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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: 2-169497628-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=169497628&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 169497628,
"ref": "G",
"alt": "A",
"effect": "missense_variant,splice_region_variant",
"transcript": "NM_152384.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.620G>A",
"hgvs_p": "p.Arg207His",
"transcript": "NM_152384.3",
"protein_id": "NP_689597.1",
"transcript_support_level": null,
"aa_start": 207,
"aa_end": null,
"aa_length": 341,
"cds_start": 620,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000295240.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_152384.3"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.620G>A",
"hgvs_p": "p.Arg207His",
"transcript": "ENST00000295240.8",
"protein_id": "ENSP00000295240.3",
"transcript_support_level": 1,
"aa_start": 207,
"aa_end": null,
"aa_length": 341,
"cds_start": 620,
"cds_end": null,
"cds_length": 1026,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_152384.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000295240.8"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ENSG00000251569",
"gene_hgnc_id": null,
"hgvs_c": "c.620G>A",
"hgvs_p": "p.Arg207His",
"transcript": "ENST00000513963.1",
"protein_id": "ENSP00000424363.1",
"transcript_support_level": 2,
"aa_start": 207,
"aa_end": null,
"aa_length": 544,
"cds_start": 620,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000513963.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.619-1858G>A",
"hgvs_p": null,
"transcript": "ENST00000392663.6",
"protein_id": "ENSP00000376431.2",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": 320,
"cds_start": null,
"cds_end": null,
"cds_length": 963,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000392663.6"
},
{
"aa_ref": "R",
"aa_alt": "H",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant",
"splice_region_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.554G>A",
"hgvs_p": "p.Arg185His",
"transcript": "ENST00000857799.1",
"protein_id": "ENSP00000527858.1",
"transcript_support_level": null,
"aa_start": 185,
"aa_end": null,
"aa_length": 319,
"cds_start": 554,
"cds_end": null,
"cds_length": 960,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857799.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.553-1858G>A",
"hgvs_p": null,
"transcript": "ENST00000950195.1",
"protein_id": "ENSP00000620254.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 298,
"cds_start": null,
"cds_end": null,
"cds_length": 897,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950195.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 6,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.523-1858G>A",
"hgvs_p": null,
"transcript": "ENST00000950194.1",
"protein_id": "ENSP00000620253.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 288,
"cds_start": null,
"cds_end": null,
"cds_length": 867,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000950194.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": 7,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "c.618+3792G>A",
"hgvs_p": null,
"transcript": "ENST00000857800.1",
"protein_id": "ENSP00000527859.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 275,
"cds_start": null,
"cds_end": null,
"cds_length": 828,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000857800.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"splice_region_variant",
"non_coding_transcript_exon_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "n.*342G>A",
"hgvs_p": null,
"transcript": "ENST00000443151.1",
"protein_id": "ENSP00000406182.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000443151.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"hgvs_c": "n.*342G>A",
"hgvs_p": null,
"transcript": "ENST00000443151.1",
"protein_id": "ENSP00000406182.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": null,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "nonsense_mediated_decay",
"feature": "ENST00000443151.1"
}
],
"gene_symbol": "BBS5",
"gene_hgnc_id": 970,
"dbsnp": "rs35487251",
"frequency_reference_population": 0.007845575,
"hom_count_reference_population": 87,
"allele_count_reference_population": 12368,
"gnomad_exomes_af": 0.00802988,
"gnomad_genomes_af": 0.00612001,
"gnomad_exomes_ac": 11437,
"gnomad_genomes_ac": 931,
"gnomad_exomes_homalt": 86,
"gnomad_genomes_homalt": 1,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.011214107275009155,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.8360000252723694,
"splice_prediction_selected": "Pathogenic",
"splice_source_selected": "dbscSNV1_RF",
"revel_score": 0.228,
"revel_prediction": "Benign",
"alphamissense_score": 0.1037,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.16,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 9.175,
"phylop100way_prediction": "Pathogenic",
"spliceai_max_score": 0.11,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": 0.981101852294291,
"dbscsnv_ada_prediction": "Pathogenic",
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -14,
"acmg_classification": "Benign",
"acmg_criteria": "PP2,PP3,BP6_Very_Strong,BS1,BS2",
"acmg_by_gene": [
{
"score": -14,
"benign_score": 16,
"pathogenic_score": 2,
"criteria": [
"PP2",
"PP3",
"BP6_Very_Strong",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "NM_152384.3",
"gene_symbol": "BBS5",
"hgnc_id": 970,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.620G>A",
"hgvs_p": "p.Arg207His"
},
{
"score": -11,
"benign_score": 12,
"pathogenic_score": 1,
"criteria": [
"PP3",
"BP6_Very_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000513963.1",
"gene_symbol": "ENSG00000251569",
"hgnc_id": null,
"effects": [
"missense_variant",
"splice_region_variant"
],
"inheritance_mode": "",
"hgvs_c": "c.620G>A",
"hgvs_p": "p.Arg207His"
}
],
"clinvar_disease": "Bardet-Biedl syndrome,not provided,not specified",
"clinvar_classification": "Benign/Likely benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "LB:1 B:6",
"phenotype_combined": "not specified|Bardet-Biedl syndrome|not provided",
"pathogenicity_classification_combined": "Benign/Likely benign",
"custom_annotations": null
}
],
"message": null
}