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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: 3-149162752-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=3&pos=149162752&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "3",
"pos": 149162752,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "NM_032383.5",
"consequences": [
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.2355G>A",
"hgvs_p": "p.Gln785Gln",
"transcript": "NM_032383.5",
"protein_id": "NP_115759.2",
"transcript_support_level": null,
"aa_start": 785,
"aa_end": null,
"aa_length": 1004,
"cds_start": 2355,
"cds_end": null,
"cds_length": 3015,
"cdna_start": 2441,
"cdna_end": null,
"cdna_length": 4611,
"mane_select": "ENST00000296051.7",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": true,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 17,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.2355G>A",
"hgvs_p": "p.Gln785Gln",
"transcript": "ENST00000296051.7",
"protein_id": "ENSP00000296051.2",
"transcript_support_level": 1,
"aa_start": 785,
"aa_end": null,
"aa_length": 1004,
"cds_start": 2355,
"cds_end": null,
"cds_length": 3015,
"cdna_start": 2441,
"cdna_end": null,
"cdna_length": 4611,
"mane_select": "NM_032383.5",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.1860G>A",
"hgvs_p": "p.Gln620Gln",
"transcript": "NM_001308258.2",
"protein_id": "NP_001295187.1",
"transcript_support_level": null,
"aa_start": 620,
"aa_end": null,
"aa_length": 839,
"cds_start": 1860,
"cds_end": null,
"cds_length": 2520,
"cdna_start": 1946,
"cdna_end": null,
"cdna_length": 4116,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 12,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.1860G>A",
"hgvs_p": "p.Gln620Gln",
"transcript": "ENST00000460120.5",
"protein_id": "ENSP00000418230.1",
"transcript_support_level": 2,
"aa_start": 620,
"aa_end": null,
"aa_length": 839,
"cds_start": 1860,
"cds_end": null,
"cds_length": 2520,
"cdna_start": 1946,
"cdna_end": null,
"cdna_length": 2745,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Q",
"aa_alt": "Q",
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"synonymous_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.2355G>A",
"hgvs_p": "p.Gln785Gln",
"transcript": "XM_047449064.1",
"protein_id": "XP_047305020.1",
"transcript_support_level": null,
"aa_start": 785,
"aa_end": null,
"aa_length": 942,
"cds_start": 2355,
"cds_end": null,
"cds_length": 2829,
"cdna_start": 2441,
"cdna_end": null,
"cdna_length": 2977,
"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": 3,
"exon_rank_end": null,
"exon_count": 8,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "n.483G>A",
"hgvs_p": null,
"transcript": "ENST00000460822.1",
"protein_id": "ENSP00000419824.1",
"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": 1958,
"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": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "n.*193C>T",
"hgvs_p": null,
"transcript": "ENST00000481169.5",
"protein_id": "ENSP00000418773.1",
"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": 3411,
"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": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "n.3071C>T",
"hgvs_p": null,
"transcript": "NR_046371.2",
"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": 3409,
"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": 13,
"exon_rank_end": null,
"exon_count": 16,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "n.2441G>A",
"hgvs_p": null,
"transcript": "XR_001740328.3",
"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": 2942,
"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": 19,
"exon_rank_end": null,
"exon_count": 19,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "n.3284C>T",
"hgvs_p": null,
"transcript": "XR_427361.4",
"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": 3622,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 6,
"exon_rank_end": null,
"exon_count": 6,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "c.*137C>T",
"hgvs_p": null,
"transcript": "ENST00000479771.5",
"protein_id": "ENSP00000420367.1",
"transcript_support_level": 5,
"aa_start": null,
"aa_end": null,
"aa_length": 225,
"cds_start": -4,
"cds_end": null,
"cds_length": 678,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 1150,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 18,
"exon_rank_end": null,
"exon_count": 18,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "n.*193C>T",
"hgvs_p": null,
"transcript": "ENST00000481169.5",
"protein_id": "ENSP00000418773.1",
"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": 3411,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "c.*137C>T",
"hgvs_p": null,
"transcript": "XM_011512435.3",
"protein_id": "XP_011510737.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1094,
"cds_start": -4,
"cds_end": null,
"cds_length": 3285,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3797,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 20,
"exon_rank_end": null,
"exon_count": 20,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "CP",
"gene_hgnc_id": 2295,
"hgvs_c": "c.*137C>T",
"hgvs_p": null,
"transcript": "XM_006713499.4",
"protein_id": "XP_006713562.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 1090,
"cds_start": -4,
"cds_end": null,
"cds_length": 3273,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3785,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": true,
"strand": true,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 13,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"hgvs_c": "c.*64G>A",
"hgvs_p": null,
"transcript": "XM_005247834.5",
"protein_id": "XP_005247891.1",
"transcript_support_level": null,
"aa_start": null,
"aa_end": null,
"aa_length": 763,
"cds_start": -4,
"cds_end": null,
"cds_length": 2292,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 2455,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "HPS3",
"gene_hgnc_id": 15597,
"dbsnp": "rs1366063625",
"frequency_reference_population": 0.000011772637,
"hom_count_reference_population": 0,
"allele_count_reference_population": 19,
"gnomad_exomes_af": 0.0000116299,
"gnomad_genomes_af": 0.0000131437,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 2,
"gnomad_exomes_homalt": 0,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.46000000834465027,
"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": -0.46,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 1.168,
"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": "NM_032383.5",
"gene_symbol": "HPS3",
"hgnc_id": 15597,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR",
"hgvs_c": "c.2355G>A",
"hgvs_p": "p.Gln785Gln"
},
{
"score": -4,
"benign_score": 4,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate",
"BP6_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000481169.5",
"gene_symbol": "CP",
"hgnc_id": 2295,
"effects": [
"non_coding_transcript_exon_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "n.*193C>T",
"hgvs_p": null
}
],
"clinvar_disease": "not provided",
"clinvar_classification": "Likely benign",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "LB:1",
"phenotype_combined": "not provided",
"pathogenicity_classification_combined": "Likely benign",
"custom_annotations": null
}
],
"message": null
}