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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: 2-26277141-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=26277141&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 26277141,
"ref": "C",
"alt": "T",
"effect": "synonymous_variant",
"transcript": "ENST00000317799.10",
"consequences": [
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADHB",
"gene_hgnc_id": 4803,
"hgvs_c": "c.423C>T",
"hgvs_p": "p.Ala141Ala",
"transcript": "NM_000183.3",
"protein_id": "NP_000174.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 474,
"cds_start": 423,
"cds_end": null,
"cds_length": 1425,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 1997,
"mane_select": "ENST00000317799.10",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADHB",
"gene_hgnc_id": 4803,
"hgvs_c": "c.423C>T",
"hgvs_p": "p.Ala141Ala",
"transcript": "ENST00000317799.10",
"protein_id": "ENSP00000325136.5",
"transcript_support_level": 1,
"aa_start": 141,
"aa_end": null,
"aa_length": 474,
"cds_start": 423,
"cds_end": null,
"cds_length": 1425,
"cdna_start": 483,
"cdna_end": null,
"cdna_length": 1997,
"mane_select": "NM_000183.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADHB",
"gene_hgnc_id": 4803,
"hgvs_c": "c.378C>T",
"hgvs_p": "p.Ala126Ala",
"transcript": "NM_001281512.2",
"protein_id": "NP_001268441.1",
"transcript_support_level": null,
"aa_start": 126,
"aa_end": null,
"aa_length": 459,
"cds_start": 378,
"cds_end": null,
"cds_length": 1380,
"cdna_start": 438,
"cdna_end": null,
"cdna_length": 1952,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADHB",
"gene_hgnc_id": 4803,
"hgvs_c": "c.378C>T",
"hgvs_p": "p.Ala126Ala",
"transcript": "ENST00000537713.5",
"protein_id": "ENSP00000444295.1",
"transcript_support_level": 2,
"aa_start": 126,
"aa_end": null,
"aa_length": 459,
"cds_start": 378,
"cds_end": null,
"cds_length": 1380,
"cdna_start": 629,
"cdna_end": null,
"cdna_length": 2142,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADHB",
"gene_hgnc_id": 4803,
"hgvs_c": "c.357C>T",
"hgvs_p": "p.Ala119Ala",
"transcript": "NM_001281513.2",
"protein_id": "NP_001268442.1",
"transcript_support_level": null,
"aa_start": 119,
"aa_end": null,
"aa_length": 452,
"cds_start": 357,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 566,
"cdna_end": null,
"cdna_length": 2080,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADHB",
"gene_hgnc_id": 4803,
"hgvs_c": "c.357C>T",
"hgvs_p": "p.Ala119Ala",
"transcript": "ENST00000545822.2",
"protein_id": "ENSP00000442665.1",
"transcript_support_level": 5,
"aa_start": 119,
"aa_end": null,
"aa_length": 452,
"cds_start": 357,
"cds_end": null,
"cds_length": 1359,
"cdna_start": 357,
"cdna_end": null,
"cdna_length": 1870,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADHB",
"gene_hgnc_id": 4803,
"hgvs_c": "c.423C>T",
"hgvs_p": "p.Ala141Ala",
"transcript": "ENST00000405867.7",
"protein_id": "ENSP00000385411.3",
"transcript_support_level": 5,
"aa_start": 141,
"aa_end": null,
"aa_length": 351,
"cds_start": 423,
"cds_end": null,
"cds_length": 1056,
"cdna_start": 496,
"cdna_end": null,
"cdna_length": 1588,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADHB",
"gene_hgnc_id": 4803,
"hgvs_c": "c.423C>T",
"hgvs_p": "p.Ala141Ala",
"transcript": "ENST00000425035.5",
"protein_id": "ENSP00000404633.1",
"transcript_support_level": 4,
"aa_start": 141,
"aa_end": null,
"aa_length": 174,
"cds_start": 423,
"cds_end": null,
"cds_length": 527,
"cdna_start": 592,
"cdna_end": null,
"cdna_length": 696,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADHB",
"gene_hgnc_id": 4803,
"hgvs_c": "c.423C>T",
"hgvs_p": "p.Ala141Ala",
"transcript": "ENST00000448743.5",
"protein_id": "ENSP00000415300.1",
"transcript_support_level": 5,
"aa_start": 141,
"aa_end": null,
"aa_length": 148,
"cds_start": 423,
"cds_end": null,
"cds_length": 449,
"cdna_start": 531,
"cdna_end": null,
"cdna_length": 557,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "A",
"aa_alt": "A",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADHB",
"gene_hgnc_id": 4803,
"hgvs_c": "c.423C>T",
"hgvs_p": "p.Ala141Ala",
"transcript": "XM_011532803.2",
"protein_id": "XP_011531105.1",
"transcript_support_level": null,
"aa_start": 141,
"aa_end": null,
"aa_length": 474,
"cds_start": 423,
"cds_end": null,
"cds_length": 1425,
"cdna_start": 632,
"cdna_end": null,
"cdna_length": 2146,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HADHB",
"gene_hgnc_id": 4803,
"hgvs_c": "n.1370C>T",
"hgvs_p": null,
"transcript": "ENST00000494615.1",
"protein_id": null,
"transcript_support_level": 2,
"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": 2883,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HADHB",
"gene_hgnc_id": 4803,
"dbsnp": "rs374569092",
"frequency_reference_population": 0.000013946453,
"hom_count_reference_population": 0,
"allele_count_reference_population": 22,
"gnomad_exomes_af": 0.0000140293,
"gnomad_genomes_af": 0.0000131686,
"gnomad_exomes_ac": 20,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.23999999463558197,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0.009999999776482582,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.24,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.223,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0.01,
"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": -3,
"acmg_classification": "Likely_benign",
"acmg_criteria": "PM2,BP4_Moderate,BP6_Moderate,BP7",
"acmg_by_gene": [
{
"score": -3,
"benign_score": 5,
"pathogenic_score": 2,
"criteria": [
"PM2",
"BP4_Moderate",
"BP6_Moderate",
"BP7"
],
"verdict": "Likely_benign",
"transcript": "ENST00000317799.10",
"gene_symbol": "HADHB",
"hgnc_id": 4803,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.423C>T",
"hgvs_p": "p.Ala141Ala"
}
],
"clinvar_disease": "Mitochondrial trifunctional protein deficiency",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "Mitochondrial trifunctional protein deficiency",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}