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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: 7-16462589-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=7&pos=16462589&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "7",
"pos": 16462589,
"ref": "G",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_015464.3",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "W",
"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": "SOSTDC1",
"gene_hgnc_id": 21748,
"hgvs_c": "c.580C>T",
"hgvs_p": "p.Arg194Trp",
"transcript": "NM_015464.3",
"protein_id": "NP_056279.1",
"transcript_support_level": null,
"aa_start": 194,
"aa_end": null,
"aa_length": 206,
"cds_start": 580,
"cds_end": null,
"cds_length": 621,
"cdna_start": 650,
"cdna_end": null,
"cdna_length": 1758,
"mane_select": "ENST00000307068.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"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": "SOSTDC1",
"gene_hgnc_id": 21748,
"hgvs_c": "c.580C>T",
"hgvs_p": "p.Arg194Trp",
"transcript": "ENST00000307068.5",
"protein_id": "ENSP00000304930.4",
"transcript_support_level": 1,
"aa_start": 194,
"aa_end": null,
"aa_length": 206,
"cds_start": 580,
"cds_end": null,
"cds_length": 621,
"cdna_start": 650,
"cdna_end": null,
"cdna_length": 1758,
"mane_select": "NM_015464.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "R",
"aa_alt": "W",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SOSTDC1",
"gene_hgnc_id": 21748,
"hgvs_c": "c.652C>T",
"hgvs_p": "p.Arg218Trp",
"transcript": "ENST00000396652.1",
"protein_id": "ENSP00000379889.1",
"transcript_support_level": 2,
"aa_start": 218,
"aa_end": null,
"aa_length": 230,
"cds_start": 652,
"cds_end": null,
"cds_length": 693,
"cdna_start": 1365,
"cdna_end": null,
"cdna_length": 2411,
"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": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CRPPA",
"gene_hgnc_id": 37276,
"hgvs_c": "c.-47+33791C>T",
"hgvs_p": null,
"transcript": "ENST00000675257.1",
"protein_id": "ENSP00000501664.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 315,
"cds_start": -4,
"cds_end": null,
"cds_length": 948,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1415,
"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": 10,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "CRPPA",
"gene_hgnc_id": 37276,
"hgvs_c": "c.-47+33791C>T",
"hgvs_p": null,
"transcript": "ENST00000674759.1",
"protein_id": "ENSP00000502749.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 300,
"cds_start": -4,
"cds_end": null,
"cds_length": 903,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1181,
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272537",
"gene_hgnc_id": null,
"hgvs_c": "n.721+1273G>A",
"hgvs_p": null,
"transcript": "ENST00000605985.2",
"protein_id": null,
"transcript_support_level": 6,
"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": 1475,
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "ENSG00000272537",
"gene_hgnc_id": null,
"hgvs_c": "n.486-8031G>A",
"hgvs_p": null,
"transcript": "ENST00000780753.1",
"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": 1241,
"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": 6,
"intron_rank": 5,
"intron_rank_end": null,
"gene_symbol": "LOC105375168",
"gene_hgnc_id": null,
"hgvs_c": "n.736+1273G>A",
"hgvs_p": null,
"transcript": "XR_007060220.1",
"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": 1492,
"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": 5,
"intron_rank": 4,
"intron_rank_end": null,
"gene_symbol": "LOC105375168",
"gene_hgnc_id": null,
"hgvs_c": "n.581-8031G>A",
"hgvs_p": null,
"transcript": "XR_007060223.1",
"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": 1336,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "SOSTDC1",
"gene_hgnc_id": 21748,
"dbsnp": "rs764846211",
"frequency_reference_population": 0.000010532185,
"hom_count_reference_population": 0,
"allele_count_reference_population": 17,
"gnomad_exomes_af": 0.0000109449,
"gnomad_genomes_af": 0.00000656892,
"gnomad_exomes_ac": 16,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.38542819023132324,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.549,
"revel_prediction": "Uncertain_significance",
"alphamissense_score": 0.3453,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.21,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.752,
"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": -5,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4,BS2",
"acmg_by_gene": [
{
"score": -5,
"benign_score": 5,
"pathogenic_score": 0,
"criteria": [
"BP4",
"BS2"
],
"verdict": "Likely_benign",
"transcript": "NM_015464.3",
"gene_symbol": "SOSTDC1",
"hgnc_id": 21748,
"effects": [
"missense_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "c.580C>T",
"hgvs_p": "p.Arg194Trp"
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000675257.1",
"gene_symbol": "CRPPA",
"hgnc_id": 37276,
"effects": [
"intron_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.-47+33791C>T",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "ENST00000780753.1",
"gene_symbol": "ENSG00000272537",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.486-8031G>A",
"hgvs_p": null
},
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "XR_007060220.1",
"gene_symbol": "LOC105375168",
"hgnc_id": null,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.736+1273G>A",
"hgvs_p": null
}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}