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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: 2-73424839-C-T (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=73424839&ref=C&alt=T&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 73424839,
"ref": "C",
"alt": "T",
"effect": "missense_variant",
"transcript": "NM_015120.4",
"consequences": [
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.1174C>T",
"hgvs_p": "p.Arg392Cys",
"transcript": "NM_001378454.1",
"protein_id": "NP_001365383.1",
"transcript_support_level": null,
"aa_start": 392,
"aa_end": null,
"aa_length": 4168,
"cds_start": 1174,
"cds_end": null,
"cds_length": 12507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "ENST00000613296.6",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_001378454.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.1174C>T",
"hgvs_p": "p.Arg392Cys",
"transcript": "ENST00000613296.6",
"protein_id": "ENSP00000482968.1",
"transcript_support_level": 1,
"aa_start": 392,
"aa_end": null,
"aa_length": 4168,
"cds_start": 1174,
"cds_end": null,
"cds_length": 12507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": "NM_001378454.1",
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000613296.6"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 4,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.1048C>T",
"hgvs_p": "p.Arg350Cys",
"transcript": "ENST00000484298.5",
"protein_id": "ENSP00000478155.1",
"transcript_support_level": 1,
"aa_start": 350,
"aa_end": null,
"aa_length": 4126,
"cds_start": 1048,
"cds_end": null,
"cds_length": 12381,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000484298.5"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.1174C>T",
"hgvs_p": "p.Arg392Cys",
"transcript": "NM_015120.4",
"protein_id": "NP_055935.4",
"transcript_support_level": null,
"aa_start": 392,
"aa_end": null,
"aa_length": 4168,
"cds_start": 1174,
"cds_end": null,
"cds_length": 12507,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "NM_015120.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.724C>T",
"hgvs_p": "p.Arg242Cys",
"transcript": "ENST00000684548.1",
"protein_id": "ENSP00000507421.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 4065,
"cds_start": 724,
"cds_end": null,
"cds_length": 12198,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000684548.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.724C>T",
"hgvs_p": "p.Arg242Cys",
"transcript": "ENST00000682859.1",
"protein_id": "ENSP00000508222.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 4041,
"cds_start": 724,
"cds_end": null,
"cds_length": 12126,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000682859.1"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 5,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.1174C>T",
"hgvs_p": "p.Arg392Cys",
"transcript": "ENST00000614410.4",
"protein_id": "ENSP00000479094.1",
"transcript_support_level": 5,
"aa_start": 392,
"aa_end": null,
"aa_length": 3859,
"cds_start": 1174,
"cds_end": null,
"cds_length": 11580,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000614410.4"
},
{
"aa_ref": "R",
"aa_alt": "C",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.724C>T",
"hgvs_p": "p.Arg242Cys",
"transcript": "ENST00000682801.1",
"protein_id": "ENSP00000507862.1",
"transcript_support_level": null,
"aa_start": 242,
"aa_end": null,
"aa_length": 3852,
"cds_start": 724,
"cds_end": null,
"cds_length": 11559,
"cdna_start": null,
"cdna_end": null,
"cdna_length": null,
"mane_select": null,
"mane_plus": null,
"biotype": "protein_coding",
"feature": "ENST00000682801.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "n.724C>T",
"hgvs_p": null,
"transcript": "ENST00000682565.1",
"protein_id": "ENSP00000507671.1",
"transcript_support_level": null,
"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": "ENST00000682565.1"
},
{
"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": 5,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "n.1134C>T",
"hgvs_p": null,
"transcript": "ENST00000682675.1",
"protein_id": null,
"transcript_support_level": null,
"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": "retained_intron",
"feature": "ENST00000682675.1"
},
{
"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": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "n.1139C>T",
"hgvs_p": null,
"transcript": "ENST00000682889.1",
"protein_id": null,
"transcript_support_level": null,
"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": "ENST00000682889.1"
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "n.526C>T",
"hgvs_p": null,
"transcript": "ENST00000683791.1",
"protein_id": "ENSP00000506916.1",
"transcript_support_level": null,
"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": "ENST00000683791.1"
}
],
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"dbsnp": "rs3813227",
"frequency_reference_population": 0.25654805,
"hom_count_reference_population": 66086,
"allele_count_reference_population": 412205,
"gnomad_exomes_af": 0.243022,
"gnomad_genomes_af": 0.385973,
"gnomad_exomes_ac": 353524,
"gnomad_genomes_ac": 58681,
"gnomad_exomes_homalt": 50242,
"gnomad_genomes_homalt": 15844,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 8.495763381688448e-7,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.029,
"revel_prediction": "Benign",
"alphamissense_score": 0.0614,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.53,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 0.089,
"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": -20,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BA1",
"acmg_by_gene": [
{
"score": -20,
"benign_score": 20,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BA1"
],
"verdict": "Benign",
"transcript": "NM_015120.4",
"gene_symbol": "ALMS1",
"hgnc_id": 428,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.1174C>T",
"hgvs_p": "p.Arg392Cys"
}
],
"clinvar_disease": "Alstrom syndrome,Cardiovascular phenotype,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:6",
"phenotype_combined": "not specified|Alstrom syndrome|Cardiovascular phenotype|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}