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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: 22-19432565-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=22&pos=19432565&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "22",
"pos": 19432565,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_003776.4",
"consequences": [
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL40",
"gene_hgnc_id": 14491,
"hgvs_c": "c.11C>T",
"hgvs_p": "p.Ser4Phe",
"transcript": "NM_003776.4",
"protein_id": "NP_003767.2",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 206,
"cds_start": 11,
"cds_end": null,
"cds_length": 621,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000333130.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_003776.4"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL40",
"gene_hgnc_id": 14491,
"hgvs_c": "c.11C>T",
"hgvs_p": "p.Ser4Phe",
"transcript": "ENST00000333130.4",
"protein_id": "ENSP00000333401.3",
"transcript_support_level": 1,
"aa_start": 4,
"aa_end": null,
"aa_length": 206,
"cds_start": 11,
"cds_end": null,
"cds_length": 621,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_003776.4",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000333130.4"
},
{
"aa_ref": "S",
"aa_alt": "F",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL40",
"gene_hgnc_id": 14491,
"hgvs_c": "c.11C>T",
"hgvs_p": "p.Ser4Phe",
"transcript": "ENST00000926344.1",
"protein_id": "ENSP00000596403.1",
"transcript_support_level": null,
"aa_start": 4,
"aa_end": null,
"aa_length": 178,
"cds_start": 11,
"cds_end": null,
"cds_length": 537,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000926344.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"5_prime_UTR_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL40",
"gene_hgnc_id": 14491,
"hgvs_c": "c.-374C>T",
"hgvs_p": null,
"transcript": "NM_001318151.2",
"protein_id": "NP_001305080.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 162,
"cds_start": null,
"cds_end": null,
"cds_length": 489,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001318151.2"
},
{
"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": 6,
"intron_rank": 1,
"intron_rank_end": null,
"gene_symbol": "HIRA",
"gene_hgnc_id": 4916,
"hgvs_c": "n.72+14813G>A",
"hgvs_p": null,
"transcript": "ENST00000452818.1",
"protein_id": "ENSP00000404792.1",
"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": "ENST00000452818.1"
},
{
"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": 24,
"intron_rank": 2,
"intron_rank_end": null,
"gene_symbol": "C22orf39",
"gene_hgnc_id": 27012,
"hgvs_c": "n.192+14813G>A",
"hgvs_p": null,
"transcript": "ENST00000509549.5",
"protein_id": "ENSP00000424903.1",
"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": "nonsense_mediated_decay",
"feature": "ENST00000509549.5"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"upstream_gene_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "MRPL40",
"gene_hgnc_id": 14491,
"hgvs_c": "n.-14C>T",
"hgvs_p": null,
"transcript": "ENST00000443660.5",
"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": "pseudogene",
"feature": "ENST00000443660.5"
}
],
"gene_symbol": "MRPL40",
"gene_hgnc_id": 14491,
"dbsnp": "rs201603828",
"frequency_reference_population": 0.000007864445,
"hom_count_reference_population": 0,
"allele_count_reference_population": 11,
"gnomad_exomes_af": 0.00000786445,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 11,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.0414031445980072,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.007,
"revel_prediction": "Benign",
"alphamissense_score": 0.0958,
"alphamissense_prediction": "Benign",
"bayesdelnoaf_score": -0.7,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -2,
"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": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Strong",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "NM_003776.4",
"gene_symbol": "MRPL40",
"hgnc_id": 14491,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.11C>T",
"hgvs_p": "p.Ser4Phe"
},
{
"score": -2,
"benign_score": 4,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Strong"
],
"verdict": "Likely_benign",
"transcript": "ENST00000509549.5",
"gene_symbol": "C22orf39",
"hgnc_id": 27012,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.192+14813G>A",
"hgvs_p": null
},
{
"score": -8,
"benign_score": 8,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000452818.1",
"gene_symbol": "HIRA",
"hgnc_id": 4916,
"effects": [
"intron_variant"
],
"inheritance_mode": "AD",
"hgvs_c": "n.72+14813G>A",
"hgvs_p": null
}
],
"clinvar_disease": "",
"clinvar_classification": "",
"clinvar_review_status": "",
"clinvar_submissions_summary": "",
"phenotype_combined": null,
"pathogenicity_classification_combined": null,
"custom_annotations": null
}
],
"message": null
}