_Strong",
"acmg_by_gene": [
{
"score": 18,
"benign_score": 0,
"pathogenic_score": 18,
"criteria": [
"PVS1",
"PM2",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000347364.7",
"gene_symbol": "MKKS",
"hgnc_id": 7108,
"effects": [
"stop_gained"
],
"inheritance_mode": "AR",
"hgvs_c": "c.119C>G",
"hgvs_p": "p.Ser40*"
},
{
"score": 14,
"benign_score": 0,
"pathogenic_score": 14,
"criteria": [
"PM2",
"PP3_Strong",
"PP5_Very_Strong"
],
"verdict": "Pathogenic",
"transcript": "ENST00000609375.1",
"gene_symbol": "ENSG00000285508",
"hgnc_id": null,
"effects": [
"downstream_gene_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.*339C>G",
"hgvs_p": null
}
],
"clinvar_disease": "Bardet-Biedl syndrome,Bardet-Biedl syndrome 6",
"clinvar_classification": "Pathogenic/Likely pathogenic",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "P:1 LP:1",
"phenotype_combined": "Bardet-Biedl syndrome 6|Bardet-Biedl syndrome",
"pathogenicity_classification_combined": "Pathogenic/Likely pathogenic",
"custom_annotations": null
}
],
"message": null
}