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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: 2-73408628-C-G (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=73408628&ref=C&alt=G&genome=hg38&allGenes=true"API Response
json
{
"message": null,
"variants": [
{
"acmg_by_gene": [
{
"benign_score": 6,
"criteria": [
"BP4_Moderate",
"BS1"
],
"effects": [
"missense_variant"
],
"gene_symbol": "ALMS1",
"hgnc_id": 428,
"hgvs_c": "c.331C>G",
"hgvs_p": "p.Pro111Ala",
"inheritance_mode": "AR,Unknown",
"pathogenic_score": 0,
"score": -6,
"transcript": "NM_015120.4",
"verdict": "Likely_benign"
}
],
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate,BS1",
"acmg_score": -6,
"allele_count_reference_population": 102,
"alphamissense_prediction": null,
"alphamissense_score": 0.2127,
"alt": "G",
"apogee2_prediction": null,
"apogee2_score": null,
"bayesdelnoaf_prediction": "Benign",
"bayesdelnoaf_score": -0.25,
"chr": "2",
"clinvar_classification": "Uncertain significance",
"clinvar_disease": "Alstrom syndrome,Retinal dystrophy,not provided",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "US:2",
"computational_prediction_selected": "Benign",
"computational_score_selected": 0.08806851506233215,
"computational_source_selected": "MetaRNN",
"consequences": [
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 4168,
"aa_ref": "P",
"aa_start": 111,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12844,
"cdna_start": 364,
"cds_end": null,
"cds_length": 12507,
"cds_start": 331,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_001378454.1",
"gene_hgnc_id": 428,
"gene_symbol": "ALMS1",
"hgvs_c": "c.331C>G",
"hgvs_p": "p.Pro111Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "ENST00000613296.6",
"protein_coding": true,
"protein_id": "NP_001365383.1",
"strand": true,
"transcript": "NM_001378454.1",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 4168,
"aa_ref": "P",
"aa_start": 111,
"biotype": "protein_coding",
"canonical": true,
"cdna_end": null,
"cdna_length": 12844,
"cdna_start": 364,
"cds_end": null,
"cds_length": 12507,
"cds_start": 331,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000613296.6",
"gene_hgnc_id": 428,
"gene_symbol": "ALMS1",
"hgvs_c": "c.331C>G",
"hgvs_p": "p.Pro111Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": "NM_001378454.1",
"protein_coding": true,
"protein_id": "ENSP00000482968.1",
"strand": true,
"transcript": "ENST00000613296.6",
"transcript_support_level": 1
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": 4126,
"aa_ref": null,
"aa_start": null,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12595,
"cdna_start": null,
"cds_end": null,
"cds_length": 12381,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 22,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000484298.5",
"gene_hgnc_id": 428,
"gene_symbol": "ALMS1",
"hgvs_c": "c.325-10495C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000478155.1",
"strand": true,
"transcript": "ENST00000484298.5",
"transcript_support_level": 1
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 4168,
"aa_ref": "P",
"aa_start": 111,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 12925,
"cdna_start": 442,
"cds_end": null,
"cds_length": 12507,
"cds_start": 331,
"consequences": [
"missense_variant"
],
"exon_count": 23,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "NM_015120.4",
"gene_hgnc_id": 428,
"gene_symbol": "ALMS1",
"hgvs_c": "c.331C>G",
"hgvs_p": "p.Pro111Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "NP_055935.4",
"strand": true,
"transcript": "NM_015120.4",
"transcript_support_level": null
},
{
"aa_alt": "A",
"aa_end": null,
"aa_length": 3859,
"aa_ref": "P",
"aa_start": 111,
"biotype": "protein_coding",
"canonical": false,
"cdna_end": null,
"cdna_length": 11700,
"cdna_start": 331,
"cds_end": null,
"cds_length": 11580,
"cds_start": 331,
"consequences": [
"missense_variant"
],
"exon_count": 16,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000614410.4",
"gene_hgnc_id": 428,
"gene_symbol": "ALMS1",
"hgvs_c": "c.331C>G",
"hgvs_p": "p.Pro111Ala",
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": true,
"protein_id": "ENSP00000479094.1",
"strand": true,
"transcript": "ENST00000614410.4",
"transcript_support_level": 5
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 1268,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 5,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000682675.1",
"gene_hgnc_id": 428,
"gene_symbol": "ALMS1",
"hgvs_c": "n.291C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000682675.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "pseudogene",
"canonical": false,
"cdna_end": null,
"cdna_length": 1570,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_count": 8,
"exon_rank": 2,
"exon_rank_end": null,
"feature": "ENST00000682889.1",
"gene_hgnc_id": 428,
"gene_symbol": "ALMS1",
"hgvs_c": "n.296C>G",
"hgvs_p": null,
"intron_rank": null,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000682889.1",
"transcript_support_level": null
},
{
"aa_alt": null,
"aa_end": null,
"aa_length": null,
"aa_ref": null,
"aa_start": null,
"biotype": "retained_intron",
"canonical": false,
"cdna_end": null,
"cdna_length": 3775,
"cdna_start": null,
"cds_end": null,
"cds_length": null,
"cds_start": null,
"consequences": [
"intron_variant"
],
"exon_count": 2,
"exon_rank": null,
"exon_rank_end": null,
"feature": "ENST00000684148.1",
"gene_hgnc_id": 428,
"gene_symbol": "ALMS1",
"hgvs_c": "n.197-10495C>G",
"hgvs_p": null,
"intron_rank": 1,
"intron_rank_end": null,
"mane_plus": null,
"mane_select": null,
"protein_coding": false,
"protein_id": null,
"strand": true,
"transcript": "ENST00000684148.1",
"transcript_support_level": null
}
],
"custom_annotations": null,
"dbscsnv_ada_prediction": null,
"dbscsnv_ada_score": null,
"dbsnp": "rs368354870",
"effect": "missense_variant",
"frequency_reference_population": 0.000063245774,
"gene_hgnc_id": 428,
"gene_symbol": "ALMS1",
"gnomad_exomes_ac": 99,
"gnomad_exomes_af": 0.0000677728,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_ac": 3,
"gnomad_genomes_af": 0.0000197379,
"gnomad_genomes_homalt": 0,
"gnomad_mito_heteroplasmic": null,
"gnomad_mito_homoplasmic": null,
"hom_count_reference_population": 1,
"mitotip_prediction": null,
"mitotip_score": null,
"pathogenicity_classification_combined": "Uncertain significance",
"phenotype_combined": "Alstrom syndrome|not provided|Retinal dystrophy",
"phylop100way_prediction": "Benign",
"phylop100way_score": 1.097,
"pos": 73408628,
"ref": "C",
"revel_prediction": "Benign",
"revel_score": 0.146,
"splice_prediction_selected": "Benign",
"splice_score_selected": 0.05999999865889549,
"splice_source_selected": "max_spliceai",
"spliceai_max_prediction": "Benign",
"spliceai_max_score": 0.06,
"transcript": "NM_015120.4"
}
]
}