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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: 3-138162100-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=138162100&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 138162100,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_016216.4",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBR1",
"gene_hgnc_id": 15594,
"hgvs_c": "c.1424T>C",
"hgvs_p": "p.Met475Thr",
"transcript": "NM_016216.4",
"protein_id": "NP_057300.2",
"transcript_support_level": null,
"aa_start": 475,
"aa_end": null,
"aa_length": 544,
"cds_start": 1424,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000260803.9",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_016216.4"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBR1",
"gene_hgnc_id": 15594,
"hgvs_c": "c.1424T>C",
"hgvs_p": "p.Met475Thr",
"transcript": "ENST00000260803.9",
"protein_id": "ENSP00000260803.4",
"transcript_support_level": 1,
"aa_start": 475,
"aa_end": null,
"aa_length": 544,
"cds_start": 1424,
"cds_end": null,
"cds_length": 1635,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_016216.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000260803.9"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBR1",
"gene_hgnc_id": 15594,
"hgvs_c": "c.1343T>C",
"hgvs_p": "p.Met448Thr",
"transcript": "ENST00000698924.1",
"protein_id": "ENSP00000514035.1",
"transcript_support_level": null,
"aa_start": 448,
"aa_end": null,
"aa_length": 517,
"cds_start": 1343,
"cds_end": null,
"cds_length": 1554,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000698924.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBR1",
"gene_hgnc_id": 15594,
"hgvs_c": "c.1199T>C",
"hgvs_p": "p.Met400Thr",
"transcript": "ENST00000698922.1",
"protein_id": "ENSP00000514033.1",
"transcript_support_level": null,
"aa_start": 400,
"aa_end": null,
"aa_length": 469,
"cds_start": 1199,
"cds_end": null,
"cds_length": 1410,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000698922.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBR1",
"gene_hgnc_id": 15594,
"hgvs_c": "c.*346T>C",
"hgvs_p": null,
"transcript": "ENST00000698925.1",
"protein_id": "ENSP00000514036.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 330,
"cds_start": null,
"cds_end": null,
"cds_length": 993,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000698925.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBR1",
"gene_hgnc_id": 15594,
"hgvs_c": "c.*346T>C",
"hgvs_p": null,
"transcript": "ENST00000698926.1",
"protein_id": "ENSP00000514037.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 72,
"cds_start": null,
"cds_end": null,
"cds_length": 219,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000698926.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBR1",
"gene_hgnc_id": 15594,
"hgvs_c": "n.1720T>C",
"hgvs_p": null,
"transcript": "ENST00000460271.6",
"protein_id": null,
"transcript_support_level": 2,
"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": "retained_intron",
"feature": "ENST00000460271.6"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 7,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBR1",
"gene_hgnc_id": 15594,
"hgvs_c": "n.1590T>C",
"hgvs_p": null,
"transcript": "ENST00000698921.1",
"protein_id": null,
"transcript_support_level": null,
"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": "retained_intron",
"feature": "ENST00000698921.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBR1",
"gene_hgnc_id": 15594,
"hgvs_c": "n.*543T>C",
"hgvs_p": null,
"transcript": "ENST00000698923.1",
"protein_id": "ENSP00000514034.1",
"transcript_support_level": null,
"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": "ENST00000698923.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "DBR1",
"gene_hgnc_id": 15594,
"hgvs_c": "n.*543T>C",
"hgvs_p": null,
"transcript": "ENST00000698923.1",
"protein_id": "ENSP00000514034.1",
"transcript_support_level": null,
"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": "ENST00000698923.1"
}
],
"gene_symbol": "DBR1",
"gene_hgnc_id": 15594,
"dbsnp": null,
"frequency_reference_population": 0.0000027361802,
"hom_count_reference_population": 0,
"allele_count_reference_population": 4,
"gnomad_exomes_af": 0.00000273618,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 4,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.34045106172561646,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.133,
"revel_prediction": "Benign",
"alphamissense_score": 0.2288,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.34,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 6.088,
"phylop100way_prediction": "Uncertain_significance",
"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": 1,
"acmg_classification": "Uncertain_significance",
"acmg_criteria": "PM2,BP4",
"acmg_by_gene": [
{
"score": 1,
"benign_score": 1,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4"
],
"verdict": "Uncertain_significance",
"transcript": "NM_016216.4",
"gene_symbol": "DBR1",
"hgnc_id": 15594,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1424T>C",
"hgvs_p": "p.Met475Thr"
}
],
"clinvar_disease": "Inborn genetic diseases,not provided",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Inborn genetic diseases|not provided",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}