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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: 1-114684239-A-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=1&pos=114684239&ref=A&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "1",
"pos": 114684239,
"ref": "A",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000520113.7",
"consequences": [
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD1",
"gene_hgnc_id": 468,
"hgvs_c": "c.507T>G",
"hgvs_p": "p.Ile169Met",
"transcript": "NM_000036.3",
"protein_id": "NP_000027.3",
"transcript_support_level": null,
"aa_start": 169,
"aa_end": null,
"aa_length": 747,
"cds_start": 507,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 582,
"cdna_end": null,
"cdna_length": 2335,
"mane_select": "ENST00000520113.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD1",
"gene_hgnc_id": 468,
"hgvs_c": "c.507T>G",
"hgvs_p": "p.Ile169Met",
"transcript": "ENST00000520113.7",
"protein_id": "ENSP00000430075.3",
"transcript_support_level": 1,
"aa_start": 169,
"aa_end": null,
"aa_length": 747,
"cds_start": 507,
"cds_end": null,
"cds_length": 2244,
"cdna_start": 582,
"cdna_end": null,
"cdna_length": 2335,
"mane_select": "NM_000036.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD1",
"gene_hgnc_id": 468,
"hgvs_c": "c.495T>G",
"hgvs_p": "p.Ile165Met",
"transcript": "NM_001172626.2",
"protein_id": "NP_001166097.2",
"transcript_support_level": null,
"aa_start": 165,
"aa_end": null,
"aa_length": 743,
"cds_start": 495,
"cds_end": null,
"cds_length": 2232,
"cdna_start": 570,
"cdna_end": null,
"cdna_length": 2323,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "I",
"aa_alt": "M",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD1",
"gene_hgnc_id": 468,
"hgvs_c": "c.495T>G",
"hgvs_p": "p.Ile165Met",
"transcript": "ENST00000369538.4",
"protein_id": "ENSP00000358551.4",
"transcript_support_level": 2,
"aa_start": 165,
"aa_end": null,
"aa_length": 743,
"cds_start": 495,
"cds_end": null,
"cds_length": 2232,
"cdna_start": 642,
"cdna_end": null,
"cdna_length": 2392,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD1",
"gene_hgnc_id": 468,
"hgvs_c": "n.381T>G",
"hgvs_p": null,
"transcript": "ENST00000485564.3",
"protein_id": null,
"transcript_support_level": 5,
"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": 441,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 14,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD1",
"gene_hgnc_id": 468,
"hgvs_c": "n.510T>G",
"hgvs_p": null,
"transcript": "ENST00000637080.1",
"protein_id": "ENSP00000489753.1",
"transcript_support_level": 5,
"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": 2051,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "AMPD1",
"gene_hgnc_id": 468,
"hgvs_c": "n.172T>G",
"hgvs_p": null,
"transcript": "ENST00000639077.1",
"protein_id": null,
"transcript_support_level": 5,
"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": 1693,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "AMPD1",
"gene_hgnc_id": 468,
"dbsnp": "rs542684385",
"frequency_reference_population": 0.0000012390345,
"hom_count_reference_population": 0,
"allele_count_reference_population": 2,
"gnomad_exomes_af": 6.84045e-7,
"gnomad_genomes_af": 0.00000656737,
"gnomad_exomes_ac": 1,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.06569832563400269,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.101,
"revel_prediction": "Benign",
"alphamissense_score": 0.0775,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.57,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -1.458,
"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": "ENST00000520113.7",
"gene_symbol": "AMPD1",
"hgnc_id": 468,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.507T>G",
"hgvs_p": "p.Ile169Met"
}
],
"clinvar_disease": "Autism,Muscle AMP deaminase deficiency",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"phenotype_combined": "Muscle AMP deaminase deficiency|Autism",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}