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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: 2-73451960-G-C (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=2&pos=73451960&ref=G&alt=C&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "2",
"pos": 73451960,
"ref": "G",
"alt": "C",
"effect": "missense_variant",
"transcript": "ENST00000613296.6",
"consequences": [
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.5433G>C",
"hgvs_p": "p.Lys1811Asn",
"transcript": "NM_001378454.1",
"protein_id": "NP_001365383.1",
"transcript_support_level": null,
"aa_start": 1811,
"aa_end": null,
"aa_length": 4168,
"cds_start": 5433,
"cds_end": null,
"cds_length": 12507,
"cdna_start": 5466,
"cdna_end": null,
"cdna_length": 12844,
"mane_select": "ENST00000613296.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.5433G>C",
"hgvs_p": "p.Lys1811Asn",
"transcript": "ENST00000613296.6",
"protein_id": "ENSP00000482968.1",
"transcript_support_level": 1,
"aa_start": 1811,
"aa_end": null,
"aa_length": 4168,
"cds_start": 5433,
"cds_end": null,
"cds_length": 12507,
"cdna_start": 5466,
"cdna_end": null,
"cdna_length": 12844,
"mane_select": "NM_001378454.1",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 7,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.5307G>C",
"hgvs_p": "p.Lys1769Asn",
"transcript": "ENST00000484298.5",
"protein_id": "ENSP00000478155.1",
"transcript_support_level": 1,
"aa_start": 1769,
"aa_end": null,
"aa_length": 4126,
"cds_start": 5307,
"cds_end": null,
"cds_length": 12381,
"cdna_start": 5418,
"cdna_end": null,
"cdna_length": 12595,
"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": 1,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "n.264G>C",
"hgvs_p": null,
"transcript": "ENST00000423048.5",
"protein_id": "ENSP00000399833.1",
"transcript_support_level": 1,
"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": 5194,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.5433G>C",
"hgvs_p": "p.Lys1811Asn",
"transcript": "NM_015120.4",
"protein_id": "NP_055935.4",
"transcript_support_level": null,
"aa_start": 1811,
"aa_end": null,
"aa_length": 4168,
"cds_start": 5433,
"cds_end": null,
"cds_length": 12507,
"cdna_start": 5544,
"cdna_end": null,
"cdna_length": 12925,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.5052G>C",
"hgvs_p": "p.Lys1684Asn",
"transcript": "ENST00000684548.1",
"protein_id": "ENSP00000507421.1",
"transcript_support_level": null,
"aa_start": 1684,
"aa_end": null,
"aa_length": 4065,
"cds_start": 5052,
"cds_end": null,
"cds_length": 12198,
"cdna_start": 5052,
"cdna_end": null,
"cdna_length": 12227,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 21,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.5052G>C",
"hgvs_p": "p.Lys1684Asn",
"transcript": "ENST00000682859.1",
"protein_id": "ENSP00000508222.1",
"transcript_support_level": null,
"aa_start": 1684,
"aa_end": null,
"aa_length": 4041,
"cds_start": 5052,
"cds_end": null,
"cds_length": 12126,
"cdna_start": 5052,
"cdna_end": null,
"cdna_length": 12427,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.5433G>C",
"hgvs_p": "p.Lys1811Asn",
"transcript": "ENST00000614410.4",
"protein_id": "ENSP00000479094.1",
"transcript_support_level": 5,
"aa_start": 1811,
"aa_end": null,
"aa_length": 3859,
"cds_start": 5433,
"cds_end": null,
"cds_length": 11580,
"cdna_start": 5433,
"cdna_end": null,
"cdna_length": 11700,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.5052G>C",
"hgvs_p": "p.Lys1684Asn",
"transcript": "ENST00000682801.1",
"protein_id": "ENSP00000507862.1",
"transcript_support_level": null,
"aa_start": 1684,
"aa_end": null,
"aa_length": 3852,
"cds_start": 5052,
"cds_end": null,
"cds_length": 11559,
"cdna_start": 5052,
"cdna_end": null,
"cdna_length": 11860,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "K",
"aa_alt": "N",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"missense_variant"
],
"exon_rank": 1,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "c.2502G>C",
"hgvs_p": "p.Lys834Asn",
"transcript": "ENST00000684460.1",
"protein_id": "ENSP00000506991.1",
"transcript_support_level": null,
"aa_start": 834,
"aa_end": null,
"aa_length": 3134,
"cds_start": 2502,
"cds_end": null,
"cds_length": 9405,
"cdna_start": 2504,
"cdna_end": null,
"cdna_length": 9692,
"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": 6,
"exon_rank_end": null,
"exon_count": 22,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "n.5052G>C",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 12428,
"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": 1,
"exon_rank_end": null,
"exon_count": 2,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "n.402G>C",
"hgvs_p": null,
"transcript": "ENST00000684197.1",
"protein_id": null,
"transcript_support_level": null,
"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": 3258,
"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": 1,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "n.2502G>C",
"hgvs_p": null,
"transcript": "ENST00000684656.1",
"protein_id": "ENSP00000508012.1",
"transcript_support_level": null,
"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": 9858,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
"exon_rank": null,
"exon_rank_end": null,
"exon_count": 15,
"intron_rank": 3,
"intron_rank_end": null,
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"hgvs_c": "n.*35+19669G>C",
"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": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 5497,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ALMS1",
"gene_hgnc_id": 428,
"dbsnp": "rs78039319",
"frequency_reference_population": 0.0017687335,
"hom_count_reference_population": 45,
"allele_count_reference_population": 2854,
"gnomad_exomes_af": 0.000927065,
"gnomad_genomes_af": 0.00986301,
"gnomad_exomes_ac": 1355,
"gnomad_genomes_ac": 1499,
"gnomad_exomes_homalt": 18,
"gnomad_genomes_homalt": 27,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.002468794584274292,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.049,
"revel_prediction": "Benign",
"alphamissense_score": 0.3474,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": -0.16,
"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": -13,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6,BS1,BS2",
"acmg_by_gene": [
{
"score": -13,
"benign_score": 13,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6",
"BS1",
"BS2"
],
"verdict": "Benign",
"transcript": "ENST00000613296.6",
"gene_symbol": "ALMS1",
"hgnc_id": 428,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.5433G>C",
"hgvs_p": "p.Lys1811Asn"
}
],
"clinvar_disease": "Alstrom syndrome,Cardiovascular phenotype,Monogenic diabetes,not provided,not specified",
"clinvar_classification": "Conflicting classifications of pathogenicity",
"clinvar_review_status": "criteria provided, conflicting classifications",
"clinvar_submissions_summary": "US:1 B:6",
"phenotype_combined": "Alstrom syndrome|not specified|Monogenic diabetes|not provided|Cardiovascular phenotype",
"pathogenicity_classification_combined": "Conflicting classifications of pathogenicity",
"custom_annotations": null
}
],
"message": null
}