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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: 1-219981454-A-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=219981454&ref=A&alt=G&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 219981454,
"ref": "A",
"alt": "G",
"effect": "missense_variant",
"transcript": "NM_004446.3",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPRS1",
"gene_hgnc_id": 3418,
"hgvs_c": "c.3377T>C",
"hgvs_p": "p.Met1126Thr",
"transcript": "NM_004446.3",
"protein_id": "NP_004437.2",
"transcript_support_level": null,
"aa_start": 1126,
"aa_end": null,
"aa_length": 1512,
"cds_start": 3377,
"cds_end": null,
"cds_length": 4539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000366923.8",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_004446.3"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPRS1",
"gene_hgnc_id": 3418,
"hgvs_c": "c.3377T>C",
"hgvs_p": "p.Met1126Thr",
"transcript": "ENST00000366923.8",
"protein_id": "ENSP00000355890.3",
"transcript_support_level": 1,
"aa_start": 1126,
"aa_end": null,
"aa_length": 1512,
"cds_start": 3377,
"cds_end": null,
"cds_length": 4539,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_004446.3",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000366923.8"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPRS1",
"gene_hgnc_id": 3418,
"hgvs_c": "c.3497T>C",
"hgvs_p": "p.Met1166Thr",
"transcript": "ENST00000927912.1",
"protein_id": "ENSP00000597971.1",
"transcript_support_level": null,
"aa_start": 1166,
"aa_end": null,
"aa_length": 1552,
"cds_start": 3497,
"cds_end": null,
"cds_length": 4659,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927912.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 25,
"exon_rank_end": null,
"exon_count": 33,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPRS1",
"gene_hgnc_id": 3418,
"hgvs_c": "c.3422T>C",
"hgvs_p": "p.Met1141Thr",
"transcript": "ENST00000927914.1",
"protein_id": "ENSP00000597973.1",
"transcript_support_level": null,
"aa_start": 1141,
"aa_end": null,
"aa_length": 1527,
"cds_start": 3422,
"cds_end": null,
"cds_length": 4584,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927914.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPRS1",
"gene_hgnc_id": 3418,
"hgvs_c": "c.3368T>C",
"hgvs_p": "p.Met1123Thr",
"transcript": "ENST00000927916.1",
"protein_id": "ENSP00000597975.1",
"transcript_support_level": null,
"aa_start": 1123,
"aa_end": null,
"aa_length": 1509,
"cds_start": 3368,
"cds_end": null,
"cds_length": 4530,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927916.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPRS1",
"gene_hgnc_id": 3418,
"hgvs_c": "c.3347T>C",
"hgvs_p": "p.Met1116Thr",
"transcript": "ENST00000927911.1",
"protein_id": "ENSP00000597970.1",
"transcript_support_level": null,
"aa_start": 1116,
"aa_end": null,
"aa_length": 1502,
"cds_start": 3347,
"cds_end": null,
"cds_length": 4509,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927911.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 24,
"exon_rank_end": null,
"exon_count": 32,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPRS1",
"gene_hgnc_id": 3418,
"hgvs_c": "c.3245T>C",
"hgvs_p": "p.Met1082Thr",
"transcript": "ENST00000927915.1",
"protein_id": "ENSP00000597974.1",
"transcript_support_level": null,
"aa_start": 1082,
"aa_end": null,
"aa_length": 1468,
"cds_start": 3245,
"cds_end": null,
"cds_length": 4407,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927915.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPRS1",
"gene_hgnc_id": 3418,
"hgvs_c": "c.3167T>C",
"hgvs_p": "p.Met1056Thr",
"transcript": "ENST00000927913.1",
"protein_id": "ENSP00000597972.1",
"transcript_support_level": null,
"aa_start": 1056,
"aa_end": null,
"aa_length": 1442,
"cds_start": 3167,
"cds_end": null,
"cds_length": 4329,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927913.1"
},
{
"aa_ref": "M",
"aa_alt": "T",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 31,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "EPRS1",
"gene_hgnc_id": 3418,
"hgvs_c": "c.3143T>C",
"hgvs_p": "p.Met1048Thr",
"transcript": "ENST00000927910.1",
"protein_id": "ENSP00000597969.1",
"transcript_support_level": null,
"aa_start": 1048,
"aa_end": null,
"aa_length": 1434,
"cds_start": 3143,
"cds_end": null,
"cds_length": 4305,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000927910.1"
},
{
"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": 18,
"intron_rank": 13,
"intron_rank_end": null,
"gene_symbol": "EPRS1",
"gene_hgnc_id": 3418,
"hgvs_c": "c.1606-2735T>C",
"hgvs_p": null,
"transcript": "ENST00000952426.1",
"protein_id": "ENSP00000622485.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 744,
"cds_start": null,
"cds_end": null,
"cds_length": 2235,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000952426.1"
}
],
"gene_symbol": "EPRS1",
"gene_hgnc_id": 3418,
"dbsnp": "rs1474000585",
"frequency_reference_population": 6.9591556e-7,
"hom_count_reference_population": 0,
"allele_count_reference_population": 1,
"gnomad_exomes_af": 6.95916e-7,
"gnomad_genomes_af": null,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": null,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": null,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.9338460564613342,
"computational_prediction_selected": "Pathogenic",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.813,
"revel_prediction": "Pathogenic",
"alphamissense_score": 0.8387,
"alphamissense_prediction": "Pathogenic",
"bayesdelnoaf_score": 0.31,
"bayesdelnoaf_prediction": "Pathogenic",
"phylop100way_score": 9.082,
"phylop100way_prediction": "Pathogenic",
"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": "Uncertain_significance",
"acmg_criteria": "PM2,PP3_Moderate,PP5",
"acmg_by_gene": [
{
"score": 5,
"benign_score": 0,
"pathogenic_score": 5,
"criteria": [
"PM2",
"PP3_Moderate",
"PP5"
],
"verdict": "Uncertain_significance",
"transcript": "NM_004446.3",
"gene_symbol": "EPRS1",
"hgnc_id": 3418,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.3377T>C",
"hgvs_p": "p.Met1126Thr"
}
],
"clinvar_disease": " 15, hypomyelinating,Leukodystrophy",
"clinvar_classification": "Pathogenic",
"clinvar_review_status": "no assertion criteria provided",
"clinvar_submissions_summary": "null",
"phenotype_combined": "Leukodystrophy, hypomyelinating, 15",
"pathogenicity_classification_combined": "Pathogenic",
"custom_annotations": null
}
],
"message": null
}